1
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Sprunger ML, Jackrel ME. The role of Matrin-3 in physiology and its dysregulation in disease. Biochem Soc Trans 2024:BST20220585. [PMID: 38813817 DOI: 10.1042/bst20220585] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
The dysfunction of many RNA-binding proteins (RBPs) that are heavily disordered, including TDP-43 and FUS, are implicated in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These proteins serve many important roles in the cell, and their capacity to form biomolecular condensates (BMCs) is key to their function, but also a vulnerability that can lead to misregulation and disease. Matrin-3 (MATR3) is an intrinsically disordered RBP implicated both genetically and pathologically in ALS/FTD, though it is relatively understudied as compared with TDP-43 and FUS. In addition to binding RNA, MATR3 also binds DNA and is implicated in many cellular processes including the DNA damage response, transcription, splicing, and cell differentiation. It is unclear if MATR3 localizes to BMCs under physiological conditions, which is brought further into question due to its lack of a prion-like domain. Here, we review recent studies regarding MATR3 and its roles in numerous physiological processes, as well as its implication in a range of diseases.
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Affiliation(s)
- Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO 63130, U.S.A
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO 63130, U.S.A
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2
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Wang J, Zhu H, Tian R, Zhang Q, Zhang H, Hu J, Wang S. Physiological and pathological effects of phase separation in the central nervous system. J Mol Med (Berl) 2024; 102:599-615. [PMID: 38441598 PMCID: PMC11055734 DOI: 10.1007/s00109-024-02435-7] [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: 05/01/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Phase separation, also known as biomolecule condensate, participates in physiological processes such as transcriptional regulation, signal transduction, gene expression, and DNA damage repair by creating a membrane-free compartment. Phase separation is primarily caused by the interaction of multivalent non-covalent bonds between proteins and/or nucleic acids. The strength of molecular multivalent interaction can be modified by component concentration, the potential of hydrogen, posttranslational modification, and other factors. Notably, phase separation occurs frequently in the cytoplasm of mitochondria, the nucleus, and synapses. Phase separation in vivo is dynamic or stable in the normal physiological state, while abnormal phase separation will lead to the formation of biomolecule condensates, speeding up the disease progression. To provide candidate suggestions for the clinical treatment of nervous system diseases, this review, based on existing studies, carefully and systematically represents the physiological roles of phase separation in the central nervous system and its pathological mechanism in neurodegenerative diseases.
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Affiliation(s)
- Jiaxin Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Hongrui Zhu
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China.
- Core Facility Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China.
| | - Ruijia Tian
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Qian Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Haoliang Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Jin Hu
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Sheng Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China.
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3
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Dey P, Rajalaxmi S, Saha P, Thakur PS, Hashmi MA, Lal H, Saini N, Singh N, Ramanathan A. Cold-shock proteome of myoblasts reveals role of RBM3 in promotion of mitochondrial metabolism and myoblast differentiation. Commun Biol 2024; 7:515. [PMID: 38688991 PMCID: PMC11061143 DOI: 10.1038/s42003-024-06196-4] [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: 06/21/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Adaptation to hypothermia is important for skeletal muscle cells under physiological stress and is used for therapeutic hypothermia (mild hypothermia at 32 °C). We show that hypothermic preconditioning at 32 °C for 72 hours improves the differentiation of skeletal muscle myoblasts using both C2C12 and primary myoblasts isolated from 3 month and 18-month-old mice. We analyzed the cold-shock proteome of myoblasts exposed to hypothermia (32 °C for 6 and 48 h) and identified significant changes in pathways related to RNA processing and central carbon, fatty acid, and redox metabolism. The analysis revealed that levels of the cold-shock protein RBM3, an RNA-binding protein, increases with both acute and chronic exposure to hypothermic stress, and is necessary for the enhanced differentiation and maintenance of mitochondrial metabolism. We also show that overexpression of RBM3 at 37 °C is sufficient to promote mitochondrial metabolism, cellular proliferation, and differentiation of C2C12 and primary myoblasts. Proteomic analysis of C2C12 myoblasts overexpressing RBM3 show significant enrichment of pathways involved in fatty acid metabolism, RNA metabolism and the electron transport chain. Overall, we show that the cold-shock protein RBM3 is a critical factor that can be used for controlling the metabolic network of myoblasts.
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Affiliation(s)
- Paulami Dey
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Srujanika Rajalaxmi
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Pushpita Saha
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Purvi Singh Thakur
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Maroof Athar Hashmi
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Heera Lal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Nistha Saini
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Nirpendra Singh
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Arvind Ramanathan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India.
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Wang J, Feng X, Liu X, Wang G, Xiong Y, Zhang L, Zhang Y, Lu H. In-Depth Profiling of 4-Hydroxy-2-nonenal Modification via Reversible Thiazolidine Chemistry. Anal Chem 2024; 96:5125-5133. [PMID: 38502245 DOI: 10.1021/acs.analchem.3c05060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Protein modification by lipid-derived electrophiles (LDEs) is associated with various signaling pathways. Among these LDEs, 4-hydroxy-2-nonenal (HNE) is the most toxic, and protein modified with HNE has been linked to various diseases, including Alzheimer's and Parkinson's. However, due to their low abundance, in-depth profiling of HNE modifications still presents challenges. This study introduces a novel strategy utilizing reversible thiazolidine chemistry to selectively capture HNE-modified proteins and a palladium-mediated cleavage reaction to release them. Thousands of HNE-modified sites in different cell lines were identified. Combined with ABPP, we discovered a set of HNE-sensitive sites that offer a new tool for studying LDE modifications in proteomes.
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Affiliation(s)
- Jun Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Xiaoxiao Feng
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Xuejiao Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Yingying Xiong
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
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5
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Islam Z, Polash A, Suzawa M, Chim B, Kuhn S, Sultana S, Cutrona N, Smith PT, Kabat J, Ganesan S, Foroushani A, Hafner M, Muljo SA. MATRIN3 deficiency triggers autoinflammation via cGAS-STING activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587645. [PMID: 38712171 PMCID: PMC11071297 DOI: 10.1101/2024.04.01.587645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Interferon-stimulated genes (ISGs) comprise a program of immune effectors important for host immune defense. When uncontrolled, ISGs play a central role in interferonopathies and other inflammatory diseases. The mechanisms responsible for turning on ISGs are not completely known. By investigating MATRIN3 (MATR3), a nuclear RNA-binding protein mutated in familial ALS, we found that perturbing MATR3 results in elevated expression of ISGs. Using an integrative approach, we elucidate a pathway that leads to activation of cGAS-STING. This outlines a plausible mechanism for pathogenesis in a subset of ALS, and suggests new diagnostic and therapeutic approaches for this fatal disease.
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Affiliation(s)
- Zohirul Islam
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
| | - Ahsan Polash
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease (NIAMS), NIH; Bethesda, Maryland 20892, USA
| | - Masataka Suzawa
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease (NIAMS), NIH; Bethesda, Maryland 20892, USA
| | - Bryan Chim
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
| | - Skyler Kuhn
- Integrated Data Sciences Section, Research Technologies Branch (RTB), NIAID, NIH; Bethesda, Maryland 20892, USA
| | - Sabrina Sultana
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
| | - Nicholas Cutrona
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
| | - Patrick T. Smith
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
| | - Juraj Kabat
- Biological Imaging Section, RTB, NIAID, NIH; Bethesda, Maryland 20892, USA
| | - Sundar Ganesan
- Biological Imaging Section, RTB, NIAID, NIH; Bethesda, Maryland 20892, USA
| | - Amir Foroushani
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease (NIAMS), NIH; Bethesda, Maryland 20892, USA
| | - Stefan A. Muljo
- Integrative Immunobiology Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, Maryland 20892, USA
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6
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Lee YJ, Rio DC. A mutation in the low-complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks. Genes Dev 2024; 38:11-30. [PMID: 38182429 PMCID: PMC10903937 DOI: 10.1101/gad.351104.123] [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: 08/21/2023] [Accepted: 12/14/2023] [Indexed: 01/07/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease characterized by loss of motor neurons. Human genetic studies have linked mutations in RNA-binding proteins as causative for this disease. The hnRNPA1 protein, a known pre-mRNA splicing factor, is mutated in some ALS patients. Here, two human cell models were generated to investigate how a mutation in the C-terminal low-complexity domain (LCD) of hnRNPA1 can cause splicing changes of thousands of transcripts that collectively are linked to the DNA damage response, cilium organization, and translation. We show that the hnRNPA1 D262V mutant protein binds to new binding sites on differentially spliced transcripts from genes that are linked to ALS. We demonstrate that this ALS-linked hnRNPA1 mutation alters normal RNA-dependent protein-protein interactions. Furthermore, cells expressing this hnRNPA1 mutant exhibit a cell aggregation phenotype, markedly reduced growth rates, changes in stress granule kinetics, and aberrant growth of neuronal processes. This study provides insight into how a single amino acid mutation in a splicing factor can alter RNA splicing networks of genes linked to ALS.
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Affiliation(s)
- Yeon J Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, USA
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7
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Liu T, Zhu Q, Kai Y, Bingham T, Wang S, Cha HJ, Mehta S, Schlaeger TM, Yuan GC, Orkin SH. Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions. Nat Commun 2024; 15:1274. [PMID: 38341433 PMCID: PMC10858947 DOI: 10.1038/s41467-024-45386-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Changes in chromatin occupancy by Matr3 also correlated with these alterations. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.
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Affiliation(s)
- Tianxin Liu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Qian Zhu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lester Sue Smith Breast Center, Department of Human Molecular Genetics, Baylor College of Medicine, 1 Moursund St, Houston, TX, 77030, USA
| | - Yan Kai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Trevor Bingham
- Stem Cell Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Stacy Wang
- Lester Sue Smith Breast Center, Department of Human Molecular Genetics, Baylor College of Medicine, 1 Moursund St, Houston, TX, 77030, USA
| | - Hye Ji Cha
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Science & Engineering, Dankook University, Cheonan, 31116, South Korea
| | - Stuti Mehta
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
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8
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Pozner A, Li L, Verma SP, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, John CM, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Mortenson KL, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97. Nat Commun 2024; 15:1165. [PMID: 38326311 PMCID: PMC10850509 DOI: 10.1038/s41467-024-45280-5] [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: 02/21/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
The t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributes with ASPSCR1::TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrate the oncogenic transcriptional signature of ASPSCR1::TFE3, by facilitating assembly of higher-order chromatin conformation structures demonstrated by HiChIP. Finally, ASPSCR1::TFE3 and VCP demonstrate co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.
