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Limone F, Mordes DA, Couto A, Joseph BJ, Mitchell JM, Therrien M, Ghosh SD, Meyer D, Zhang Y, Goldman M, Bortolin L, Cobos I, Stevens B, McCarroll SA, Kadiu I, Burberry A, Pietiläinen O, Eggan K. Single-nucleus sequencing reveals enriched expression of genetic risk factors in extratelencephalic neurons sensitive to degeneration in ALS. NATURE AGING 2024:10.1038/s43587-024-00640-0. [PMID: 38907103 DOI: 10.1038/s43587-024-00640-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/01/2024] [Indexed: 06/23/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by a progressive loss of motor function linked to degenerating extratelencephalic neurons/Betz cells (ETNs). The reasons why these neurons are selectively affected remain unclear. Here, to understand the unique molecular properties that may sensitize ETNs to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In both patients and unaffected individuals, we found significantly higher expression of ALS risk genes in THY1+ ETNs, regardless of diagnosis. In patients, this was accompanied by the induction of genes involved in protein homeostasis and stress responses that were significantly induced in a wide collection of ETNs. Examination of oligodendroglial and microglial nuclei revealed patient-specific downregulation of myelinating genes in oligodendrocytes and upregulation of an endolysosomal reactive state in microglia. Our findings suggest that selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitizing them to genetics and mechanisms of degeneration.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian J Joseph
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jana M Mitchell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martine Therrien
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Sulagna Dia Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yingying Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Laura Bortolin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Inma Cobos
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Beth Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Irena Kadiu
- Neuroinflammation Focus Area, UCB Pharma, Braine-l'Alleud, Belgium
| | - Aaron Burberry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Olli Pietiläinen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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2
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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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3
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Cheng F, Chapman T, Zhang S, Morsch M, Chung R, Lee A, Rayner SL. Understanding age-related pathologic changes in TDP-43 functions and the consequence on RNA splicing and signalling in health and disease. Ageing Res Rev 2024; 96:102246. [PMID: 38401571 DOI: 10.1016/j.arr.2024.102246] [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: 10/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
TAR DNA binding protein-43 (TDP-43) is a key component in RNA splicing which plays a crucial role in the aging process. In neurodegenerative diseases such as amyotrophic lateral sclerosis, frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, TDP-43 can be mutated, mislocalised out of the nucleus of neurons and glial cells and form cytoplasmic inclusions. These TDP-43 alterations can lead to its RNA splicing dysregulation and contribute to mis-splicing of various types of RNA, such as mRNA, microRNA, and circular RNA. These changes can result in the generation of an altered transcriptome and proteome within cells, ultimately changing the diversity and quantity of gene products. In this review, we summarise the findings of novel atypical RNAs resulting from TDP-43 dysfunction and their potential as biomarkers or targets for therapeutic development.
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Affiliation(s)
- Flora Cheng
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
| | - Tyler Chapman
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Selina Zhang
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Marco Morsch
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Roger Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Stephanie L Rayner
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
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4
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Krus KL, Benitez AM, Strickland A, Milbrandt J, Bloom AJ, DiAntonio A. Reduced STMN2 and pathogenic TDP-43, two hallmarks of ALS, synergize to accelerate motor decline in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585052. [PMID: 38562780 PMCID: PMC10983882 DOI: 10.1101/2024.03.19.585052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pathological TDP-43 loss from the nucleus and cytoplasmic aggregation occurs in almost all cases of ALS and half of frontotemporal dementia patients. Stathmin2 (Stmn2) is a key target of TDP-43 regulation and aberrantly spliced Stmn2 mRNA is found in patients with ALS, frontotemporal dementia, and Alzheimer's Disease. STMN2 participates in the axon injury response and its depletion in vivo partially replicates ALS-like symptoms including progressive motor deficits and distal NMJ denervation. The interaction between STMN2 loss and TDP-43 dysfunction has not been studied in mice because TDP-43 regulates human but not murine Stmn2 splicing. Therefore, we generated trans-heterozygous mice that lack one functional copy of Stmn2 and express one mutant TDP-43Q331K knock-in allele to investigate whether reduced STMN2 function exacerbates TDP-43-dependent pathology. Indeed, we observe synergy between these two alleles, resulting in an early onset, progressive motor deficit. Surprisingly, this behavioral defect is not accompanied by detectable neuropathology in the brain, spinal cord, peripheral nerves or at neuromuscular junctions (NMJs). However, the trans-heterozygous mice exhibit abnormal mitochondrial morphology in their distal axons and NMJs. As both STMN2 and TDP-43 affect mitochondrial dynamics, and neuronal mitochondrial dysfunction is a cardinal feature of many neurodegenerative diseases, this abnormality likely contributes to the observed motor deficit. These findings demonstrate that partial loss of STMN2 significantly exacerbates TDP-43-associated phenotypes, suggesting that STMN2 restoration could ameliorate TDP-43 related disease before the onset of degeneration.
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Affiliation(s)
- Kelsey L. Krus
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
| | - Ana Morales Benitez
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
| | - Amy Strickland
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
| | - A. Joseph Bloom
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
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5
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San Gil R, Pascovici D, Venturato J, Brown-Wright H, Mehta P, Madrid San Martin L, Wu J, Luan W, Chui YK, Bademosi AT, Swaminathan S, Naidoo S, Berning BA, Wright AL, Keating SS, Curtis MA, Faull RLM, Lee JD, Ngo ST, Lee A, Morsch M, Chung RS, Scotter E, Lisowski L, Mirzaei M, Walker AK. A transient protein folding response targets aggregation in the early phase of TDP-43-mediated neurodegeneration. Nat Commun 2024; 15:1508. [PMID: 38374041 PMCID: PMC10876645 DOI: 10.1038/s41467-024-45646-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Understanding the mechanisms that drive TDP-43 pathology is integral to combating amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD) and other neurodegenerative diseases. Here we generated a longitudinal quantitative proteomic map of the cortex from the cytoplasmic TDP-43 rNLS8 mouse model of ALS and FTLD, and developed a complementary open-access webtool, TDP-map ( https://shiny.rcc.uq.edu.au/TDP-map/ ). We identified distinct protein subsets enriched for diverse biological pathways with temporal alterations in protein abundance, including increases in protein folding factors prior to disease onset. This included increased levels of DnaJ homolog subfamily B member 5, DNAJB5, which also co-localized with TDP-43 pathology in diseased human motor cortex. DNAJB5 over-expression decreased TDP-43 aggregation in cell and cortical neuron cultures, and knockout of Dnajb5 exacerbated motor impairments caused by AAV-mediated cytoplasmic TDP-43 expression in mice. Together, these findings reveal molecular mechanisms at distinct stages of ALS and FTLD progression and suggest that protein folding factors could be protective in neurodegenerative diseases.
