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Huang WP, Ellis BCS, Hodgson RE, Sanchez Avila A, Kumar V, Rayment J, Moll T, Shelkovnikova TA. Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion. Cell Rep 2024; 43:114421. [PMID: 38941189 DOI: 10.1016/j.celrep.2024.114421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024] Open
Abstract
TDP-43 protein is dysregulated in several neurodegenerative diseases, which often have a multifactorial nature and may have extrinsic stressors as a "second hit." TDP-43 undergoes reversible nuclear condensation in stressed cells including neurons. Here, we demonstrate that stress-inducible nuclear TDP-43 condensates are RNA-depleted, non-liquid assemblies distinct from the known nuclear bodies. Their formation requires TDP-43 oligomerization and ATP and is inhibited by RNA. Using a confocal nanoscanning assay, we find that amyotrophic lateral sclerosis (ALS)-linked mutations alter stress-induced TDP-43 condensation by changing its affinity to liquid-like ribonucleoprotein assemblies. Stress-induced nuclear condensation transiently inactivates TDP-43, leading to loss of interaction with its protein binding partners and loss of function in splicing. Splicing changes are especially prominent and persisting for STMN2 RNA, and STMN2 protein becomes rapidly depleted early during stress. Our results point to early pathological changes to TDP-43 in the nucleus and support therapeutic modulation of stress response in ALS.
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Affiliation(s)
- Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Brittany C S Ellis
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Anna Sanchez Avila
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Vedanth Kumar
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Jessica Rayment
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK.
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Deng X, Seguinot BO, Bradshaw G, Lee JS, Coy S, Kalocsay M, Santagata S, Mitchison T. STMND1 is a phylogenetically ancient stathmin which localizes to motile cilia and exhibits nuclear translocation that is inhibited when soluble tubulin concentration increases. Mol Biol Cell 2024; 35:ar82. [PMID: 38630521 DOI: 10.1091/mbc.e23-12-0514] [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: 05/14/2024] Open
Abstract
Stathmins are small, unstructured proteins that bind tubulin dimers and are implicated in several human diseases, but whose function remains unknown. We characterized a new stathmin, STMND1 (Stathmin Domain Containing 1) as the human representative of an ancient subfamily. STMND1 features a N-terminal myristoylated and palmitoylated motif which directs it to membranes and a tubulin-binding stathmin-like domain (SLD) that contains an internal nuclear localization signal. Biochemistry and proximity labeling showed that STMND1 binds tubulin, and live imaging showed that tubulin binding inhibits translocation from cellular membranes to the nucleus. STMND1 is highly expressed in multiciliated epithelial cells, where it localizes to motile cilia. Overexpression in a model system increased the length of primary cilia. Our study suggests that the most ancient stathmins have cilium-related functions that involve sensing soluble tubulin.
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Affiliation(s)
- Xiang Deng
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Bryan O Seguinot
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Gary Bradshaw
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Jong Suk Lee
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Shannon Coy
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Marian Kalocsay
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Sandro Santagata
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Timothy Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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Nguyen L. Updates on Disease Mechanisms and Therapeutics for Amyotrophic Lateral Sclerosis. Cells 2024; 13:888. [PMID: 38891021 PMCID: PMC11172142 DOI: 10.3390/cells13110888] [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: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS), or Lou Gehrig's disease, is a motor neuron disease. In ALS, upper and lower motor neurons in the brain and spinal cord progressively degenerate during the course of the disease, leading to the loss of the voluntary movement of the arms and legs. Since its first description in 1869 by a French neurologist Jean-Martin Charcot, the scientific discoveries on ALS have increased our understanding of ALS genetics, pathology and mechanisms and provided novel therapeutic strategies. The goal of this review article is to provide a comprehensive summary of the recent findings on ALS mechanisms and related therapeutic strategies to the scientific audience. Several highlighted ALS research topics discussed in this article include the 2023 FDA approved drug for SOD1 ALS, the updated C9orf72 GGGGCC repeat-expansion-related mechanisms and therapeutic targets, TDP-43-mediated cryptic splicing and disease markers and diagnostic and therapeutic options offered by these recent discoveries.