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Affiliation(s)
- Amir Pozner
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Li Li
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shiv Prakash Verma
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shuxin Wang
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jared J Barrott
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Mary L Nelson
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Ju-Fen Zhu
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sydney L Lambert
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Lara S Carroll
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kyllie Smith-Fry
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael G Stewart
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarmishta Kannan
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Bodrie Jensen
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Cini M John
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Saif Sikdar
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Hongrui Liu
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer Bourdage
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jinxiu Li
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Katelyn L Mortenson
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - John S Groundland
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Rosanna Wustrack
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Donna L Senger
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, McGill University and Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Franz J Zemp
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Douglas J Mahoney
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Xiaoyang Zhang
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Alexander J Lazar
- Departments of Anatomic Pathology, Translational Molecular Pathology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Peter S Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Kevin B Jones
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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9
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Khan M, Chen XXL, Dias M, Santos JR, Kour S, You J, van Bruggen R, Youssef MMM, Wan YW, Liu Z, Rosenfeld JA, Tan Q, Pandey UB, Yalamanchili HK, Park J. MATR3 pathogenic variants differentially impair its cryptic splicing repression function. FEBS Lett 2024; 598:415-436. [PMID: 38320753 DOI: 10.1002/1873-3468.14806] [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: 12/06/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Matrin-3 (MATR3) is an RNA-binding protein implicated in neurodegenerative and neurodevelopmental diseases. However, little is known regarding the role of MATR3 in cryptic splicing within the context of functional genes and how disease-associated variants impact this function. We show that loss of MATR3 leads to cryptic exon inclusion in many transcripts. We reveal that ALS-linked S85C pathogenic variant reduces MATR3 solubility but does not impair RNA binding. In parallel, we report a novel neurodevelopmental disease-associated M548T variant, located in the RRM2 domain, which reduces protein solubility and impairs RNA binding and cryptic splicing repression functions of MATR3. Altogether, our research identifies cryptic events within functional genes and demonstrates how disease-associated variants impact MATR3 cryptic splicing repression function.
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Affiliation(s)
- Mashiat Khan
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Xiao Xiao Lily Chen
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Michelle Dias
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jhune Rizsan Santos
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Justin You
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Rebekah van Bruggen
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Mohieldin M M Youssef
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Qiumin Tan
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeehye Park
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
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10
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Chong ZZ, Menkes DL, Souayah N. Pathogenesis underlying hexanucleotide repeat expansions in C9orf72 gene in amyotrophic lateral sclerosis. Rev Neurosci 2024; 35:85-97. [PMID: 37525497 DOI: 10.1515/revneuro-2023-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder. Mutations in C9orf72 and the resulting hexanucleotide repeat (GGGGCC) expansion (HRE) has been identified as a major cause of familial ALS, accounting for about 40 % of familial and 6 % of sporadic cases of ALS in Western patients. The pathological outcomes of HRE expansion in ALS have been recognized as the results of two mechanisms that include both the toxic gain-of-function and loss-of-function of C9ORF72. The gain of toxicity results from RNA and dipeptide repeats (DPRs). The HRE can be bidirectionally transcribed into RNA foci, which can bind to and disrupt RNA splicing, transport, and translation. The DPRs that include poly-glycine-alanine, poly-glycine-proline, poly-glycine- arginine, poly-proline-alanine, and poly-proline-arginine can induce toxicity by direct binding and sequestrating other proteins to interfere rRNA synthesis, ribosome biogenesis, translation, and nucleocytoplasmic transport. The C9ORF72 functions through binding to its partners-Smith-Magenis chromosome regions 8 (SMCR8) and WD repeat-containing protein (WDR41). Loss of C9ORF72 function results in impairment of autophagy, deregulation of autoimmunity, increased stress, and disruption of nucleocytoplasmic transport. Further insight into the mechanism in C9ORF72 HRE pathogenesis will facilitate identifying novel and effective therapeutic targets for ALS.
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Affiliation(s)
- Zhao Zhong Chong
- Department of Neurology, Rutgers University, New Jersey Medical School, 185 S. Orange Ave, Newark, NJ 07103, USA
| | - Daniel L Menkes
- Department of Neurology, Oakland University William Beaumont School of Medicine, 3555 West 13 Mile Road, Suite N120, Royal Oak, MI 48073, USA
| | - Nizar Souayah
- Department of Neurology, Rutgers University, New Jersey Medical School, 90 Bergen Street DOC 8100, Newark, NJ 07101, USA
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11
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He H, Jamal M, Zeng X, Lei Y, Xiao D, Wei Z, Zhang C, Zhang X, Pan S, Ding Q, Tan H, Xie S, Zhang Q. Matrin-3 acts as a potential biomarker and promotes hepatocellular carcinoma progression by interacting with cell cycle-regulating genes. Cell Cycle 2024; 23:15-35. [PMID: 38252499 PMCID: PMC11005806 DOI: 10.1080/15384101.2024.2305535] [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: 01/15/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. The oncogenic role of Matrin-3 (MATR3), an a nuclear matrix protein, in HCC remains largely unknown. Here, we document the biological function of MATR3 in HCC based on integrated bioinformatics analysis and functional studies. According to the TCGA database, MATR3 expression was found to be positively correlated with clinicopathological characteristics in HCC. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve displayed the diagnostic and prognostic potentials of MATR3 in HCC patients, respectively. Pathway enrichment analysis represented the enrichment of MATR3 in various molecular pathways, including the regulation of the cell cycle. Functional assays in HCC cell lines showed reduced proliferation of cells with stable silencing of MATR3. At the same time, the suppressive effects of MATR3 depletion on HCC development were verified by xenograft tumor experiments. Moreover, MATR3 repression also resulted in cell cycle arrest by modulating the expression of cell cycle-associated genes. In addition, the interaction of MATR3 with cell cycle-regulating factors in HCC cells was further corroborated with co-immunoprecipitation and mass spectrometry (Co-IP/MS). Furthermore, CIBERSORT and TIMER analyses showed an association between MATR3 and immune infiltration in HCC. In general, this study highlights the novel oncogenic function of MATR3 in HCC, which could comprehensively address how aberrant changes in the cell cycle promote HCC development. MATR3 might serve as a prognostic predictor and therapeutic target for HCC patients.
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Affiliation(s)
- Hengjing He
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Muhammad Jamal
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xingruo Zeng
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yufei Lei
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Di Xiao
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zimeng Wei
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Chengjie Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shan Pan
- School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Qianshan Ding
- School of Medicine, Northwest University, Xian, China
| | - Haiyan Tan
- Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Songping Xie
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qiuping Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan, China
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12
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Cilleros-Holgado P, Gómez-Fernández D, Piñero-Pérez R, Romero-Domínguez JM, Reche-López D, López-Cabrera A, Álvarez-Córdoba M, Munuera-Cabeza M, Talaverón-Rey M, Suárez-Carrillo A, Romero-González A, Sánchez-Alcázar JA. Mitochondrial Quality Control via Mitochondrial Unfolded Protein Response (mtUPR) in Ageing and Neurodegenerative Diseases. Biomolecules 2023; 13:1789. [PMID: 38136659 PMCID: PMC10741690 DOI: 10.3390/biom13121789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Mitochondria play a key role in cellular functions, including energy production and oxidative stress regulation. For this reason, maintaining mitochondrial homeostasis and proteostasis (homeostasis of the proteome) is essential for cellular health. Therefore, there are different mitochondrial quality control mechanisms, such as mitochondrial biogenesis, mitochondrial dynamics, mitochondrial-derived vesicles (MDVs), mitophagy, or mitochondrial unfolded protein response (mtUPR). The last item is a stress response that occurs when stress is present within mitochondria and, especially, when the accumulation of unfolded and misfolded proteins in the mitochondrial matrix surpasses the folding capacity of the mitochondrion. In response to this, molecular chaperones and proteases as well as the mitochondrial antioxidant system are activated to restore mitochondrial proteostasis and cellular function. In disease contexts, mtUPR modulation holds therapeutic potential by mitigating mitochondrial dysfunction. In particular, in the case of neurodegenerative diseases, such as primary mitochondrial diseases, Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), Amyotrophic Lateral Sclerosis (ALS), or Friedreich's Ataxia (FA), there is a wealth of evidence demonstrating that the modulation of mtUPR helps to reduce neurodegeneration and its associated symptoms in various cellular and animal models. These findings underscore mtUPR's role as a promising therapeutic target in combating these devastating disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Jose Antonio Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (P.C.-H.); (D.G.-F.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.); (M.Á.-C.); (M.M.-C.); (M.T.-R.); (A.S.-C.); (A.R.-G.)
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13
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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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14
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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15
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Theme 04 - In Vivo Experimetal Models. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:128-139. [PMID: 37966319 DOI: 10.1080/21678421.2023.2260194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
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16
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Webber CJ, Murphy CN, Rondón-Ortiz AN, van der Spek SJF, Kelly EX, Lampl NM, Chiesa G, Khalil AS, Emili A, Wolozin B. Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways. Hum Mol Genet 2023; 32:2966-2980. [PMID: 37522762 PMCID: PMC10549787 DOI: 10.1093/hmg/ddad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023] Open
Abstract
Aggregation of TAR DNA-binding protein 43 kDa (TDP-43) is thought to drive the pathophysiology of amyotrophic lateral sclerosis and some frontotemporal dementias. TDP-43 is normally a nuclear protein that in neurons translocates to the cytoplasm and can form insoluble aggregates upon activation of the integrated stress response (ISR). Viruses evolved to control the ISR. In the case of Herpesvirus 8, the protein ORF57 acts to bind protein kinase R, inhibit phosphorylation of eIF2α and reduce activation of the ISR. We hypothesized that ORF57 might also possess the ability to inhibit aggregation of TDP-43. ORF57 was expressed in the neuronal SH-SY5Y line and its effects on TDP-43 aggregation characterized. We report that ORF57 inhibits TDP-43 aggregation by 55% and elicits a 2.45-fold increase in the rate of dispersion of existing TDP-43 granules. These changes were associated with a 50% decrease in cell death. Proteomic studies were carried out to identify the protein interaction network of ORF57. We observed that ORF57 directly binds to TDP-43 as well as interacts with many components of the ISR, including elements of the proteostasis machinery known to reduce TDP-43 aggregation. We propose that viral proteins designed to inhibit a chronic ISR can be engineered to remove aggregated proteins and dampen a chronic ISR.