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Affiliation(s)
- Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Dana Pascovici
- Insight Stats, Croydon Park, NSW, Australia
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde Sydney, NSW, Australia
| | - Juliana Venturato
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Heledd Brown-Wright
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Prachi Mehta
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Lidia Madrid San Martin
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jemma Wu
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde Sydney, NSW, Australia
| | - Wei Luan
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Yi Kit Chui
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Adekunle T Bademosi
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Shilpa Swaminathan
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Serey Naidoo
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Britt A Berning
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda L Wright
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sean S Keating
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Maurice A Curtis
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - John D Lee
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Shyuan T Ngo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Marco Morsch
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Roger S Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Emma Scotter
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Leszek Lisowski
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Westmead, NSW, Australia
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde Sydney, NSW, Australia
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
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6
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Iguchi Y, Takahashi Y, Li J, Araki K, Amakusa Y, Kawakami Y, Kobayashi K, Yokoi S, Katsuno M. IκB kinase phosphorylates cytoplasmic TDP-43 and promotes its proteasome degradation. J Cell Biol 2024; 223:e202302048. [PMID: 38197897 PMCID: PMC10783433 DOI: 10.1083/jcb.202302048] [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: 02/19/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024] Open
Abstract
Cytoplasmic aggregation of TDP-43 in neurons is a pathological feature common to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). We demonstrate that the IκB kinase (IKK) complex promotes the degradation of cytoplasmic TDP-43 through proteasomes. While IKKβ is a major factor in TDP-43 degradation, IKKα acts as a cofactor, and NEMO functions as a scaffold for the recruitment of TDP-43 to the IKK complex. Furthermore, we identified IKKβ-induced phosphorylation sites of TDP-43 and found that phosphorylation at Thr8 and Ser92 is important for the reduction of TDP-43 by IKK. TDP-43 phosphorylation at Ser92 was detected in a pattern different from that of C-terminal phosphorylation in the pathological inclusion of ALS. IKKβ was also found to significantly reduce the expression level and toxicity of the disease-causing TDP-43 mutation. Finally, the favorable effect of IKKβ on TDP-43 aggregation was confirmed in the hippocampus of mice. IKK and the N-terminal phosphorylation of TDP-43 are potential therapeutic targets for ALS and FTLD.
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Affiliation(s)
- Yohei Iguchi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhei Takahashi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jiayi Li
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kunihiko Araki
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Medical Faculty, Institute of Experimental Epileptology and Cognition Research, University of Bonn, Bonn, Germany
| | - Yoshinobu Amakusa
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yu Kawakami
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Okazaki, Japan
| | - Satoshi Yokoi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, Nagoya, Japan
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7
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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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8
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Irwin KE, Jasin P, Braunstein KE, Sinha IR, Garret MA, Bowden KD, Chang K, Troncoso JC, Moghekar A, Oh ES, Raitcheva D, Bartlett D, Miller T, Berry JD, Traynor BJ, Ling JP, Wong PC. A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS-FTD. Nat Med 2024; 30:382-393. [PMID: 38278991 PMCID: PMC10878965 DOI: 10.1038/s41591-023-02788-5] [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: 01/24/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
Although loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well documented in postmortem tissues of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects loss of function of TDP-43, and thus detection of proteins containing cryptic exon-encoded neoepitopes in cerebrospinal fluid (CSF) or blood could reveal the earliest stages of TDP-43 dysregulation in patients. Here we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found in HDGFL2) to show that loss of TDP-43 splicing repression occurs in ALS-FTD, including in presymptomatic C9orf72 mutation carriers. Cryptic hepatoma-derived growth factor-like protein 2 (HDGFL2) accumulates in CSF at significantly higher levels in familial ALS-FTD and sporadic ALS compared with controls and is elevated earlier than neurofilament light and phosphorylated neurofilament heavy chain protein levels in familial disease. Cryptic HDGFL2 can also be detected in blood of individuals with ALS-FTD, including in presymptomatic C9orf72 mutation carriers, and accumulates at levels highly correlated with those in CSF. Our findings indicate that loss of TDP-43 cryptic splicing repression occurs early in disease progression, even presymptomatically, and that detection of the HDGFL2 cryptic neoepitope serves as a potential diagnostic biomarker for ALS, which should facilitate patient recruitment and measurement of target engagement in clinical trials.
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Affiliation(s)
- Katherine E Irwin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Pei Jasin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | - Irika R Sinha
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Mark A Garret
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Kyra D Bowden
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Esther S Oh
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | | | - Timothy Miller
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - James D Berry
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- National Institute of Neurological Disorders, National Institutes of Health, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA.
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9
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Agra Almeida Quadros AR, Li Z, Wang X, Ndayambaje IS, Aryal S, Ramesh N, Nolan M, Jayakumar R, Han Y, Stillman H, Aguilar C, Wheeler HJ, Connors T, Lopez-Erauskin J, Baughn MW, Melamed Z, Beccari MS, Olmedo Martínez L, Canori M, Lee CZ, Moran L, Draper I, Kopin AS, Oakley DH, Dickson DW, Cleveland DW, Hyman BT, Das S, Ertekin-Taner N, Lagier-Tourenne C. Cryptic splicing of stathmin-2 and UNC13A mRNAs is a pathological hallmark of TDP-43-associated Alzheimer's disease. Acta Neuropathol 2024; 147:9. [PMID: 38175301 PMCID: PMC10766724 DOI: 10.1007/s00401-023-02655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Nuclear clearance and cytoplasmic accumulations of the RNA-binding protein TDP-43 are pathological hallmarks in almost all patients with amyotrophic lateral sclerosis (ALS) and up to 50% of patients with frontotemporal dementia (FTD) and Alzheimer's disease. In Alzheimer's disease, TDP-43 pathology is predominantly observed in the limbic system and correlates with cognitive decline and reduced hippocampal volume. Disruption of nuclear TDP-43 function leads to abnormal RNA splicing and incorporation of erroneous cryptic exons in numerous transcripts including Stathmin-2 (STMN2, also known as SCG10) and UNC13A, recently reported in tissues from patients with ALS and FTD. Here, we identify both STMN2 and UNC13A cryptic exons in Alzheimer's disease patients, that correlate with TDP-43 pathology burden, but not with amyloid-β or tau deposits. We also demonstrate that processing of the STMN2 pre-mRNA is more sensitive to TDP-43 loss of function than UNC13A. In addition, full-length RNAs encoding STMN2 and UNC13A are suppressed in large RNA-seq datasets generated from Alzheimer's disease post-mortem brain tissue. Collectively, these results open exciting new avenues to use STMN2 and UNC13A as potential therapeutic targets in a broad range of neurodegenerative conditions with TDP-43 proteinopathy including Alzheimer's disease.