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Affiliation(s)
- Lien Nguyen
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Luo Q, Wang J, Ge W, Li Z, Mao Y, Wang C, Zhang L. Exploration of the potential causative genes for inflammatory bowel disease: Transcriptome-wide association analysis, Mendelian randomization analysis and Bayesian colocalisation. Heliyon 2024; 10:e28944. [PMID: 38617957 PMCID: PMC11015108 DOI: 10.1016/j.heliyon.2024.e28944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
Background Inflammatory bowel disease (IBD) poses a complex challenge due to its intricate underlying mechanisms, and curative treatments remain elusive. Consequently, there is an urgent need to identify genes causally associated with IBD. Methods We extracted blood eQTL data from the GTExv8.ALL.Whole_Blood database, genome-wide association studies (GWAS) summary statistics of IBD from the IEU GWAS database, and performed a three-fold analysis protocol, including transcriptome-wide association analysis, Mendelian randomisation analysis, Bayesian colocalisation, and subsequent potential therapeutic agents identification. Results We identified four pathogenic genes, namely CARD9, RTEL1, STMN3 and ARFRP1, that promote the development of IBD, encompassing both ulcerative colitis (UC) and Crohn's disease (CD). Notably, ARFRP1 exhibited the ability to suppress IBD (encompassing UC and CD) development. Regarding drug prediction, cyclophosphamide emerged as a promising novel therapeutic option for IBD, encompassing UC and CD. Conclusion We identified several potential genes related to IBD (UC and CD), including CARD9, RTEL1, STMN3 and ARFRP1, warranting further investigation in functional studies to elucidate underlying disease mechanisms. Additionally, clinical studies exploring the potential of cyclophosphamide as a treatment avenue for IBD are warranted.
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Affiliation(s)
- Qinghua Luo
- Clinical Medical College, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Jiawen Wang
- Department of Proctology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Ge
- Department of Proctology, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zihao Li
- Office of the President, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Yuanting Mao
- Clinical Medical College, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Chen Wang
- Department of Proctology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Leichang Zhang
- Formula-Pattern Research Center, Jiangxi University of Chinese Medicine, Jiangxi, China
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Xu J, Hörner M, Nagel M, Korneck M, Noß M, Hauser S, Schöls L, Admard J, Casadei N, Schüle R. Unraveling Axonal Transcriptional Landscapes: Insights from iPSC-Derived Cortical Neurons and Implications for Motor Neuron Degeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586780. [PMID: 38585749 PMCID: PMC10996649 DOI: 10.1101/2024.03.26.586780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment specific analysis. In this study, we employ a robust RNA-sequencing (RNA-seq) approach, using microfluidic devices, to generate high-quality axonal transcriptomes from iPSC-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, ribosomal proteins (RPs), mitochondrial-encoded RNAs, and long non-coding RNAs (lncRNAs). Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a subset of previously unreported TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analyzed KIF1C-knockout (KO) CNs, modeling hereditary spastic paraplegia (HSP), a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in KIF1C-KO axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of KIF1C on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment specific disease mechanisms.
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Kim YS, Seo N, Kim JH, Kang S, Park JW, Park KD, Lee HA, Park M. Exploring the Functional Heterogeneity of Directly Reprogrammed Neural Stem Cell-Derived Neurons via Single-Cell RNA Sequencing. Cells 2023; 12:2818. [PMID: 38132138 PMCID: PMC10742074 DOI: 10.3390/cells12242818] [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: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
The therapeutic potential of directly reprogrammed neural stem cells (iNSCs) for neurodegenerative diseases relies on reducing the innate tumorigenicity of pluripotent stem cells. However, the heterogeneity within iNSCs is a major hurdle in quality control prior to clinical applications. Herein, we generated iNSCs from human fibroblasts, by transfecting transcription factors using Sendai virus particles, and characterized the expression of iNSC markers. Using immunostaining and quantitative real time -polymerase chain reaction (RT -qPCR), no differences were observed between colonies of iNSCs and iNSC-derived neurons. Unexpectedly, patch-clamp analysis of iNSC-derived neurons revealed distinctive action potential firing even within the same batch product. We performed single-cell RNA sequencing in fibroblasts, iNSCs, and iNSC-derived neurons to dissect their functional heterogeneity and identify cell fate regulators during direct reprogramming followed by neuronal differentiation. Pseudotime trajectory analysis revealed distinct cell types depending on their gene expression profiles. Differential gene expression analysis showed distinct NEUROG1, PEG3, and STMN2 expression patterns in iNSCs and iNSC-derived neurons. Taken together, we recommend performing a predictable functional assessment with appropriate surrogate markers to ensure the quality control of iNSCs and their differentiated neurons, particularly before cell banking for regenerative cell therapy.
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Affiliation(s)
- Yoo Sung Kim
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
| | - NaRi Seo
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
| | - Ji-Hye Kim
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
| | - Soyeong Kang
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
| | - Ji Won Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
| | - Ki Dae Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
| | - Hyang-Ae Lee
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea;
| | - Misun Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (Y.S.K.); (N.S.); (J.-H.K.); (S.K.); (J.W.P.); (K.D.P.)
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