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Affiliation(s)
- Chelsea J Webber
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Caroline N Murphy
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Alejandro N Rondón-Ortiz
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Sophie J F van der Spek
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Elena X Kelly
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Noah M Lampl
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
| | - Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
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17
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Pozner A, Verma SP, Li L, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, Mortenson KL, John C, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560242. [PMID: 37873234 PMCID: PMC10592841 DOI: 10.1101/2023.09.29.560242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The t(X,17) chromosomal translocation, generating the ASPSCR1-TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCC), frustrating efforts to identify therapeutic targets for these rare cancers. Proteomic analysis showed that VCP/p97, an AAA+ ATPase with known segregase function, was strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1-TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1-TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributed with ASPSCR1-TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrated the oncogenic transcriptional signature of ASPSCR1-TFE3, by facilitating assembly of higher-order chromatin conformation structures as demonstrated by HiChIP. Finally, ASPSCR1-TFE3 and VCP demonstrated co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.
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18
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Akçimen F, Lopez ER, Landers JE, Nath A, Chiò A, Chia R, Traynor BJ. Amyotrophic lateral sclerosis: translating genetic discoveries into therapies. Nat Rev Genet 2023; 24:642-658. [PMID: 37024676 PMCID: PMC10611979 DOI: 10.1038/s41576-023-00592-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 04/08/2023]
Abstract
Recent advances in sequencing technologies and collaborative efforts have led to substantial progress in identifying the genetic causes of amyotrophic lateral sclerosis (ALS). This momentum has, in turn, fostered the development of putative molecular therapies. In this Review, we outline the current genetic knowledge, emphasizing recent discoveries and emerging concepts such as the implication of distinct types of mutation, variability in mutated genes in diverse genetic ancestries and gene-environment interactions. We also propose a high-level model to synthesize the interdependent effects of genetics, environmental and lifestyle factors, and ageing into a unified theory of ALS. Furthermore, we summarize the current status of therapies developed on the basis of genetic knowledge established for ALS over the past 30 years, and we discuss how developing treatments for ALS will advance our understanding of targeting other neurological diseases.
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Affiliation(s)
- Fulya Akçimen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Elia R Lopez
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute for Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R, Rome, Italy
- Azienda Ospedaliero Universitaria Citta' della Salute e della Scienza, Turin, Italy
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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19
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Guareschi S, Ravasi M, Baldessari D, Pozzi S, Zaffino T, Melazzini M, Ambrosini A. The positive impact on translational research of Fondazione italiana di ricerca per la Sclerosi Laterale Amiotrofica (AriSLA), a non-profit foundation focused on amyotrophic lateral sclerosis. Convergence of ex-ante evaluation and ex-post outcomes when goals are set upfront. Front Res Metr Anal 2023; 8:1067981. [PMID: 37601533 PMCID: PMC10436489 DOI: 10.3389/frma.2023.1067981] [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: 10/12/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
Charities investing on rare disease research greatly contribute to generate ground-breaking knowledge with the clear goal of finding a cure for their condition of interest. Although the amount of their investments may be relatively small compared to major funders, the advocacy groups' clear mission promotes innovative research and aggregates highly motivated and mission-oriented scientists. Here, we illustrate the case of Fondazione italiana di ricerca per la Sclerosi Laterale Amiotrofica (AriSLA), the main Italian funding agency entirely dedicated to amyotrophic lateral sclerosis research. An international benchmark analysis of publications derived from AriSLA-funded projects indicated that their mean relative citation ratio values (iCite dashboard, National Institutes of Health, U.S.) were very high, suggesting a strong influence on the referring international scientific community. An interesting trend of research toward translation based on the "triangle of biomedicine" and paper citations (iCite) was also observed. Qualitative analysis on researchers' accomplishments was convergent with the bibliometric data, indicating a high level of performance of several working groups, lines of research that speak of progression toward clinical translation, and one study that has progressed from the investigation of cellular mechanisms to a Phase 2 international clinical trial. The key elements of the success of the AriSLA investment lie in: (i) the clear definition of the objectives (research with potential impact on patients, no matter how far), (ii) a rigorous peer-review process entrusted to an international panel of experts, (iii) diversification of the portfolio with ad hoc selection criteria, which also contributed to bringing new experts and younger scientists to the field, and (iv) a close interaction of AriSLA stakeholders with scientists, who developed a strong sense of belonging. Periodic review of the portfolio of investments is a vital practice for funding agencies. Sharing information between funding agencies about their own policies and research assessment methods and outcomes help guide the international debate on funding strategies and research directions to be undertaken, particularly in the field of rare diseases, where synergy is a relevant enabling factor.
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Affiliation(s)
| | | | | | | | | | | | - Anna Ambrosini
- Fondazione AriSLA ETS, Milan, Italy
- Fondazione Telethon ETS, Milan, Italy
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20
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Bagyinszky E, Hulme J, An SSA. Studies of Genetic and Proteomic Risk Factors of Amyotrophic Lateral Sclerosis Inspire Biomarker Development and Gene Therapy. Cells 2023; 12:1948. [PMID: 37566027 PMCID: PMC10417729 DOI: 10.3390/cells12151948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease affecting the upper and lower motor neurons, leading to muscle weakness, motor impairments, disabilities and death. Approximately 5-10% of ALS cases are associated with positive family history (familial ALS or fALS), whilst the remainder are sporadic (sporadic ALS, sALS). At least 50 genes have been identified as causative or risk factors for ALS. Established pathogenic variants include superoxide dismutase type 1 (SOD1), chromosome 9 open reading frame 72 (c9orf72), TAR DNA Binding Protein (TARDBP), and Fused In Sarcoma (FUS); additional ALS-related genes including Charged Multivesicular Body Protein 2B (CHMP2B), Senataxin (SETX), Sequestosome 1 (SQSTM1), TANK Binding Kinase 1 (TBK1) and NIMA Related Kinase 1 (NEK1), have been identified. Mutations in these genes could impair different mechanisms, including vesicle transport, autophagy, and cytoskeletal or mitochondrial functions. So far, there is no effective therapy against ALS. Thus, early diagnosis and disease risk predictions remain one of the best options against ALS symptomologies. Proteomic biomarkers, microRNAs, and extracellular vehicles (EVs) serve as promising tools for disease diagnosis or progression assessment. These markers are relatively easy to obtain from blood or cerebrospinal fluids and can be used to identify potential genetic causative and risk factors even in the preclinical stage before symptoms appear. In addition, antisense oligonucleotides and RNA gene therapies have successfully been employed against other diseases, such as childhood-onset spinal muscular atrophy (SMA), which could also give hope to ALS patients. Therefore, an effective gene and biomarker panel should be generated for potentially "at risk" individuals to provide timely interventions and better treatment outcomes for ALS patients as soon as possible.
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Affiliation(s)
- Eva Bagyinszky
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - John Hulme
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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21
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Roy B, Peck A, Evangelista T, Pfeffer G, Wang L, Diaz‐Manera J, Korb M, Wicklund MP, Milone M, Freimer M, Kushlaf H, Villar‐Quiles R, Stojkovic T, Needham M, Palmio J, Lloyd TE, Keung B, Mozaffar T, Weihl CC, Kimonis V. Provisional practice recommendation for the management of myopathy in VCP-associated multisystem proteinopathy. Ann Clin Transl Neurol 2023; 10:686-695. [PMID: 37026610 PMCID: PMC10187720 DOI: 10.1002/acn3.51760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Valosin-containing protein (VCP)-associated multisystem proteinopathy (MSP) is a rare genetic disorder with abnormalities in the autophagy pathway leading to various combinations of myopathy, bone diseases, and neurodegeneration. Ninety percent of patients with VCP-associated MSP have myopathy, but there is no consensus-based guideline. The goal of this working group was to develop a best practice set of provisional recommendations for VCP myopathy which can be easily implemented across the globe. As an initiative by Cure VCP Disease Inc., a patient advocacy organization, an online survey was initially conducted to identify the practice gaps in VCP myopathy. All prior published literature on VCP myopathy was reviewed to better understand the different aspects of management of VCP myopathy, and several working group sessions were conducted involving international experts to develop this provisional recommendation. VCP myopathy has a heterogeneous clinical phenotype and should be considered in patients with limb-girdle muscular dystrophy phenotype, or any myopathy with an autosomal dominant pattern of inheritance. Genetic testing is the only definitive way to diagnose VCP myopathy, and single-variant testing in the case of a known familial VCP variant, or multi-gene panel sequencing in undifferentiated cases can be considered. Muscle biopsy is important in cases of diagnostic uncertainty or lack of a definitive pathogenic genetic variant since rimmed vacuoles (present in ~40% cases) are considered a hallmark of VCP myopathy. Electrodiagnostic studies and magnetic resonance imaging can also help rule out disease mimics. Standardized management of VCP myopathy will optimize patient care and help future research initiatives.