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Affiliation(s)
- Ana Rita Agra Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Zhaozhi Li
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandeep Aryal
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Nandini Ramesh
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rojashree Jayakumar
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Han
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Stillman
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hayden J Wheeler
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theresa Connors
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jone Lopez-Erauskin
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Michael W Baughn
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Laura Olmedo Martínez
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Canori
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Moran
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Bradley T Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
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10
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López-Erauskin J, Bravo-Hernandez M, Presa M, Baughn MW, Melamed Z, Beccari MS, Agra de Almeida Quadros AR, Arnold-Garcia O, Zuberi A, Ling K, Platoshyn O, Niño-Jara E, Ndayambaje IS, McAlonis-Downes M, Cabrera L, Artates JW, Ryan J, Hermann A, Ravits J, Bennett CF, Jafar-Nejad P, Rigo F, Marsala M, Lutz CM, Cleveland DW, Lagier-Tourenne C. Stathmin-2 loss leads to neurofilament-dependent axonal collapse driving motor and sensory denervation. Nat Neurosci 2024; 27:34-47. [PMID: 37996528 PMCID: PMC10842032 DOI: 10.1038/s41593-023-01496-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/16/2023] [Indexed: 11/25/2023]
Abstract
The mRNA transcript of the human STMN2 gene, encoding for stathmin-2 protein (also called SCG10), is profoundly impacted by TAR DNA-binding protein 43 (TDP-43) loss of function. The latter is a hallmark of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Using a combination of approaches, including transient antisense oligonucleotide-mediated suppression, sustained shRNA-induced depletion in aging mice, and germline deletion, we show that stathmin-2 has an important role in the establishment and maintenance of neurofilament-dependent axoplasmic organization that is critical for preserving the caliber and conduction velocity of myelinated large-diameter axons. Persistent stathmin-2 loss in adult mice results in pathologies found in ALS, including reduced interneurofilament spacing, axonal caliber collapse that drives tearing within outer myelin layers, diminished conduction velocity, progressive motor and sensory deficits, and muscle denervation. These findings reinforce restoration of stathmin-2 as an attractive therapeutic approach for ALS and other TDP-43-dependent neurodegenerative diseases.
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Affiliation(s)
- Jone López-Erauskin
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Mariana Bravo-Hernandez
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | | | - Michael W Baughn
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Medical Neurobiology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melinda S Beccari
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ana Rita Agra de Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olatz Arnold-Garcia
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), Madrid, Spain
| | | | - Karen Ling
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Oleksandr Platoshyn
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Elkin Niño-Jara
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Melissa McAlonis-Downes
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Larissa Cabrera
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Jonathan W Artates
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Anita Hermann
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Martin Marsala
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Don W Cleveland
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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11
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Frazel PW, Labib D, Fisher T, Brosh R, Pirjanian N, Marchildon A, Boeke JD, Fossati V, Liddelow SA. Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols. Nat Neurosci 2023; 26:1726-1738. [PMID: 37697111 PMCID: PMC10763608 DOI: 10.1038/s41593-023-01424-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence during the development of the brain and spinal cord. Here we used single-cell/single-nucleus RNA sequencing (scRNA-seq/snRNA-seq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human-induced pluripotent stem cells. We computationally identify candidate genes involved in the fate specification of glia in both species and report heterogeneous expression of astrocyte surface markers across differentiating cells. We then used our transcriptomic data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multi-omic, dual single-nuclei (sn)RNA-seq/snATAC-seq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets will enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.
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Affiliation(s)
- Paul W Frazel
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA.
| | - David Labib
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Theodore Fisher
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York City, NY, USA
| | - Nicolette Pirjanian
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Anne Marchildon
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York City, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA.
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York City, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York City, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York City, NY, USA.
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12
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Lin JP, Brake A, Donadieu M, Lee A, Kawaguchi R, Sati P, Geschwind DH, Jacobson S, Schafer DP, Reich DS. A 4D transcriptomic map for the evolution of multiple sclerosis-like lesions in the marmoset brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559371. [PMID: 37808784 PMCID: PMC10557631 DOI: 10.1101/2023.09.25.559371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Single-time-point histopathological studies on postmortem multiple sclerosis (MS) tissue fail to capture lesion evolution dynamics, posing challenges for therapy development targeting development and repair of focal inflammatory demyelination. To close this gap, we studied experimental autoimmune encephalitis (EAE) in the common marmoset, the most faithful animal model of these processes. Using MRI-informed RNA profiling, we analyzed ~600,000 single-nucleus and ~55,000 spatial transcriptomes, comparing them against EAE inoculation status, longitudinal radiological signals, and histopathological features. We categorized 5 groups of microenvironments pertinent to neural function, immune and glial responses, tissue destruction and repair, and regulatory network at brain borders. Exploring perilesional microenvironment diversity, we uncovered central roles of EAE-associated astrocytes, oligodendrocyte precursor cells, and ependyma in lesion formation and resolution. We pinpointed imaging and molecular features capturing the pathological trajectory of WM, offering potential for assessing treatment outcomes using marmoset as a platform.
