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Tejwani L, Ravindra NG, Lee C, Cheng Y, Nguyen B, Luttik K, Ni L, Zhang S, Morrison LM, Gionco J, Xiang Y, Yoon J, Ro H, Haidery F, Grijalva RM, Bae E, Kim K, Martuscello RT, Orr HT, Zoghbi HY, McLoughlin HS, Ranum LPW, Shakkottai VG, Faust PL, Wang S, van Dijk D, Lim J. Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1. Neuron 2024; 112:362-383.e15. [PMID: 38016472 PMCID: PMC10922326 DOI: 10.1016/j.neuron.2023.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 09/10/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
Abstract
Neurodegeneration is a protracted process involving progressive changes in myriad cell types that ultimately results in the death of vulnerable neuronal populations. To dissect how individual cell types within a heterogeneous tissue contribute to the pathogenesis and progression of a neurodegenerative disorder, we performed longitudinal single-nucleus RNA sequencing of mouse and human spinocerebellar ataxia type 1 (SCA1) cerebellar tissue, establishing continuous dynamic trajectories of each cell population. Importantly, we defined the precise transcriptional changes that precede loss of Purkinje cells and, for the first time, identified robust early transcriptional dysregulation in unipolar brush cells and oligodendroglia. Finally, we applied a deep learning method to predict disease state accurately and identified specific features that enable accurate distinction of wild-type and SCA1 cells. Together, this work reveals new roles for diverse cerebellar cell types in SCA1 and provides a generalizable analysis framework for studying neurodegeneration.
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Affiliation(s)
- Leon Tejwani
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Neal G Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06510, USA
| | - Changwoo Lee
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yubao Cheng
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Billy Nguyen
- University of California, San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Kimberly Luttik
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Luhan Ni
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shupei Zhang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Logan M Morrison
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - John Gionco
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center and the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Yangfei Xiang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Hannah Ro
- Yale College, New Haven, CT 06510, USA
| | | | - Rosalie M Grijalva
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Kristen Kim
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA
| | - Regina T Martuscello
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center and the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hayley S McLoughlin
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Laura P W Ranum
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, College of Medicine, Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Vikram G Shakkottai
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Phyllis L Faust
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center and the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA.
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06510, USA.
| | - Janghoo Lim
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale School of Medicine, New Haven, CT 06510, USA.
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Olmos V, Gogia N, Luttik K, Haidery F, Lim J. The extra-cerebellar effects of spinocerebellar ataxia type 1 (SCA1): looking beyond the cerebellum. Cell Mol Life Sci 2022; 79:404. [PMID: 35802260 PMCID: PMC9993484 DOI: 10.1007/s00018-022-04419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/28/2022]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is one of nine polyglutamine (polyQ) diseases and is characterized as an adult late-onset, progressive, dominantly inherited genetic disease. SCA1 is caused by an increase in the number of CAG repeats in the ATXN1 gene leading to an expanded polyQ tract in the ATAXIN-1 protein. ATAXIN-1 is broadly expressed throughout the brain. However, until recently, SCA1 research has primarily centered on the cerebellum, given the characteristic cerebellar Purkinje cell loss observed in patients, as well as the progressive motor deficits, including gait and limb incoordination, that SCA1 patients present with. There are, however, also other symptoms such as respiratory problems, cognitive defects and memory impairment, anxiety, and depression observed in SCA1 patients and mouse models, which indicate that there are extra-cerebellar effects of SCA1 that cannot be explained solely through changes in the cerebellar region of the brain alone. The existing gap between human and mouse model studies of extra-cerebellar regions in SCA1 makes it difficult to answer many important questions in the field. This review will cover both the cerebellar and extra-cerebellar effects of SCA1 and highlight the need for further investigations into the impact of mutant ATXN1 expression in these regions. This review will also discuss implications of extra-cerebellar effects not only for SCA1 but other neurodegenerative diseases showing diverse pathology as well.
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Affiliation(s)
- Victor Olmos
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA
| | - Neha Gogia
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA
| | - Kimberly Luttik
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA
| | | | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA.
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA.
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA.
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA.
- Yale Stem Cell Center, Yale School of Medicine, 295 Congress Avenue, BCMM 154E, New Haven, CT, 06510, USA.
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Gogia N, Ni L, Olmos V, Haidery F, Luttik K, Lim J. Exploring the Role of Posttranslational Modifications in Spinal and Bulbar Muscular Atrophy. Front Mol Neurosci 2022; 15:931301. [PMID: 35726299 PMCID: PMC9206542 DOI: 10.3389/fnmol.2022.931301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Spinal and Bulbar Muscular Atrophy (SBMA) is an X-linked adult-onset progressive neuromuscular disease that affects the spinal and bulbar motor neurons and skeletal muscles. SBMA is caused by expansion of polymorphic CAG trinucleotide repeats in the Androgen Receptor (AR) gene, resulting in expanded glutamine tract in the AR protein. Polyglutamine (polyQ) expansion renders the mutant AR protein toxic, resulting in the formation of mutant protein aggregates and cell death. This classifies SBMA as one of the nine known polyQ diseases. Like other polyQ disorders, the expansion of the polyQ tract in the AR protein is the main genetic cause of the disease; however, multiple other mechanisms besides the polyQ tract expansion also contribute to the SBMA disease pathophysiology. Posttranslational modifications (PTMs), including phosphorylation, acetylation, methylation, ubiquitination, and SUMOylation are a category of mechanisms by which the functionality of AR has been found to be significantly modulated and can alter the neurotoxicity of SBMA. This review summarizes the different PTMs and their effects in regulating the AR function and discusses their pathogenic or protective roles in context of SBMA. This review also includes the therapeutic approaches that target the PTMs of AR in an effort to reduce the mutant AR-mediated toxicity in SBMA.
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Affiliation(s)
- Neha Gogia
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Luhan Ni
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Victor Olmos
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Fatema Haidery
- Yale College, Yale University, New Haven, CT, United States
| | - Kimberly Luttik
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States,Interdepartmental Neuroscience Program, Yale University, New Haven, CT, United States
| | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States,Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States,Interdepartmental Neuroscience Program, Yale University, New Haven, CT, United States,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, Yale University, New Haven, CT, United States
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