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Affiliation(s)
- Bhaskar Roy
- Department of NeurologyYale School of MedicineNew HavenConnecticutUSA
| | | | - Teresinha Evangelista
- GH Pitié‐Salpêtrière, Sorbonne Université‐Inserm UMRS97, Institut de MyologieParisFrance
| | - Gerald Pfeffer
- Hotchkiss Brain Institute, Department of Clinical NeurosciencesUniversity of Calgary Cumming School of MedicineCalgaryAlbertaCanada
| | - Leo Wang
- Department of NeurologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jordi Diaz‐Manera
- John Walton Muscular Dystrophy Research CentreNewcastle UniversityNewcastle upon TyneUK
| | - Manisha Korb
- Department of NeurologyUniversity of California—Irvine School of MedicineOrangeCaliforniaUSA
| | | | | | - Miriam Freimer
- Department of NeurologyOhio State UniversityColumbusOhioUSA
| | - Hani Kushlaf
- Department of Neurology and Rehabilitation MedicineUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Rocio‐Nur Villar‐Quiles
- APHP, Reference Center for Neuromuscular Disorders, Center of Research in MyologySorbonne Université‐Inserm UMRS974, Pitié‐Salpêtrière HospitalParisFrance
| | - Tanya Stojkovic
- APHP, Reference Center for Neuromuscular Disorders, Center of Research in MyologySorbonne Université‐Inserm UMRS974, Pitié‐Salpêtrière HospitalParisFrance
| | - Merrilee Needham
- University of Notre Dame, Murdoch University and Fiona Stanley HospitalPerthAustralia
| | - Johanna Palmio
- Neuromuscular Research CenterTampere University HospitalTampereFinland
| | - Thomas E. Lloyd
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMassachusettsUSA
- Department of Neuroscience and PathologyJohns Hopkins University School of MedicineBaltimoreMassachusettsUSA
| | - Benison Keung
- Department of NeurologyYale School of MedicineNew HavenConnecticutUSA
| | - Tahseen Mozaffar
- Department of NeurologyUniversity of California—Irvine School of MedicineOrangeCaliforniaUSA
| | - Conrad Chris Weihl
- Department of NeurologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Virginia Kimonis
- Department of NeurologyUniversity of California—Irvine School of MedicineOrangeCaliforniaUSA
- Department of PediatricsUniversity of California—Irvine School of MedicineOrangeCaliforniaUSA
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22
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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23
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Malik AM, Wu JJ, Gillies CA, Doctrove QA, Li X, Huang H, Tank EHM, Shakkottai VG, Barmada S. Neuronal activity regulates Matrin 3 abundance and function in a calcium-dependent manner through calpain-mediated cleavage and calmodulin binding. Proc Natl Acad Sci U S A 2023; 120:e2206217120. [PMID: 37011198 PMCID: PMC10104577 DOI: 10.1073/pnas.2206217120] [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: 04/08/2022] [Accepted: 02/14/2023] [Indexed: 04/05/2023] Open
Abstract
RNA-binding protein (RBP) dysfunction is a fundamental hallmark of amyotrophic lateral sclerosis (ALS) and related neuromuscular disorders. Abnormal neuronal excitability is also a conserved feature in ALS patients and disease models, yet little is known about how activity-dependent processes regulate RBP levels and functions. Mutations in the gene encoding the RBP Matrin 3 (MATR3) cause familial disease, and MATR3 pathology has also been observed in sporadic ALS, suggesting a key role for MATR3 in disease pathogenesis. Here, we show that glutamatergic activity drives MATR3 degradation through an NMDA receptor-, Ca2+-, and calpain-dependent mechanism. The most common pathogenic MATR3 mutation renders it resistant to calpain degradation, suggesting a link between activity-dependent MATR3 regulation and disease. We also demonstrate that Ca2+ regulates MATR3 through a nondegradative process involving the binding of Ca2+/calmodulin to MATR3 and inhibition of its RNA-binding ability. These findings indicate that neuronal activity impacts both the abundance and function of MATR3, underscoring the effect of activity on RBPs and providing a foundation for further study of Ca2+-coupled regulation of RBPs implicated in ALS and related neurological diseases.
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Affiliation(s)
- Ahmed M. Malik
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI48109
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI48109
- Department of Neurology, University of Michigan, Ann Arbor, MI48109
| | - Josephine J. Wu
- Department of Neurology, University of Michigan, Ann Arbor, MI48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI48109
| | - Christie A. Gillies
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI48109
| | - Quinlan A. Doctrove
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI48109
- Postbac Research Education Program, University of Michigan, Ann Arbor, MI48109
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI48109
| | - Haoran Huang
- University of Texas Southwestern Medical Center, Dallas, TX 75390
| | | | | | - Sami Barmada
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI48109
- Department of Neurology, University of Michigan, Ann Arbor, MI48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI48109
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24
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van Hummel A, Sabale M, Przybyla M, van der Hoven J, Chan G, Feiten AF, Chung RS, Ittner LM, Ke YD. TDP-43 pathology and functional deficits in wild-type and ALS/FTD mutant cyclin F mouse models. Neuropathol Appl Neurobiol 2023; 49:e12902. [PMID: 36951214 PMCID: PMC10946706 DOI: 10.1111/nan.12902] [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: 10/31/2022] [Revised: 03/08/2023] [Accepted: 03/18/2023] [Indexed: 03/24/2023]
Abstract
AIMS Amyotrophic lateral sclerosis (ALS) is characterised by a progressive loss of upper and lower motor neurons leading to muscle weakness and eventually death. Frontotemporal dementia (FTD) presents clinically with significant behavioural decline. Approximately 10% of cases have a known family history, and disease-linked mutations in multiple genes have been identified in FTD and ALS. More recently, ALS and FTD-linked variants have been identified in the CCNF gene, which accounts for an estimated 0.6% to over 3% of familial ALS cases. METHODS In this study, we developed the first mouse models expressing either wild-type (WT) human CCNF or its mutant pathogenic variant S621G to recapitulate key clinical and neuropathological features of ALS and FTD linked to CCNF disease variants. We expressed human CCNF WT or CCNFS621G throughout the murine brain by intracranial delivery of adeno-associated virus (AAV) to achieve widespread delivery via somatic brain transgenesis. RESULTS These mice developed behavioural abnormalities, similar to the clinical symptoms of FTD patients, as early as 3 months of age, including hyperactivity and disinhibition, which progressively deteriorated to include memory deficits by 8 months of age. Brains of mutant CCNF_S621G mice displayed an accumulation of ubiquitinated proteins with elevated levels of phosphorylated TDP-43 present in both CCNF_WT and mutant CCNF_S621G mice. We also investigated the effects of CCNF expression on interaction targets of CCNF and found elevated levels of insoluble splicing factor proline and glutamine-rich (SFPQ). Furthermore, cytoplasmic TDP-43 inclusions were found in both CCNF_WT and mutant CCNF_S621G mice, recapitulating the key hallmark of FTD/ALS pathology. CONCLUSIONS In summary, CCNF expression in mice reproduces clinical presentations of ALS, including functional deficits and TDP-43 neuropathology with altered CCNF-mediated pathways contributing to the pathology observed.
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Affiliation(s)
- Annika van Hummel
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Miheer Sabale
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Magdalena Przybyla
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Julia van der Hoven
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Gabriella Chan
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Astrid F. Feiten
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of MedicineLudwig‐Maximilians‐Universität MünchenMunich81377Germany
| | - Roger S. Chung
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Lars M. Ittner
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Yazi D. Ke
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
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25
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Muys BR, Shrestha RL, Anastasakis DG, Pongor L, Li XL, Grammatikakis I, Polash A, Chari R, Gorospe M, Harris CC, Aladjem MI, Basrai MA, Hafner M, Lal A. Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B. Cell Rep 2023; 42:112260. [PMID: 36924503 PMCID: PMC10132239 DOI: 10.1016/j.celrep.2023.112260] [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: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Matrin3 is an RNA-binding protein that regulates diverse RNA-related processes, including mRNA splicing. Although Matrin3 has been intensively studied in neurodegenerative diseases, its function in cancer remains unclear. Here, we report Matrin3-mediated regulation of mitotic spindle dynamics in colorectal cancer (CRC) cells. We comprehensively identified RNAs bound and regulated by Matrin3 in CRC cells and focused on CDC14B, one of the top Matrin3 targets. Matrin3 knockdown results in increased inclusion of an exon containing a premature termination codon in the CDC14B transcript and simultaneous down-regulation of the standard CDC14B transcript. Knockdown of CDC14B phenocopies the defects in mitotic spindle dynamics upon Matrin3 knockdown, and the elongated and misoriented mitotic spindle observed upon Matrin3 knockdown are rescued upon overexpression of CDC14B, suggesting that CDC14B is a key downstream effector of Matrin3. Collectively, these data reveal a role for the Matrin3/CDC14B axis in control of mitotic spindle dynamics.
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Affiliation(s)
- Bruna R Muys
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA
| | | | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA
| | - Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA
| | - Ahsan Polash
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD 21701, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, CCR, NCI, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA.
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA.
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26
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Dominick M, Houchins N, Venugopal V, Zuberi AR, Lutz CM, Meechooveet B, Van Keuren-Jensen K, Bowser R, Medina DX. MATR3 P154S knock-in mice do not exhibit motor, muscle or neuropathologic features of ALS. Biochem Biophys Res Commun 2023; 645:164-172. [PMID: 36689813 PMCID: PMC10046992 DOI: 10.1016/j.bbrc.2023.01.032] [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: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Matrin 3 is a nuclear matrix protein that has many roles in RNA processing including splicing and transport of mRNA. Many missense mutations in the Matrin 3 gene (MATR3) have been linked to familial forms of amyotrophic lateral sclerosis (ALS) and distal myopathy. However, the exact role of MATR3 mutations in ALS and myopathy pathogenesis is not understood. To demonstrate a role of MATR3 mutations in vivo, we generated a novel CRISPR/Cas9 mediated knock-in mouse model harboring the MATR3 P154S mutation expressed under the control of the endogenous promoter. The P154S variant of the MATR3 gene has been linked to familial forms of ALS. Heterozygous and homozygous MATR3 P154S knock-in mice did not develop progressive motor deficits compared to wild-type mice. In addition, ALS-like pathology did not develop in nervous or muscle tissue in either heterozygous or homozygous mice. Our results suggest that the MATR3 P154S variant is not sufficient to produce ALS-like pathology in vivo.
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Affiliation(s)
- Marissa Dominick
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ, 85013, USA
| | - Nicole Houchins
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ, 85013, USA
| | - Vinisha Venugopal
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ, 85013, USA
| | - Aamir R Zuberi
- Rare and Orphan Disease Translational Center, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Cathleen M Lutz
- Rare and Orphan Disease Translational Center, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Bessie Meechooveet
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Robert Bowser
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ, 85013, USA
| | - David X Medina
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ, 85013, USA.
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27
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Oliveira Santos M, Gromicho M, Pronto-Laborinho A, de Carvalho M. Sporadic Spinal-Onset Amyotrophic Lateral Sclerosis Associated with Myopathy in Three Unrelated Portuguese Patients. Brain Sci 2023; 13:brainsci13020220. [PMID: 36831763 PMCID: PMC9953916 DOI: 10.3390/brainsci13020220] [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: 11/13/2022] [Revised: 01/15/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and myopathy have been already described as part of a common genetic syndrome called multisystem proteinopathy. They may occur together or not, and can be associated with other clinical features such as frontotemporal dementia and Paget's bone disease. In addition, primary skeletal muscle involvement has been also reported in inherited forms of lower motor neuron disease, in spinal-bulbar muscular atrophy and in spinal muscular atrophy. We aim to characterize three sporadic, spinal-onset ALS patients, one with a concurrent non-specific myopathy, and two with a previous diagnosis of myopathy before upper and lower motor neuron signs emerged. Perhaps our sporadic ALS cases associated with myopathy share a common, but still unknown, pathogenic background. These cases raise the paradigm of a possible interplay between skeletal muscle degeneration and motor neuron damage.