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Affiliation(s)
- Jing-Ping Lin
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Alexis Brake
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Maxime Donadieu
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Amanda Lee
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Riki Kawaguchi
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA
| | - Pascal Sati
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA
| | - Daniel H Geschwind
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA
- Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Dorothy P Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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13
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Estades Ayuso V, Pickles S, Todd T, Yue M, Jansen-West K, Song Y, González Bejarano J, Rawlinson B, DeTure M, Graff-Radford NR, Boeve BF, Knopman DS, Petersen RC, Dickson DW, Josephs KA, Petrucelli L, Prudencio M. TDP-43-regulated cryptic RNAs accumulate in Alzheimer's disease brains. Mol Neurodegener 2023; 18:57. [PMID: 37605276 PMCID: PMC10441763 DOI: 10.1186/s13024-023-00646-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Inclusions of TAR DNA-binding protein 43 kDa (TDP-43) has been designated limbic-predominant, age-related TDP-43 encephalopathy (LATE), with or without co-occurrence of Alzheimer's disease (AD). Approximately, 30-70% AD cases present TDP-43 proteinopathy (AD-TDP), and a greater disease severity compared to AD patients without TDP-43 pathology. However, it remains unclear to what extent TDP-43 dysfunction is involved in AD pathogenesis. METHODS To investigate whether TDP-43 dysfunction is a prominent feature in AD-TDP cases, we evaluated whether non-conserved cryptic exons, which serve as a marker of TDP-43 dysfunction in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP), accumulate in AD-TDP brains. We assessed a cohort of 192 post-mortem brains from three different brain regions: amygdala, hippocampus, and frontal cortex. Following RNA and protein extraction, qRT-PCR and immunoassays were performed to quantify the accumulation of cryptic RNA targets and phosphorylated TDP-43 pathology, respectively. RESULTS We detected the accumulation of misspliced cryptic or skiptic RNAs of STMN2, KCNQ2, UNC13A, CAMK2B, and SYT7 in the amygdala and hippocampus of AD-TDP cases. The topographic distribution of cryptic RNA accumulation mimicked that of phosphorylated TDP-43, regardless of TDP-43 subtype classification. Further, cryptic RNAs efficiently discriminated AD-TDP cases from controls. CONCLUSIONS Overall, our results indicate that cryptic RNAs may represent an intriguing new therapeutic and diagnostic target in AD, and that methods aimed at detecting and measuring these species in patient biofluids could be used as a reliable tool to assess TDP-43 pathology in AD. Our work also raises the possibility that TDP-43 dysfunction and related changes in cryptic splicing could represent a common molecular mechanism shared between AD-TDP and FTLD-TDP.
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Affiliation(s)
- Virginia Estades Ayuso
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Tiffany Todd
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Yuping Song
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | | | | | | | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | | | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA.
- Department of Research, Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.
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14
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Mann JR, McKenna ED, Mawrie D, Papakis V, Alessandrini F, Anderson EN, Mayers R, Ball HE, Kaspi E, Lubinski K, Baron DM, Tellez L, Landers JE, Pandey UB, Kiskinis E. Loss of function of the ALS-associated NEK1 kinase disrupts microtubule homeostasis and nuclear import. SCIENCE ADVANCES 2023; 9:eadi5548. [PMID: 37585529 PMCID: PMC10431718 DOI: 10.1126/sciadv.adi5548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Loss-of-function variants in NIMA-related kinase 1 (NEK1) constitute a major genetic cause of amyotrophic lateral sclerosis (ALS), accounting for 2 to 3% of all cases. However, how NEK1 mutations cause motor neuron (MN) dysfunction is unknown. Using mass spectrometry analyses for NEK1 interactors and NEK1-dependent expression changes, we find functional enrichment for proteins involved in the microtubule cytoskeleton and nucleocytoplasmic transport. We show that α-tubulin and importin-β1, two key proteins involved in these processes, are phosphorylated by NEK1 in vitro. NEK1 is essential for motor control and survival in Drosophila models in vivo, while using several induced pluripotent stem cell (iPSC)-MN models, including NEK1 knockdown, kinase inhibition, and a patient mutation, we find evidence for disruptions in microtubule homeostasis and nuclear import. Notably, stabilizing microtubules with two distinct classes of drugs restored NEK1-dependent deficits in both pathways. The capacity of NEK1 to modulate these processes that are critically involved in ALS pathophysiology renders this kinase a formidable therapeutic candidate.
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Affiliation(s)
- Jacob R. Mann
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth D. McKenna
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Francesco Alessandrini
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric N. Anderson
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Ryan Mayers
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hannah E. Ball
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evan Kaspi
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Katherine Lubinski
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Desiree M. Baron
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Liana Tellez
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Udai B. Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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15
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Menge S, Decker L, Freischmidt A. Restoring expression of Stathmin-2: a novel strategy to treat TDP-43 proteinopathies. Signal Transduct Target Ther 2023; 8:266. [PMID: 37433765 DOI: 10.1038/s41392-023-01533-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/24/2023] [Accepted: 06/04/2023] [Indexed: 07/13/2023] Open
Affiliation(s)
- Sonja Menge
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Lorena Decker
- Department of Neurology, Ulm University, 89081, Ulm, Germany
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16
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Thornburg-Suresh EJC, Richardson JE, Summers DW. The Stathmin-2 membrane-targeting domain is required for axon protection and regulated degradation by DLK signaling. J Biol Chem 2023; 299:104861. [PMID: 37236359 PMCID: PMC10404615 DOI: 10.1016/j.jbc.2023.104861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Axon integrity is essential for functional connectivity in the nervous system. The degeneration of stressed or damaged axons is a common and sometimes initiating event in neurodegenerative disorders. Stathmin-2 (Stmn2) is an axon maintenance factor that is depleted in amyotrophic lateral sclerosis, and replenishment of Stmn2 can restore neurite outgrowth in diseased neurons. However, mechanisms responsible for Stmn2-mediated axon maintenance in injured neurons are not known. We used primary sensory neurons to interrogate the role of Stmn2 in the degeneration of severed axons. We discover that membrane association of Stmn2 is critical for its axon-protective activity. Structure-function studies revealed that axonal enrichment of Stmn2 is driven by palmitoylation as well as tubulin interaction. Using live imaging, we discover that another Stmn, Stmn3, comigrates with Stmn2-containing vesicles. We also demonstrate that Stmn3 undergoes regulated degradation through dual leucine zipper kinase (DLK)-c-Jun N-terminal kinase signaling. The Stmn2 membrane-targeting domain is both necessary and sufficient for localization to a specific vesicle population and confers sensitivity to DLK-dependent degradation. Our findings reveal a broader role for DLK in tuning the local abundance of palmitoylated Stmns in axon segments. Moreover, palmitoylation is a critical component of Stmn-mediated axon protection, and defining the Stmn2-containing vesicle population will provide important clues toward mechanisms of axon maintenance.