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Affiliation(s)
- Miguel Oliveira Santos
- Department of Neurosciences and Mental Health, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, 1649-028 Lisbon, Portugal
- Instituto de Fisiologia, Instituto de Medicina Molecular, Centro de Estudos Egas Moniz, Faculdade de Medicina, Universidade de Lisboa, 1648-028 Lisbon, Portugal
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Centro de Estudos Egas Moniz, Faculdade de Medicina, Universidade de Lisboa, 1648-028 Lisbon, Portugal
| | - Ana Pronto-Laborinho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Centro de Estudos Egas Moniz, Faculdade de Medicina, Universidade de Lisboa, 1648-028 Lisbon, Portugal
| | - Mamede de Carvalho
- Department of Neurosciences and Mental Health, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, 1649-028 Lisbon, Portugal
- Instituto de Fisiologia, Instituto de Medicina Molecular, Centro de Estudos Egas Moniz, Faculdade de Medicina, Universidade de Lisboa, 1648-028 Lisbon, Portugal
- Correspondence: ; Tel./Fax: +351-217-805-219
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28
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Udine E, Jain A, van Blitterswijk M. Advances in sequencing technologies for amyotrophic lateral sclerosis research. Mol Neurodegener 2023; 18:4. [PMID: 36635726 PMCID: PMC9838075 DOI: 10.1186/s13024-022-00593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is caused by upper and lower motor neuron loss and has a fairly rapid disease progression, leading to fatality in an average of 2-5 years after symptom onset. Numerous genes have been implicated in this disease; however, many cases remain unexplained. Several technologies are being used to identify regions of interest and investigate candidate genes. Initial approaches to detect ALS genes include, among others, linkage analysis, Sanger sequencing, and genome-wide association studies. More recently, next-generation sequencing methods, such as whole-exome and whole-genome sequencing, have been introduced. While those methods have been particularly useful in discovering new ALS-linked genes, methodological advances are becoming increasingly important, especially given the complex genetics of ALS. Novel sequencing technologies, like long-read sequencing, are beginning to be used to uncover the contribution of repeat expansions and other types of structural variation, which may help explain missing heritability in ALS. In this review, we discuss how popular and/or upcoming methods are being used to discover ALS genes, highlighting emerging long-read sequencing platforms and their role in aiding our understanding of this challenging disease.
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Affiliation(s)
- Evan Udine
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Angita Jain
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Center for Clinical and Translational Sciences, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL, 32224, USA.
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Huang K, Fan X, Jiang Y, Jin S, Huang J, Pang L, Wang Y, Wu Y, Sun X. Integrative identification of hub genes in development of atrial fibrillation related stroke. PLoS One 2023; 18:e0283617. [PMID: 36952494 PMCID: PMC10035830 DOI: 10.1371/journal.pone.0283617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND As the most common arrhythmia, atrial fibrillation (AF) is associated with a significantly increased risk of stroke, which causes high disability and mortality. To date, the underlying mechanism of stroke occurring after AF remains unclear. Herein, we studied hub genes and regulatory pathways involved in AF and secondary stroke and aimed to reveal biomarkers and therapeutic targets of AF-related stroke. METHODS The GSE79768 and GSE58294 datasets were used to analyze AF- and stroke-related differentially expressed genes (DEGs) to obtain a DEG1 dataset. Weighted correlation network analysis (WGCNA) was used to identify modules associated with AF-related stroke in GSE66724 (DEG2). DEG1 and DEG2 were merged, and hub genes were identified based on protein-protein interaction networks. Gene Ontology terms were used to analyze the enriched pathways. The GSE129409 and GSE70887 were applied to construct a circRNA-miRNA-mRNA network in AF-related stroke. Hub genes were verified in patients using quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS We identified 3,132 DEGs in blood samples and 253 DEGs in left atrial specimens. Co-expressed hub genes of EIF4E3, ZNF595, ZNF700, MATR3, ACKR4, ANXA3, SEPSECS-AS1, and RNF166 were significantly associated with AF-related stroke. The hsa_circ_0018657/hsa-miR-198/EIF4E3 pathway was explored as the regulating axis in AF-related stroke. The qRT-PCR results were consistent with the bioinformatic analysis. CONCLUSIONS Hub genes EIF4E3, ZNF595, ZNF700, MATR3, ACKR4, ANXA3, SEPSECS-AS1, and RNF166 have potential as novel biomarkers and therapeutic targets in AF-related stroke. The hsa_circ_0018657/hsa-miR-198/EIF4E3 axis could play an important role regulating the development of AF-related stroke.
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Affiliation(s)
- Kai Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Xi Fan
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yuwen Jiang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Sheng Jin
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Jiechun Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Liewen Pang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yiqing Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yuming Wu
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Xiaotian Sun
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
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Muzio L, Ghirelli A, Agosta F, Martino G. Novel therapeutic approaches for motor neuron disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 196:523-537. [PMID: 37620088 DOI: 10.1016/b978-0-323-98817-9.00027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to the neurodegeneration and death of upper and lower motor neurons (MNs). Although MNs are the main cells involved in the process of neurodegeneration, a growing body of evidence points toward other cell types as concurrent to disease initiation and propagation. Given the current absence of effective therapies, the quest for other therapeutic targets remains open and still challenges the scientific community. Both neuronal and extra-neuronal mechanisms of cellular stress and damage have been studied and have posed the basis for the development of novel therapies that have been investigated on both animal models and humans. In this chapter, a thorough review of the main mechanisms of cellular damage and the respective therapeutic attempts targeting them is reported. The main areas covered include neuroinflammation, protein aggregation, RNA metabolism, and oxidative stress.
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Affiliation(s)
- Luca Muzio
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy
| | - Alma Ghirelli
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Agosta
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Gianvito Martino
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
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31
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Savarese M, Jokela M, Udd B. Distal myopathy. HANDBOOK OF CLINICAL NEUROLOGY 2023; 195:497-519. [PMID: 37562883 DOI: 10.1016/b978-0-323-98818-6.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Distal myopathies are a group of genetic, primary muscle diseases. Patients develop progressive weakness and atrophy of the muscles of forearm, hands, lower leg, or feet. Currently, over 20 different forms, presenting a variable age of onset, clinical presentation, disease progression, muscle involvement, and histological findings, are known. Some of them are dominant and some recessive. Different variants in the same gene are often associated with either dominant or recessive forms, although there is a lack of a comprehensive understanding of the genotype-phenotype correlations. This chapter provides a description of the clinicopathologic and genetic aspects of distal myopathies emphasizing known etiologic and pathophysiologic mechanisms.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland; Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, Tampere, Finland; Division of Clinical Neurosciences, Department of Neurology, Turku University Hospital, Turku, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland; Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland; Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, Tampere, Finland; Department of Neurology, Vaasa Central Hospital, Vaasa, Finland.
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32
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Yuan A, Nixon RA. Posttranscriptional regulation of neurofilament proteins and tau in health and disease. Brain Res Bull 2023; 192:115-127. [PMID: 36441047 PMCID: PMC9907725 DOI: 10.1016/j.brainresbull.2022.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 01/16/2023]
Abstract
Neurofilament and tau proteins are neuron-specific cytoskeletal proteins that are enriched in axons, regulated by many of the same protein kinases, interact physically, and are the principal constituents of neurofibrillary lesions in major adult-onset dementias. Both proteins share functions related to the modulation of stability and functions of the microtubule network in axons, axonal transport and scaffolding of organelles, long-term synaptic potentiation, and learning and memory. Expression of these proteins is regulated not only at the transcriptional level but also through posttranscriptional control of pre-mRNA splicing, mRNA stability, transport, localization, local translation and degradation. Current evidence suggests that posttranscriptional determinants of their levels are usually regulated by RNA-binding proteins and microRNAs primarily through 3'-untranslated regions of neurofilament and tau mRNAs. Dysregulations of neurofilament and tau expression caused by mutations or pathologies of RNA-binding proteins such as TDP43, FUS and microRNAs are increasingly recognized in association with varied neurological disorders. In this review, we summarize the current understanding of posttranscriptional control of neurofilament and tau by examining the posttranscriptional regulation of neurofilament and tau by RNA-binding proteins and microRNAs implicated in health and diseases.
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Affiliation(s)
- Aidong Yuan
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University Langone Health, New York, NY 10016, USA; NYU Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA.
| | - Ralph A. Nixon
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA,Department of Psychiatry, New York University Langone Health, New York, NY 10016, USA,Department of Cell Biology, New York University Langone Health, New York, NY 10016, USA,NYU Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA,Correspondence to: Center for Dementia Research, Nathan Kline Institute, New York University Langone Health, New York, NY 10016, USA, (A. Yuan), (R.A. Nixon)
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Kumar R, Malik Z, Singh M, Rachana R, Mani S, Ponnusamy K, Haider S. Amyotrophic Lateral Sclerosis Risk Genes and Suppressor. Curr Gene Ther 2023; 23:148-162. [PMID: 36366843 DOI: 10.2174/1566523223666221108113330] [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: 04/11/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to death by progressive paralysis and respiratory failure within 2-4 years of onset. About 90-95% of ALS cases are sporadic (sALS), and 5-10% are inherited through family (fALS). Though the mechanisms of the disease are still poorly understood, so far, approximately 40 genes have been reported as ALS causative genes. The mutations in some crucial genes, like SOD1, C9ORF72, FUS, and TDP-43, are majorly associated with ALS, resulting in ROS-associated oxidative stress, excitotoxicity, protein aggregation, altered RNA processing, axonal and vesicular trafficking dysregulation, and mitochondrial dysfunction. Recent studies show that dysfunctional cellular pathways get restored as a result of the repair of a single pathway in ALS. In this review article, our aim is to identify putative targets for therapeutic development and the importance of a single suppressor to reduce multiple symptoms by focusing on important mutations and the phenotypic suppressors of dysfunctional cellular pathways in crucial genes as reported by other studies.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - Zubbair Malik
- School of Computational and Integrative Science, Jawaharlal Nehru University, New Delhi-110067, India
| | - Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - R Rachana
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - Shalini Mani
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | | | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
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Sung W, Nahm M, Lim SM, Noh MY, Lee S, Hwang SM, Kim YH, Park J, Oh KW, Ki CS, Kim YE, Kim SH. Clinical and genetic characteristics of amyotrophic lateral sclerosis patients with ANXA11 variants. Brain Commun 2022; 4:fcac299. [PMID: 36458208 PMCID: PMC9707645 DOI: 10.1093/braincomms/fcac299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/26/2022] [Accepted: 11/16/2022] [Indexed: 08/12/2023] Open
Abstract
Increasing genetic evidence supports the hypothesis that variants in the annexin A11 gene (ANXA11 ) contribute to amyotrophic lateral sclerosis pathogenesis. Therefore, we studied the clinical aspects of sporadic amyotrophic lateral sclerosis patients carrying ANXA11 variants. We also implemented functional experiments to verify the pathogenicity of the hotspot variants associated with amyotrophic lateral sclerosis-frontotemporal dementia. Korean patients diagnosed with amyotrophic lateral sclerosis (n = 882) underwent genetic evaluations through next-generation sequencing, which identified 16 ANXA11 variants in 26 patients. We analysed their clinical features, such as the age of onset, progression rate, initial symptoms and cognitive status. To evaluate the functional significance of the ANXA11 variants in amyotrophic lateral sclerosis-frontotemporal dementia pathology, we additionally utilized patient fibroblasts carrying frontotemporal dementia-linked ANXA11 variants (p.P36R and p.D40G ) to perform a series of in vitro studies, including calcium imaging, stress granule dynamics and protein translation. The frequency of the pathogenic or likely pathogenic variants of ANXA11 was 0.3% and the frequency of variants classified as variants of unknown significance was 2.6%. The patients with variants in the low-complexity domain presented unique clinical features, including late-onset, a high prevalence of amyotrophic lateral sclerosis-frontotemporal dementia, a fast initial progression rate and a high tendency for bulbar-onset compared with patients carrying variants in the C-terminal repeated annexin homology domains. In addition, functional studies using amyotrophic lateral sclerosis-frontotemporal dementia patient fibroblasts revealed that the ANXA11 variants p.P36R and p.D40G impaired intracellular calcium homeostasis, stress granule disassembly and protein translation. This study suggests that the clinical manifestations of amyotrophic lateral sclerosis and amyotrophic lateral sclerosis-frontotemporal dementia spectrum patients with ANXA11 variants could be distinctively characterized depending upon the location of the variant.
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Affiliation(s)
- Wonjae Sung
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Minyeop Nahm
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Su Min Lim
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Min-Young Noh
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Sanggon Lee
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Sung-Min Hwang
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Yong Ho Kim
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Jinseok Park
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Ki-Wook Oh
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | | | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
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35
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Lee J, Cho H, Kwon I. Phase separation of low-complexity domains in cellular function and disease. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1412-1422. [PMID: 36175485 PMCID: PMC9534829 DOI: 10.1038/s12276-022-00857-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the ways in which recent studies of low-complexity (LC) domains have challenged our understanding of the mechanisms underlying cellular organization. LC sequences, long believed to function in the absence of a molecular structure, are abundant in the proteomes of all eukaryotic organisms. Over the past decade, the phase separation of LC domains has emerged as a fundamental mechanism driving dynamic multivalent interactions of many cellular processes. We review the key evidence showing the role of phase separation of individual proteins in organizing cellular assemblies and facilitating biological function while implicating the dynamics of phase separation as a key to biological validity and functional utility. We also highlight the evidence showing that pathogenic LC proteins alter various phase separation-dependent interactions to elicit debilitating human diseases, including cancer and neurodegenerative diseases. Progress in understanding the biology of phase separation may offer useful hints toward possible therapeutic interventions to combat the toxicity of pathogenic proteins.
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Affiliation(s)
- Jiwon Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Hana Cho
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
| | - Ilmin Kwon
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
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36
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Alexander GM, Heiman-Patterson TD, Bearoff F, Sher RB, Hennessy L, Terek S, Caccavo N, Cox GA, Philip VM, Blankenhorn EA. Identification of quantitative trait loci for survival in the mutant dynactin p150Glued mouse model of motor neuron disease. PLoS One 2022; 17:e0274615. [PMID: 36107978 PMCID: PMC9477371 DOI: 10.1371/journal.pone.0274615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/01/2022] [Indexed: 11/19/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common degenerative motor neuron disorder. Although most cases of ALS are sporadic, 5-10% of cases are familial, with mutations associated with over 40 genes. There is variation of ALS symptoms within families carrying the same mutation; the disease may develop in one sibling and not in another despite the presence of the mutation in both. Although the cause of this phenotypic variation is unknown, it is likely related to genetic modifiers of disease expression. The identification of ALS causing genes has led to the development of transgenic mouse models of motor neuron disease. Similar to families with familial ALS, there are background-dependent differences in disease phenotype in transgenic mouse models of ALS suggesting that, as in human ALS, differences in phenotype may be ascribed to genetic modifiers. These genetic modifiers may not cause ALS rather their expression either exacerbates or ameliorates the effect of the mutant ALS causing genes. We have reported that in both the G93A-hSOD1 and G59S-hDCTN1 mouse models, SJL mice demonstrated a more severe phenotype than C57BL6 mice. From reciprocal intercrosses between G93A-hSOD1 transgenic mice on SJL and C57BL6 strains, we identified a major quantitative trait locus (QTL) on mouse chromosome 17 that results in a significant shift in lifespan. In this study we generated reciprocal intercrosses between transgenic G59S-hDCTN1 mice on SJL and C57BL6 strains and identified survival QTLs on mouse chromosomes 17 and 18. The chromosome 17 survival QTL on G93A-hSOD1 and G59S-hDCTN1 mice partly overlap, suggesting that the genetic modifiers located in this region may be shared by these two ALS models despite the fact that motor neuron degeneration is caused by mutations in different proteins. The overlapping region contains eighty-seven genes with non-synonymous variations predicted to be deleterious and/or damaging. Two genes in this segment, NOTCH3 and Safb/SAFB1, have been associated with motor neuron disease. The identification of genetic modifiers of motor neuron disease, especially those modifiers that are shared by SOD1 and dynactin-1 transgenic mice, may result in the identification of novel targets for therapies that can alter the course of this devastating illness.
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Affiliation(s)
| | - Terry D. Heiman-Patterson
- Department of Neurology, Lewis Katz School of Medicine of Temple University, Philadelphia, Pennsylvania, United States of America
| | - Frank Bearoff
- Department of Microbiology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Roger B. Sher
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| | - Laura Hennessy
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Shannon Terek
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Nicole Caccavo
- Department of Neurology, Lewis Katz School of Medicine of Temple University, Philadelphia, Pennsylvania, United States of America
| | - Gregory A. Cox
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Vivek M. Philip
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Elizabeth A. Blankenhorn
- Department of Microbiology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
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Cao MC, Scotter EL. Novel and known transcriptional targets of ALS/FTD protein TDP-43: Meta-analysis and interactive graphical database. Dis Model Mech 2022; 15:276263. [PMID: 35946434 PMCID: PMC9509890 DOI: 10.1242/dmm.049418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Abstract
TDP-43 proteinopathy is the major pathology in amyotrophic lateral sclerosis (ALS) and tau-negative frontotemporal dementia (FTD). Mounting evidence implicates loss of normal TDP-43 RNA processing function as a key pathomechanism. However, the RNA targets of TDP-43 differ by report, and have never been formally collated or compared between models and disease, hampering understanding of TDP-43 function. Here, we conducted re-analysis and meta-analysis of publicly available RNA-sequencing datasets from six TDP-43-knockdown models, and TDP-43-immunonegative neuronal nuclei from ALS/ FTD brain, to identify differentially expressed genes (DEGs) and exon usage (DEU) events. There was little overlap in DEGs between knockdown models, but PFKP, STMN2, CFP, KIAA1324 and TRHDE were common targets and were also differentially expressed in TDP-43-immunonegative neurons. DEG enrichment analysis revealed diverse biological pathways including immune and synaptic functions. Common DEU events in human datasets included well-known targets POLDIP3 and STMN2, and novel targets EXD3, MMAB, DLG5 and GOSR2. Our interactive database https://phpstack-449938-2576646.cloudwaysapps.com/ allows further exploration of TDP-43 DEG and DEU targets. Together, these data identify TDP-43 targets that can be exploited therapeutically or to validate loss-of-function processes.
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Affiliation(s)
- Maize C Cao
- School of Biological Sciences and Centre for Brain Research, University of Auckland, Auckland, New Zealand. 3A Symonds Street, Auckland 1010, New Zealand
| | - Emma L Scotter
- School of Biological Sciences and Centre for Brain Research, University of Auckland, Auckland, New Zealand. 3A Symonds Street, Auckland 1010, New Zealand
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Secchi M, Lodola C, Garbelli A, Bione S, Maga G. DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective. Cancers (Basel) 2022; 14:cancers14153820. [PMID: 35954483 PMCID: PMC9367324 DOI: 10.3390/cancers14153820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies. Abstract RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.
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Regulating Phase Transition in Neurodegenerative Diseases by Nuclear Import Receptors. BIOLOGY 2022; 11:biology11071009. [PMID: 36101390 PMCID: PMC9311884 DOI: 10.3390/biology11071009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
RNA-binding proteins (RBPs) with a low-complexity prion-like domain (PLD) can undergo aberrant phase transitions and have been implicated in neurodegenerative diseases such as ALS and FTD. Several nuclear RBPs mislocalize to cytoplasmic inclusions in disease conditions. Impairment in nucleocytoplasmic transport is another major event observed in ageing and in neurodegenerative disorders. Nuclear import receptors (NIRs) regulate the nucleocytoplasmic transport of different RBPs bearing a nuclear localization signal by restoring their nuclear localization. NIRs can also specifically dissolve or prevent the aggregation and liquid–liquid phase separation of wild-type or disease-linked mutant RBPs, due to their chaperoning activity. This review focuses on the LLPS of intrinsically disordered proteins and the role of NIRs in regulating LLPS in neurodegeneration. This review also discusses the implication of NIRs as therapeutic agents in neurogenerative diseases.