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Affiliation(s)
- Emma J C Thornburg-Suresh
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, Iowa, USA; Department of Biology, University of Iowa, Iowa City, Iowa, USA
| | | | - Daniel W Summers
- Department of Biology, University of Iowa, Iowa City, Iowa, USA; Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA.
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17
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Jiang X, Gatt A, Lashley T. HnRNP Pathologies in Frontotemporal Lobar Degeneration. Cells 2023; 12:1633. [PMID: 37371103 DOI: 10.3390/cells12121633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Frontotemporal dementia (FTD) is the second most common form of young-onset (<65 years) dementia. Clinically, it primarily manifests as a disorder of behavioural, executive, and/or language functions. Pathologically, frontotemporal lobar degeneration (FTLD) is the predominant cause of FTD. FTLD is a proteinopathy, and the main pathological proteins identified so far are tau, TAR DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). As TDP-43 and FUS are members of the heterogeneous ribonucleic acid protein (hnRNP) family, many studies in recent years have expanded the research on the relationship between other hnRNPs and FTLD pathology. Indeed, these studies provide evidence for an association between hnRNP abnormalities and FTLD. In particular, several studies have shown that multiple hnRNPs may exhibit nuclear depletion and cytoplasmic mislocalisation within neurons in FTLD cases. However, due to the diversity and complex association of hnRNPs, most studies are still at the stage of histological discovery of different hnRNP abnormalities in FTLD. We herein review the latest studies relating hnRNPs to FTLD. Together, these studies outline an important role of multiple hnRNPs in the pathogenesis of FTLD and suggest that future research into FTLD should include the whole spectrum of this protein family.
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Affiliation(s)
- Xinwa Jiang
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ariana Gatt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
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18
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Allen SP, Al Sultan A, Kabucho Kibirige E, Tonkiss E, Hamer KJ, Castelli LM, Lin YH, Roscoe S, Stefanidis N, Mead RJ, Highley JR, Cooper-Knock J, Hautbergue GM, Heath PR, Kirby J, Shaw PJ. A Y374X TDP43 truncation leads to an altered metabolic profile in amyotrophic lateral sclerosis fibroblasts driven by pyruvate and TCA cycle intermediate alterations. Front Aging Neurosci 2023; 15:1151848. [PMID: 37251807 PMCID: PMC10213779 DOI: 10.3389/fnagi.2023.1151848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
A p.Y374X truncation in TARDBP was recently shown to reduce expression of TDP43 in fibroblasts isolated from ALS cases. In this follow up study focused on assessing the downstream phenotypic consequences of loss of TDP43 in the context of the truncation, we have shown a striking effect on the fibroblast metabolic profile. Phenotypic metabolic screening uncovered a distinct metabolic profile in TDP43-Y374X fibroblasts compared to controls, which was driven by alterations in key metabolic checkpoint intermediates including pyruvate, alpha-ketoglutarate and succinate. These metabolic alterations were confirmed using transcriptomics and bioenergetic flux analysis. These data suggest that TDP43 truncation directly compromises glycolytic and mitochondrial function, identifying potential therapeutic targets for mitigating the effects of TDP43-Y374X truncation.
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Affiliation(s)
- Scott P. Allen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
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19
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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20
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Zhou T, Chen Y, Liao Z, Zhang L, Su D, Li Z, Yang X, Ke X, Liu H, Chen Y, Weng R, Shen H, Xu C, Wan Y, Xu R, Su P. Spatiotemporal Characterization of Human Early Intervertebral Disc Formation at Single-Cell Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206296. [PMID: 36965031 DOI: 10.1002/advs.202206296] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/28/2023] [Indexed: 05/18/2023]
Abstract
The intervertebral disc (IVD) acts as a fibrocartilaginous joint to anchor adjacent vertebrae. Although several studies have demonstrated the cellular heterogeneity of adult mature IVDs, a single-cell transcriptomic atlas mapping early IVD formation is still lacking. Here, the authors generate a spatiotemporal and single cell-based transcriptomic atlas of human IVD formation at the embryonic stage and a comparative mouse transcript landscape. They identify two novel human notochord (NC)/nucleus pulposus (NP) clusters, SRY-box transcription factor 10 (SOX10)+ and cathepsin K (CTSK)+ , that are distributed in the early and late stages of IVD formation and they are validated by lineage tracing experiments in mice. Matrisome NC/NP clusters, T-box transcription factor T (TBXT)+ and CTSK+ , are responsible for the extracellular matrix homeostasis. The IVD atlas suggests that a subcluster of the vertebral chondrocyte subcluster might give rise to an inner annulus fibrosus of chondrogenic origin, while the fibroblastic outer annulus fibrosus preferentially expresseds transgelin and fibromodulin . Through analyzing intercellular crosstalk, the authors further find that notochordal secreted phosphoprotein 1 (SPP1) is a novel cue in the IVD microenvironment, and it is associated with IVD development and degeneration. In conclusion, the single-cell transcriptomic atlas will be leveraged to develop preventative and regenerative strategies for IVD degeneration.
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Affiliation(s)
- Taifeng Zhou
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yu Chen
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhiheng Liao
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Long Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Deying Su
- Guangdong Provincial Key Laboratory of Proteomics and State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhuling Li
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoming Yang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiaona Ke
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hengyu Liu
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuyu Chen
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Ricong Weng
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Huimin Shen
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Caixia Xu
- Research Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yong Wan
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Peiqiang Su
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
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21
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Baughn MW, Melamed Z, López-Erauskin J, Beccari MS, Ling K, Zuberi A, Presa M, Gil EG, Maimon R, Vazquez-Sanchez S, Chaturvedi S, Bravo-Hernández M, Taupin V, Moore S, Artates JW, Acks E, Ndayambaje IS, de Almeida Quadros ARA, Jafar-nejad P, Rigo F, Bennett CF, Lutz C, Lagier-Tourenne C, Cleveland DW. Mechanism of STMN2 cryptic splice-polyadenylation and its correction for TDP-43 proteinopathies. Science 2023; 379:1140-1149. [PMID: 36927019 PMCID: PMC10148063 DOI: 10.1126/science.abq5622] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 02/02/2023] [Indexed: 03/18/2023]
Abstract
Loss of nuclear TDP-43 is a hallmark of neurodegeneration in TDP-43 proteinopathies, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP-43 mislocalization results in cryptic splicing and polyadenylation of pre-messenger RNAs (pre-mRNAs) encoding stathmin-2 (also known as SCG10), a protein that is required for axonal regeneration. We found that TDP-43 binding to a GU-rich region sterically blocked recognition of the cryptic 3' splice site in STMN2 pre-mRNA. Targeting dCasRx or antisense oligonucleotides (ASOs) suppressed cryptic splicing, which restored axonal regeneration and stathmin-2-dependent lysosome trafficking in TDP-43-deficient human motor neurons. In mice that were gene-edited to contain human STMN2 cryptic splice-polyadenylation sequences, ASO injection into cerebral spinal fluid successfully corrected Stmn2 pre-mRNA misprocessing and restored stathmin-2 expression levels independently of TDP-43 binding.
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Affiliation(s)
- Michael W. Baughn
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Ze’ev Melamed
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Medical Neurobiology, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Jone López-Erauskin
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Melinda S Beccari
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Karen Ling
- Ionis Pharmaceuticals; Carlsbad, CA 92010, USA
| | - Aamir Zuberi
- Rare Disease Translation Center, The Jackson Laboratory; Bar Harbor, ME 04609
| | - Maximilliano Presa
- Rare Disease Translation Center, The Jackson Laboratory; Bar Harbor, ME 04609
| | - Elena Gonzalo Gil
- Rare Disease Translation Center, The Jackson Laboratory; Bar Harbor, ME 04609
| | - Roy Maimon
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Sonia Vazquez-Sanchez
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Som Chaturvedi
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Mariana Bravo-Hernández
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Vanessa Taupin
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Stephen Moore
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Jonathan W. Artates
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - Eitan Acks
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
| | - I. Sandra Ndayambaje
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School; Boston, MA 02114, USA
| | - Ana R. Agra de Almeida Quadros
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School; Boston, MA 02114, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals; Carlsbad, CA 92010, USA
| | | | - Cathleen Lutz
- Rare Disease Translation Center, The Jackson Laboratory; Bar Harbor, ME 04609
| | - Clotilde Lagier-Tourenne
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School; Boston, MA 02114, USA
- Broad Institute of Harvard University and MIT; Cambridge, MA 02142, USA
| | - Don W. Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego; La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego; La Jolla, CA 92093, USA
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22
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Mehta PR, Brown AL, Ward ME, Fratta P. The era of cryptic exons: implications for ALS-FTD. Mol Neurodegener 2023; 18:16. [PMID: 36922834 PMCID: PMC10018954 DOI: 10.1186/s13024-023-00608-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
TDP-43 is an RNA-binding protein with a crucial nuclear role in splicing, and mislocalises from the nucleus to the cytoplasm in a range of neurodegenerative disorders. TDP-43 proteinopathy spans a spectrum of incurable, heterogeneous, and increasingly prevalent neurodegenerative diseases, including the amyotrophic lateral sclerosis and frontotemporal dementia disease spectrum and a significant fraction of Alzheimer's disease. There are currently no directed disease-modifying therapies for TDP-43 proteinopathies, and no way to distinguish who is affected before death. It is now clear that TDP-43 proteinopathy leads to a number of molecular changes, including the de-repression and inclusion of cryptic exons. Importantly, some of these cryptic exons lead to the loss of crucial neuronal proteins and have been shown to be key pathogenic players in disease pathogenesis (e.g., STMN2), as well as being able to modify disease progression (e.g., UNC13A). Thus, these aberrant splicing events make promising novel therapeutic targets to restore functional gene expression. Moreover, presence of these cryptic exons is highly specific to patients and areas of the brain affected by TDP-43 proteinopathy, offering the potential to develop biomarkers for early detection and stratification of patients. In summary, the discovery of cryptic exons gives hope for novel diagnostics and therapeutics on the horizon for TDP-43 proteinopathies.
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Affiliation(s)
- Puja R Mehta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL Queen Square Motor Neuron Disease Centre, London, WC1N 3BG, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL Queen Square Motor Neuron Disease Centre, London, WC1N 3BG, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL Queen Square Motor Neuron Disease Centre, London, WC1N 3BG, UK.
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23
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Ni W, Wang S, Cheng D, Song F. Focusing on in vivo and in vitro axonal-degeneration models optimization may better evaluate the role of STMN2. J Neurosci Res 2023; 101:295-297. [PMID: 36523135 DOI: 10.1002/jnr.25155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/26/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Wenting Ni
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shuai Wang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dong Cheng
- Department of Health Test and Detection, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Fuyong Song
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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24
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Linares GR, Li Y, Chang WH, Rubin-Sigler J, Mendonca S, Hong S, Eoh Y, Guo W, Huang YH, Chang J, Tu S, Dorjsuren N, Santana M, Hung ST, Yu J, Perez J, Chickering M, Cheng TY, Huang CC, Lee SJJ, Deng HJ, Bach KT, Gray K, Subramanyam V, Rosenfeld J, Alworth SV, Goodarzi H, Ichida JK. SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS. Cell Stem Cell 2023; 30:171-187.e14. [PMID: 36736291 PMCID: PMC10062011 DOI: 10.1016/j.stem.2023.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/16/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by many diverse genetic etiologies. Although therapeutics that specifically target causal mutations may rescue individual types of ALS, such approaches cannot treat most patients since they have unknown genetic etiology. Thus, there is a critical need for therapeutic strategies that rescue multiple forms of ALS. Here, we combine phenotypic chemical screening on a diverse cohort of ALS patient-derived neurons with bioinformatic analysis of large chemical and genetic perturbational datasets to identify broadly effective genetic targets for ALS. We show that suppressing the gene-encoding, spliceosome-associated factor SYF2 alleviates TDP-43 aggregation and mislocalization, improves TDP-43 activity, and rescues C9ORF72 and causes sporadic ALS neuron survival. Moreover, Syf2 suppression ameliorates neurodegeneration, neuromuscular junction loss, and motor dysfunction in TDP-43 mice. Thus, suppression of spliceosome-associated factors such as SYF2 may be a broadly effective therapeutic approach for ALS.