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Nelson RS, Dammer EB, Santiago JV, Seyfried NT, Rangaraju S. Brain Cell Type-Specific Nuclear Proteomics Is Imperative to Resolve Neurodegenerative Disease Mechanisms. Front Neurosci 2022; 16:902146. [PMID: 35784845 PMCID: PMC9243337 DOI: 10.3389/fnins.2022.902146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 01/19/2023] Open
Abstract
Neurodegenerative diseases (NDs) involve complex cellular mechanisms that are incompletely understood. Emerging findings have revealed that disruption of nuclear processes play key roles in ND pathogenesis. The nucleus is a nexus for gene regulation and cellular processes that together, may underlie pathomechanisms of NDs. Furthermore, many genetic risk factors for NDs encode proteins that are either present in the nucleus or are involved in nuclear processes (for example, RNA binding proteins, epigenetic regulators, or nuclear-cytoplasmic transport proteins). While recent advances in nuclear transcriptomics have been significant, studies of the nuclear proteome in brain have been relatively limited. We propose that a comprehensive analysis of nuclear proteomic alterations of various brain cell types in NDs may provide novel biological and therapeutic insights. This may be feasible because emerging technical advances allow isolation and investigation of intact nuclei from post-mortem frozen human brain tissue with cell type-specific and single-cell resolution. Accordingly, nuclei of various brain cell types harbor unique protein markers which can be used to isolate cell-type specific nuclei followed by down-stream proteomics by mass spectrometry. Here we review the literature providing a rationale for investigating proteomic changes occurring in nuclei in NDs and then highlight the potential for brain cell type-specific nuclear proteomics to enhance our understanding of distinct cellular mechanisms that drive ND pathogenesis.
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Affiliation(s)
- Ruth S. Nelson
- Department of Neurology, Emory University, Atlanta, GA, United States
| | - Eric B. Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, United States
| | | | | | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, United States,*Correspondence: Srikant Rangaraju
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Azari A, Goodarzi A, Jafarkhani B, Eghbali M, Karimi Z, Hosseini Balef SS, Irannejad H. Novel molecular targets and mechanisms for neuroprotective modulation in neurodegenerative disorders. Cent Nerv Syst Agents Med Chem 2022; 22:88-107. [PMID: 35713146 DOI: 10.2174/1871524922666220616092132] [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: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuronal death underlies the symptoms of several human neurological disorders, including Alzheimer's, Parkinson's and Huntington's diseases, and amyotrophic lateral sclerosis that their precise pathophysiology have not yet been elucidated. According to various studies the prohibition is the best therapy with neuroprotective approaches which are advanced and safe methods. METHODS This review summarizes some of the already-known and newly emerged neuroprotective targets and strategies that their experimental effects have been reported. Accordingly, literature was studied from 2000 to 2021 and appropriate articles were searched in Google Scholar and Scopus with the keywords given in the Keywords section of the current review. RESULTS Lewy bodies are the histopathologic characteristics of neurodegenerative disorders and are protein-rich intracellular deposits in which Alpha-Synuclein is its major protein. Alpha-Synuclein's toxic potential provides a compelling rationale for therapeutic strategies aimed at decreasing its burden in neuronal cells through numerous pathways including ubiquitin-proteasome system and autophagy-lysosome Pathway, proteolytic breakdown via cathepsin D, kallikrein-6 (neurosin), calpain-1 or MMP9, heat shock proteins, and proteolysis targeting chimera which consists of a target protein ligand and an E3 ubiquitin ligase (E3) followed by target protein ubiquitination (PROTACs). Other targets that have been noticed recently are the mutant huntingtin, tau proteins and glycogen synthase kinase 3β that their accumulation proceeds extensive neuronal damage and up to the minute approach such as Proteolysis Targeting Chimera promotes its degradation in cells. As various studies demonstrated that Mendelian gene mutations can result into the neurodegenerative diseases, additional target that has gained much interest is epigenetics such as mutation, phosphodiesterase, RNA binding proteins and Nuclear respiratory factor 1. CONCLUSION The novel molecular targets and new strategies compiled and introduced here can be used by scientists to design and discover more efficient small molecule drugs against the neurodegenerative diseases. And also the genes in which their mutations can lead to the α-synuclein aggregation or accumulation are discussed and considered a valuable information of epigenetics in dementia.
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Affiliation(s)
- Aala Azari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amin Goodarzi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Behrouz Jafarkhani
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Eghbali
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zohreh Karimi
- Department of Obstetrics & Gynecology, Imam Khomeini hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Sajad Hosseini Balef
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hamid Irannejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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42
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Lambert-Smith IA, Saunders DN, Yerbury JJ. Progress in biophysics and molecular biology proteostasis impairment and ALS. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 174:3-27. [PMID: 35716729 DOI: 10.1016/j.pbiomolbio.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disease that results from the loss of both upper and lower motor neurons. It is the most common motor neuron disease and currently has no effective treatment. There is mounting evidence to suggest that disturbances in proteostasis play a significant role in ALS pathogenesis. Proteostasis is the maintenance of the proteome at the right level, conformation and location to allow a cell to perform its intended function. In this review, we present a thorough synthesis of the literature that provides evidence that genetic mutations associated with ALS cause imbalance to a proteome that is vulnerable to such pressure due to its metastable nature. We propose that the mechanism underlying motor neuron death caused by defects in mRNA metabolism and protein degradation pathways converges on proteostasis dysfunction. We propose that the proteostasis network may provide an effective target for therapeutic development in ALS.
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Affiliation(s)
- Isabella A Lambert-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Darren N Saunders
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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43
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Tarutani A, Adachi T, Akatsu H, Hashizume Y, Hasegawa K, Saito Y, Robinson AC, Mann DMA, Yoshida M, Murayama S, Hasegawa M. Ultrastructural and biochemical classification of pathogenic tau, α-synuclein and TDP-43. Acta Neuropathol 2022; 143:613-640. [PMID: 35513543 PMCID: PMC9107452 DOI: 10.1007/s00401-022-02426-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/12/2022] [Accepted: 04/23/2022] [Indexed: 12/20/2022]
Abstract
Intracellular accumulation of abnormal proteins with conformational changes is the defining neuropathological feature of neurodegenerative diseases. The pathogenic proteins that accumulate in patients' brains adopt an amyloid-like fibrous structure and exhibit various ultrastructural features. The biochemical analysis of pathogenic proteins in sarkosyl-insoluble fractions extracted from patients' brains also shows disease-specific features. Intriguingly, these ultrastructural and biochemical features are common within the same disease group. These differences among the pathogenic proteins extracted from patients' brains have important implications for definitive diagnosis of the disease, and also suggest the existence of pathogenic protein strains that contribute to the heterogeneity of pathogenesis in neurodegenerative diseases. Recent experimental evidence has shown that prion-like propagation of these pathogenic proteins from host cells to recipient cells underlies the onset and progression of neurodegenerative diseases. The reproduction of the pathological features that characterize each disease in cellular and animal models of prion-like propagation also implies that the structural differences in the pathogenic proteins are inherited in a prion-like manner. In this review, we summarize the ultrastructural and biochemical features of pathogenic proteins extracted from the brains of patients with neurodegenerative diseases that accumulate abnormal forms of tau, α-synuclein, and TDP-43, and we discuss how these disease-specific properties are maintained in the brain, based on recent experimental insights.
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Affiliation(s)
- Airi Tarutani
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Tadashi Adachi
- Division of Neuropathology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, 683-8503, Japan
| | - Hiroyasu Akatsu
- Department of Neuropathology, Choju Medical Institute, Fukushimura Hospital, Aichi, 441-8124, Japan
- Department of Community-Based Medical Education, Nagoya City University Graduate School of Medical Sciences, Aichi, 467-8601, Japan
| | - Yoshio Hashizume
- Department of Neuropathology, Choju Medical Institute, Fukushimura Hospital, Aichi, 441-8124, Japan
| | - Kazuko Hasegawa
- Division of Neurology, National Hospital Organization, Sagamihara National Hospital, Kanagawa, 252-0392, Japan
| | - Yuko Saito
- Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, 173-0015, Japan
- Department of Pathology and Laboratory Medicine, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, 187-8551, Japan
| | - Andrew C Robinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience and Experimental Psychology, Salford Royal Hospital, The University of Manchester, Salford, M6 8HD, UK
| | - David M A Mann
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience and Experimental Psychology, Salford Royal Hospital, The University of Manchester, Salford, M6 8HD, UK
| | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Aichi, 480-1195, Japan
| | - Shigeo Murayama
- Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, 173-0015, Japan
- Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Osaka, 565-0871, Japan
| | - Masato Hasegawa
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
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44
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Pfeffer G, Lee G, Pontifex CS, Fanganiello RD, Peck A, Weihl CC, Kimonis V. Multisystem Proteinopathy Due to VCP Mutations: A Review of Clinical Heterogeneity and Genetic Diagnosis. Genes (Basel) 2022; 13:genes13060963. [PMID: 35741724 PMCID: PMC9222868 DOI: 10.3390/genes13060963] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
In this work, we review clinical features and genetic diagnosis of diseases caused by mutations in the gene encoding valosin-containing protein (VCP/p97), the functionally diverse AAA-ATPase. VCP is crucial to a multitude of cellular functions including protein quality control, stress granule formation and clearance, and genomic integrity functions, among others. Pathogenic mutations in VCP cause multisystem proteinopathy (VCP-MSP), an autosomal dominant, adult-onset disorder causing dysfunction in several tissue types. It can result in complex neurodegenerative conditions including inclusion body myopathy, frontotemporal dementia, amyotrophic lateral sclerosis, or combinations of these. There is also an association with other neurodegenerative phenotypes such as Alzheimer-type dementia and Parkinsonism. Non-neurological presentations include Paget disease of bone and may also include cardiac dysfunction. We provide a detailed discussion of genotype-phenotype correlations, recommendations for genetic diagnosis, and genetic counselling implications of VCP-MSP.
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Affiliation(s)
- Gerald Pfeffer
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence:
| | - Grace Lee
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California Irvine Medical Center, Orange, CA 92868, USA; (G.L.); (V.K.)
| | - Carly S. Pontifex
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Roberto D. Fanganiello
- Oral Ecology Research Group, Faculty of Dental Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Allison Peck
- Cure VCP Disease, Inc., Americus, GA 31709, USA;
| | - Conrad C. Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Virginia Kimonis
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California Irvine Medical Center, Orange, CA 92868, USA; (G.L.); (V.K.)