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Affiliation(s)
- Gabriel R Linares
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Yichen Li
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | | | - Jasper Rubin-Sigler
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | | | - Sarah Hong
- AcuraStem Incorporated, Monrovia, CA 91016, USA
| | - Yunsun Eoh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Wenxuan Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Yi-Hsuan Huang
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Jonathan Chang
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Sharon Tu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Nomongo Dorjsuren
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Manuel Santana
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Shu-Ting Hung
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Johnny Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94158, USA
| | - Joscany Perez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Michael Chickering
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | | | | | | | - Hao-Jen Deng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Kieu-Tram Bach
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Kamden Gray
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Vishvak Subramanyam
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94158, USA
| | - Jeffrey Rosenfeld
- Department of Neurology, Loma Linda University, Loma Linda, CA 92350, USA
| | | | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94158, USA
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA 90033, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
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25
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Limone F, Guerra San Juan I, Mitchell JM, Smith JLM, Raghunathan K, Meyer D, Ghosh SD, Couto A, Klim JR, Joseph BJ, Gold J, Mello CJ, Nemesh J, Smith BM, Verhage M, McCarroll SA, Pietiläinen O, Nehme R, Eggan K. Efficient generation of lower induced motor neurons by coupling Ngn2 expression with developmental cues. Cell Rep 2023; 42:111896. [PMID: 36596304 PMCID: PMC10117176 DOI: 10.1016/j.celrep.2022.111896] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/01/2022] [Accepted: 12/08/2022] [Indexed: 01/03/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) are a powerful tool for disease modeling of hard-to-access tissues (such as the brain). Current protocols either direct neuronal differentiation with small molecules or use transcription-factor-mediated programming. In this study, we couple overexpression of transcription factor Neurogenin2 (Ngn2) with small molecule patterning to differentiate hPSCs into lower induced motor neurons (liMoNes/liMNs). This approach induces canonical MN markers including MN-specific Hb9/MNX1 in more than 95% of cells. liMNs resemble bona fide hPSC-derived MN, exhibit spontaneous electrical activity, express synaptic markers, and can contact muscle cells in vitro. Pooled, multiplexed single-cell RNA sequencing on 50 hPSC lines reveals reproducible populations of distinct subtypes of cervical and brachial MNs that resemble their in vivo, embryonic counterparts. Combining small molecule patterning with Ngn2 overexpression facilitates high-yield, reproducible production of disease-relevant MN subtypes, which is fundamental in propelling our knowledge of MN biology and its disruption in disease.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Leiden University Medical Center, LUMC, 2333 ZA Leiden, the Netherlands.
| | - Irune Guerra San Juan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, the Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jana M Mitchell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Janell L M Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Dia Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian J Joseph
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Departments of Pathology and Cell Biology, Columbia University Irving Medical Centre, New York, NY 10032, USA
| | - John Gold
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Curtis J Mello
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Nemesh
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brittany M Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthijs Verhage
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, the Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Steven A McCarroll
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietiläinen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ralda Nehme
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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26
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Lépine S, Castellanos-Montiel MJ, Durcan TM. TDP-43 dysregulation and neuromuscular junction disruption in amyotrophic lateral sclerosis. Transl Neurodegener 2022; 11:56. [PMID: 36575535 PMCID: PMC9793560 DOI: 10.1186/s40035-022-00331-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a disease characterized by upper and lower motor neuron (MN) loss with a signature feature of cytoplasmic aggregates containing TDP-43, which are detected in nearly all patients. Mutations in the gene that encodes TDP-43 (TARBDP) are known to result in both familial and sporadic ALS. In ALS, disruption of neuromuscular junctions (NMJs) constitutes a critical event in disease pathogenesis, leading to denervation atrophy, motor impairments and disability. Morphological defects and impaired synaptic transmission at NMJs have been reported in several TDP-43 animal models and in vitro, linking TDP-43 dysregulation to the loss of NMJ integrity in ALS. Through the lens of the dying-back and dying-forward hypotheses of ALS, this review discusses the roles of TDP-43 related to synaptic function, with a focus on the potential molecular mechanisms occurring within MNs, skeletal muscles and glial cells that may contribute to NMJ disruption in ALS.
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Affiliation(s)
- Sarah Lépine
- grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, 3801 University Street, Montreal, QC H3A 2B4 Canada ,grid.14709.3b0000 0004 1936 8649Faculty of Medicine and Health Sciences, McGill University, 3605 De La Montagne, Montreal, QC H3G 2M1 Canada
| | - Maria José Castellanos-Montiel
- grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, 3801 University Street, Montreal, QC H3A 2B4 Canada
| | - Thomas Martin Durcan
- grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, 3801 University Street, Montreal, QC H3A 2B4 Canada
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27
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Platform Communications: Abstract Book – 33rd International Symposium on ALS/MND (Complete printable file). Amyotroph Lateral Scler Frontotemporal Degener 2022. [DOI: 10.1080/21678421.2022.2082738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Sekar D, Tusubira D, Ross K. TDP-43 and NEAT long non-coding RNA: Roles in neurodegenerative disease. Front Cell Neurosci 2022; 16:954912. [PMID: 36385948 PMCID: PMC9650703 DOI: 10.3389/fncel.2022.954912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/11/2022] [Indexed: 01/03/2023] Open
Abstract
Understanding and ameliorating neurodegenerative diseases represents a key challenge for supporting the health span of the aging population. Diverse protein aggregates have been implicated in such neurodegenerative disorders, including amyloid-β, α-synuclein, tau, fused in sarcoma (FUS), and transactivation response element (TAR) DNA-binding protein 43 (TDP-43). Recent years have seen significant growth in our mechanistic knowledge of relationships between these proteins and some of the membrane-less nuclear structures that fulfill key roles in the cell function. These include the nucleolus, nuclear speckles, and paraspeckles. The ability of macromolecular protein:RNA complexes to partition these nuclear condensates through biophysical processes that involve liquid-liquid phase separation (LLPS) has also gained attention recently. The paraspeckle, which is scaffolded by the architectural long-non-coding RNA nuclear enriched abundant transcript 1 (NEAT1) plays central roles in RNA processing and metabolism and has been linked dynamically to TDP-43. In this mini-review, we outline essential early and recent insights in relation to TDP-43 proteinopathies. We then appraise the relationships between TDP-43 and NEAT1 in the context of neuronal paraspeckles and neuronal stress. We highlight key areas for investigation based on recent advances in our understanding of how TDP-43 affects neuronal function, especially in relation to messenger ribosomal nucleic acid (mRNA) splicing. Finally, we offer perspectives that should be considered for translational pipelines in order to improve health outcomes for the management of neurodegenerative diseases.
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Affiliation(s)
- Durairaj Sekar
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Deusdedit Tusubira
- Department of Biochemistry, Mbarara University of Science and Technology, Mbarara, Uganda,*Correspondence: Deusdedit Tusubira, ; orcid.org/0000-0002-4698-424X
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom,Institute for Health Research, Liverpool John Moores University, Liverpool, United Kingdom,Kehinde Ross, ; orcid.org/0000-0003-0252-1152
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29
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Abstract
PURPOSE OF REVIEW ALS genetics are highly dynamic and of great interest for the ALS research community. Each year, by using ever-growing datasets and cutting-edge methodology, an array of novel ALS-associated genes and downstream pathomechanisms are discovered. The increasing plenty and complexity of insights warrants regular summary by-reviews. RECENT FINDINGS Most recent disease gene discoveries constitute the candidate and risk genes SPTLC1 , KANK1 , CAV1 , HTT , and WDR7 , as well as seven novel risk loci. Cell type and functional enrichment analyses enlighten the genetic basis of selective motor neuron vulnerability in ALS demonstrating high expression of ALS-associated genes in cortical motor neurons and highlight the pathogenic significance of cell-autonomous processes. Major pathomechanistic insights have been gained regarding known ALS genes/proteins, specifically C9orf72 , TDP43, ANXA11 , and KIF5A . The first ASO-based gene-specific therapy trials in familial forms of ALS have yielded equivocal results stressing the re-evaluation of pathomechanisms linked to SOD1 and C9orf72 mutations. SUMMARY The genetic and molecular basis of ALS is increasingly examined on single-cell resolution. In the past 2 years, the understanding of the downstream mechanisms of several ALS genes and TDP-43 proteinopathy has been considerably extended. These insights will result in novel gene specific therapy approaches for sporadic ALS and genetic subtypes.
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30
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Altered TDP-43 Structure and Function: Key Insights into Aberrant RNA, Mitochondrial, and Cellular and Systemic Metabolism in Amyotrophic Lateral Sclerosis. Metabolites 2022; 12:metabo12080709. [PMID: 36005581 PMCID: PMC9415507 DOI: 10.3390/metabo12080709] [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: 07/13/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 12/10/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neuromuscular disorder with no cure available and limited treatment options. ALS is a highly heterogeneous disease, whereby patients present with vastly different phenotypes. Despite this heterogeneity, over 97% of patients will exhibit pathological TAR-DNA binding protein-43 (TDP-43) cytoplasmic inclusions. TDP-43 is a ubiquitously expressed RNA binding protein with the capacity to bind over 6000 RNA and DNA targets—particularly those involved in RNA, mitochondrial, and lipid metabolism. Here, we review the unique structure and function of TDP-43 and its role in affecting the aforementioned metabolic processes in ALS. Considering evidence published specifically in TDP-43-relevant in vitro, in vivo, and ex vivo models we posit that TDP-43 acts in a positive feedback loop with mRNA transcription/translation, stress granules, cytoplasmic aggregates, and mitochondrial proteins causing a relentless cycle of disease-like pathology eventuating in neuronal toxicity. Given its undeniable presence in ALS pathology, TDP-43 presents as a promising target for mechanistic disease modelling and future therapeutic investigations.
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31
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Krus KL, Strickland A, Yamada Y, Devault L, Schmidt RE, Bloom AJ, Milbrandt J, DiAntonio A. Loss of Stathmin-2, a hallmark of TDP-43-associated ALS, causes motor neuropathy. Cell Rep 2022; 39:111001. [PMID: 35767949 PMCID: PMC9327139 DOI: 10.1016/j.celrep.2022.111001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/18/2022] [Accepted: 06/02/2022] [Indexed: 12/03/2022] Open
Abstract
TDP-43 mediates proper Stathmin-2 (STMN2) mRNA splicing, and STMN2 protein is reduced in the spinal cord of most patients with amyotrophic lateral sclerosis (ALS). To test the hypothesis that STMN2 loss contributes to ALS pathogenesis, we generated constitutive and conditional STMN2 knockout mice. Constitutive STMN2 loss results in early-onset sensory and motor neuropathy featuring impaired motor behavior and dramatic distal neuromuscular junction (NMJ) denervation of fast-fatigable motor units, which are selectively vulnerable in ALS, without axon or motoneuron degeneration. Selective excision of STMN2 in motoneurons leads to similar NMJ pathology. STMN2 knockout heterozygous mice, which better model the partial loss of STMN2 protein found in patients with ALS, display a slowly progressive, motor-selective neuropathy with functional deficits and NMJ denervation. Thus, our findings strongly support the hypothesis that STMN2 reduction owing to TDP-43 pathology contributes to ALS pathogenesis.
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Affiliation(s)
- Kelsey L Krus
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Amy Strickland
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yurie Yamada
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura Devault
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert E Schmidt
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - A Joseph Bloom
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO 63110, USA.
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO 63110, USA.
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32
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Akiyama T, Koike Y, Petrucelli L, Gitler AD. Cracking the cryptic code in amyotrophic lateral sclerosis and frontotemporal dementia: Towards therapeutic targets and biomarkers. Clin Transl Med 2022; 12:e818. [PMID: 35567447 PMCID: PMC9098226 DOI: 10.1002/ctm2.818] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 12/19/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two devastating human neurodegenerative diseases. A hallmark pathological feature of both diseases is the depletion of the RNA-binding protein TDP-43 from the nucleus in the brain and spinal cord of patients. A major function of TDP-43 is to repress the inclusion of cryptic exons during RNA splicing. When it becomes depleted from the nucleus in disease, this function is lost, and recently, several key cryptic splicing targets of TDP-43 have emerged, including STMN2, UNC13A, and others. UNC13A is a major ALS/FTD risk gene, and the genetic variations that increase the risk for disease seem to do so by making the gene more susceptible to cryptic exon inclusion when TDP-43 function is impaired. Here, we discuss the prospects and challenges of harnessing these cryptic splicing events as novel therapeutic targets and biomarkers. Deciphering this new cryptic code may be a touchstone for ALS and FTD diagnosis and treatment.
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Affiliation(s)
- Tetsuya Akiyama
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
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