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45
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Calabrese G, Molzahn C, Mayor T. Protein interaction networks in neurodegenerative diseases: from physiological function to aggregation. J Biol Chem 2022; 298:102062. [PMID: 35623389 PMCID: PMC9234719 DOI: 10.1016/j.jbc.2022.102062] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/26/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
The accumulation of protein inclusions is linked to many neurodegenerative diseases that typically develop in older individuals, due to a combination of genetic and environmental factors. In rare familial neurodegenerative disorders, genes encoding for aggregation-prone proteins are often mutated. While the underlying mechanism leading to these diseases still remains to be fully elucidated, efforts in the past 20 years revealed a vast network of protein–protein interactions that play a major role in regulating the aggregation of key proteins associated with neurodegeneration. Misfolded proteins that can oligomerize and form insoluble aggregates associate with molecular chaperones and other elements of the proteolytic machineries that are the frontline workers attempting to protect the cells by promoting clearance and preventing aggregation. Proteins that are normally bound to aggregation-prone proteins can become sequestered and mislocalized in protein inclusions, leading to their loss of function. In contrast, mutations, posttranslational modifications, or misfolding of aggregation-prone proteins can lead to gain of function by inducing novel or altered protein interactions, which in turn can impact numerous essential cellular processes and organelles, such as vesicle trafficking and the mitochondria. This review examines our current knowledge of protein–protein interactions involving several key aggregation-prone proteins that are associated with Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, or amyotrophic lateral sclerosis. We aim to provide an overview of the protein interaction networks that play a central role in driving or mitigating inclusion formation, while highlighting some of the key proteomic studies that helped to uncover the extent of these networks.
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Affiliation(s)
- Gaetano Calabrese
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada.
| | - Cristen Molzahn
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada
| | - Thibault Mayor
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada.
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46
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Zhang JQ, Pan JQ, Wei ZY, Ren CY, Ru FX, Xia SY, He YS, Lin K, Chen JH. Brain Epitranscriptomic Analysis Revealed Altered A-to-I RNA Editing in Septic Patients. Front Genet 2022; 13:887001. [PMID: 35559016 PMCID: PMC9086164 DOI: 10.3389/fgene.2022.887001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Recent studies suggest that RNA editing is associated with impaired brain function and neurological and psychiatric disorders. However, the role of A-to-I RNA editing during sepsis-associated encephalopathy (SAE) remains unclear. In this study, we analyzed adenosine-to-inosine (A-to-I) RNA editing in postmortem brain tissues from septic patients and controls. A total of 3024 high-confidence A-to-I RNA editing sites were identified. In sepsis, there were fewer A-to-I RNA editing genes and editing sites than in controls. Among all A-to-I RNA editing sites, 42 genes showed significantly differential RNA editing, with 23 downregulated and 19 upregulated in sepsis compared to controls. Notably, more than 50% of these genes were highly expressed in the brain and potentially related to neurological diseases. Notably, cis-regulatory analysis showed that the level of RNA editing in six differentially edited genes was significantly correlated with the gene expression, including HAUS augmin-like complex subunit 2 (HAUS2), protein phosphatase 3 catalytic subunit beta (PPP3CB), hook microtubule tethering protein 3 (HOOK3), CUB and Sushi multiple domains 1 (CSMD1), methyltransferase-like 7A (METTL7A), and kinesin light chain 2 (KLC2). Furthermore, enrichment analysis showed that fewer gene functions and KEGG pathways were enriched by edited genes in sepsis compared to controls. These results revealed alteration of A-to-I RNA editing in the human brain associated with sepsis, thus providing an important basis for understanding its role in neuropathology in SAE.
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Affiliation(s)
- Jing-Qian Zhang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
| | - Jia-Qi Pan
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
| | - Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
| | - Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
| | - Fu-Xia Ru
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China.,Jieyang People's Hospital, Jieyang, China
| | - Shou-Yue Xia
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
| | | | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Joint Primate Research Center for Chronic Diseases, Wuxi School of Medicine, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Jiangnan University, Wuxi, China.,Jiangnan University Brain Institute, Wuxi, China
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47
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Sprunger ML, Lee K, Sohn BS, Jackrel ME. Molecular determinants and modifiers of Matrin-3 toxicity, condensate dynamics, and droplet morphology. iScience 2022; 25:103900. [PMID: 35252808 PMCID: PMC8889142 DOI: 10.1016/j.isci.2022.103900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Matrin-3 (MATR3) is a DNA- and RNA-binding protein implicated in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and distal myopathy. Here, we report the development of a yeast model of MATR3 proteotoxicity and aggregation. MATR3 is toxic and forms dynamic shell-like nuclear condensates in yeast. Disease-associated mutations in MATR3 impair condensate dynamics and disrupt condensate morphology. MATR3 toxicity is largely driven by its RNA-recognitions motifs (RRMs). Further, deletion of one or both RRMs drives coalescence of these condensates. Aberrant phase separation of several different RBPs underpins ALS/FTD, and we have engineered Hsp104 variants to reverse this misfolding. Here, we demonstrate that these same variants also counter MATR3 toxicity. We suggest that these Hsp104 variants which rescue MATR3, TDP-43, and FUS toxicity might be employed against a range of ALS/FTD-associated proteins. We anticipate that our yeast model could be a useful platform to screen for modulators of MATR3 misfolding.
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Affiliation(s)
- Macy L. Sprunger
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Ken Lee
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Brian S. Sohn
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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48
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Todd TW, Petrucelli L. Modelling amyotrophic lateral sclerosis in rodents. Nat Rev Neurosci 2022; 23:231-251. [PMID: 35260846 DOI: 10.1038/s41583-022-00564-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
The efficient study of human disease requires the proper tools, one of the most crucial of which is an accurate animal model that faithfully recapitulates the human condition. The study of amyotrophic lateral sclerosis (ALS) is no exception. Although the majority of ALS cases are considered sporadic, most animal models of this disease rely on genetic mutations identified in familial cases. Over the past decade, the number of genes associated with ALS has risen dramatically and, with each new genetic variant, there is a drive to develop associated animal models. Rodent models are of particular importance as they allow for the study of ALS in the context of a living mammal with a comparable CNS. Such models not only help to verify the pathogenicity of novel mutations but also provide critical insight into disease mechanisms and are crucial for the testing of new therapeutics. In this Review, we aim to summarize the full spectrum of ALS rodent models developed to date.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA.
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49
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Selective Loss of MATR3 in Spinal Interneurons, Upper Motor Neurons and Hippocampal CA1 Neurons in a MATR3 S85C Knock-In Mouse Model of Amyotrophic Lateral Sclerosis. BIOLOGY 2022; 11:biology11020298. [PMID: 35205163 PMCID: PMC8869279 DOI: 10.3390/biology11020298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting the motor neurons in the brain and spinal cord. Mutations in the gene Matr3 have been linked to ALS, including the autosomal dominant missense mutation S85C. We previously created a mouse model containing the S85C mutation in the Matr3 gene to understand how it causes ALS. The S85C mice exhibited MATR3 staining loss in selective populations of degenerating neurons, such as Purkinje cells in the cerebellum and α-motor neurons in the lumbar spinal cord. However, studies have shown that neurons other than motor neurons may be involved in contributing to ALS; therefore, we investigated additional neuronal cell types in the spinal cord and brain. Here, we found that MATR3 staining is selectively reduced in interneurons and α-motor neurons of the cervical and thoracic regions of the spinal cord, as well as in subsets of upper motor neurons and hippocampal neurons. These neurons did not exhibit cell body loss; however, how the MATR3 loss affects neuronal function remains to be determined. Overall, these findings demonstrate that the MATR3 S85C mutation affects other neuronal types of the brain and spinal cord in addition to motor neurons, suggesting that these additional neuronal types are involved in ALS pathogenesis. Abstract The neuropathological hallmark of amyotrophic lateral sclerosis (ALS) is motor neuron degeneration in the spinal cord and cortex. Accumulating studies report that other neurons in the central nervous system (CNS) are also affected in ALS. Mutations in Matr3, which encodes a nuclear matrix protein involved in RNA splicing, have been linked to ALS. Previously, we generated a MATR3 S85C knock-in (KI) mouse model that recapitulates early-stage features of ALS. We reported that MATR3 S85C KI mice exhibit defects in lumbar spinal cord motor neurons and in cerebellar Purkinje cells, which are associated with reduced MATR3 immunoreactivity. Here, we show that neurons in various other regions of the CNS are affected in MATR3 S85C KI mice. Using histological analyses, we found selective loss of MATR3 staining in α-motor neurons, but not γ-motor neurons in the cervical and thoracic spinal cord. Loss of MATR3 was also found in parvalbumin-positive interneurons in the cervical, thoracic and lumbar spinal cord. In addition, we found the loss of MATR3 in subsets of upper motor neurons and hippocampal CA1 neurons. Collectively, our findings suggest that these additional neuronal types may contribute to the disease process in MATR3 S85C KI mice.
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50
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Jiang LL, Guan WL, Wang JY, Zhang SX, Hu HY. RNA-assisted sequestration of RNA-binding proteins by cytoplasmic inclusions of the C-terminal 35-kDa fragment of TDP-43. J Cell Sci 2022; 135:274331. [PMID: 35142363 DOI: 10.1242/jcs.259380] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022] Open
Abstract
TDP-43 is a nuclear splicing factor functioning in pre-mRNA processing. Its C-terminal 35-kDa fragment (TDP-35) forms inclusions or aggregates in cytoplasm, and sequesters full-length TDP-43 into the inclusions through binding with RNA. We extended the research to investigate whether TDP-35 inclusions sequester other RNA-binding proteins (RBPs) and how RNA-binding specificity exerts the function in this sequestration process. We have characterized TIA1 (T-cell restricted intracellular antigen-1) and other RBPs that can be sequestered into the TDP-35 inclusions through specific RNA binding, and found that this sequestration leads to dysfunction of TIA1 in maturation of target pre-mRNA. Moreover, we directly visualized the dynamic sequestration of TDP-43 by the cytoplasmic TDP-35 inclusions by live-cell imaging. Our results demonstrate that TDP-35 sequesters some specific RBPs and this sequestration is assisted by binding with sequence-specific RNA. This study provides further evidence in supporting the hijacking hypothesis for RNA-assisted sequestration and will be beneficial to further understanding of the TDP-43 proteinopathies.
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Affiliation(s)
- Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Wen-Liang Guan
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian-Yang Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shu-Xian Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
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