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Li SJ, Zheng QW, Zheng J, Zhang JB, Liu H, Tie JJ, Zhang KL, Wu FF, Li XD, Zhang S, Sun X, Yang YL, Wang YY. Mitochondria transplantation transiently rescues cerebellar neurodegeneration improving mitochondrial function and reducing mitophagy in mice. Nat Commun 2025; 16:2839. [PMID: 40121210 PMCID: PMC11929859 DOI: 10.1038/s41467-025-58189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 03/13/2025] [Indexed: 03/25/2025] Open
Abstract
Cerebellar ataxia is the primary manifestation of cerebellar degenerative diseases, and mitochondrial dysfunction in Purkinje cells (PCs) plays a critical role in disease progression. In this study, we investigated the feasibility of mitochondria transplantation as a potential therapeutic approach to rescue cerebellar neurodegeneration and elucidate the associated mechanisms. We constructed a conditional Drp1 knockout model in PCs (PCKO mice), characterized by progressive ataxia. Drp1 knockout resulted in pervasive and progressive apoptosis of PCs and significant activation of surrounding glial cells. Mitochondrial dysfunction, which triggers mitophagy, is a key pathogenic factor contributing to morphological and functional damage in PCs. Transplanting liver-derived mitochondria into the cerebellum of 1-month-old PCKO mice improved mitochondrial function, reduced mitophagy, delayed apoptosis of PCs, and alleviated cerebellar ataxia for up to 3 weeks. These findings demonstrate that mitochondria transplantation holds promise as a therapeutic approach for cerebellar degenerative diseases.
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Affiliation(s)
- Shu-Jiao Li
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Qian-Wen Zheng
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Jie Zheng
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Jin-Bao Zhang
- Department of pediatrics, Xi-Jing Hospital, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Hui Liu
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Jing-Jing Tie
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Kun-Long Zhang
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
- Department of Rehabilitation Medicine, Xi-Jing Hospital, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Fei-Fei Wu
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Xiao-Dong Li
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Shuai Zhang
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China
| | - Xin Sun
- Department of pediatrics, Xi-Jing Hospital, Air Force Medical University (Fourth Military Medical University), Xi'an, China.
| | - Yan-Ling Yang
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Air Force Medical University (Fourth Military Medical University), Xi'an, China.
| | - Ya-Yun Wang
- Specific Lab for Mitochondrial Plasticity Underlying Nervous System Diseases, National Teaching Demonstration Center, School of Basic Medicine, Air Force Medical University (Fourth Military Medical University), Xi'an, China.
- State Key Laboratory of Military Stomatology, School of Stomatology, Air Force Medical University (Fourth Military Medical University), Xi'an, China.
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Ahn SH, Jang Y, Jang BS, Moon J, Lee WJ, Park DK, Yu JS, Son H, Kim H, Han D, Seok H, Kim Y, Shin SY, Lee ST, Park KI, Jung KH, Jeon D, Lee SK, Chu K. Multi-omic insights into molecular mechanism and therapeutic targets in spinocerebellar ataxia type 7. MOLECULAR THERAPY. NUCLEIC ACIDS 2025; 36:102414. [PMID: 39817193 PMCID: PMC11733039 DOI: 10.1016/j.omtn.2024.102414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Accepted: 12/03/2024] [Indexed: 01/18/2025]
Abstract
Recent advances in molecular science have significantly enlightened our mechanistic understanding of spinocerebellar ataxia type 7. To further close remaining gaps, we performed a multi-omics analysis using SCA7266Q/5Q mice. Entire brain tissue samples were collected from 12-week-old mice, and RNA sequencing, methylation analysis, and proteomic analysis were performed. Results were integrated to identify genes with identical trends in expression across all three analyses. Data from RNA sequencing and methylation analysis revealed 58 significantly hypomethylated-upregulated genes and 62 hypermethylated-downregulated genes, mostly enriched in GO terms of regulation of axonogenesis, channel activity, and monoamine signaling. In the proteomic analysis, 211 upregulated and 281 downregulated DEPs associated mostly with immune response and cellular mobility were identified. Two genes, Fam107b and Tph2, showed differential expressions in both transcriptomic and proteomic analyses. Findings were validated in RT-qPCR as well as open data source analysis. Our study is the first to perform multi-omics analysis in SCA7 mice and will serve as an important reference for future studies.
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Affiliation(s)
- Soo Hyun Ahn
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
| | - Yoonhyuk Jang
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
- The National Strategic Technology Research Institute, Seoul 03080, Republic of Korea
| | - Bum-Sup Jang
- Department of Radiation Oncology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jangsup Moon
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Woo-Jin Lee
- Department of Neurology, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea
| | - Dong-Kyu Park
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
- Advanced Neural Technologies, Seoul 03087, Republic of Korea
| | - Jung-Suk Yu
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
- Advanced Neural Technologies, Seoul 03087, Republic of Korea
| | - Hyoshin Son
- Department of Neurology, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 03312, Republic of Korea
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Heeyoung Seok
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Yongmoo Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
| | - Seo-Yi Shin
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
| | - Soon-Tae Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
| | - Kyung-Il Park
- Department of Neurology, Seoul National University Hospital Healthcare System Gangnam Center, Seoul 06236, Republic of Korea
| | - Keun-Hwa Jung
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
| | - Daejong Jeon
- Advanced Neural Technologies, Seoul 03087, Republic of Korea
| | - Sang Kun Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
| | - Kon Chu
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Laboratory for Neurotherapeutics, Department of Neurology, Comprehensive Epilepsy Center, Center for Medical Innovation, Biomedical Research Institute, Seoul National University College of Medicine and Hospital, Seoul 03080, Republic of Korea
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3
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Aliyeva A, Lennon CD, Cleary JD, Shorrock HK, Berglund JA. Dysregulation of alternative splicing is a transcriptomic feature of patient-derived fibroblasts from CAG repeat expansion spinocerebellar ataxias. Hum Mol Genet 2025; 34:239-250. [PMID: 39589088 PMCID: PMC11792238 DOI: 10.1093/hmg/ddae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/25/2024] [Accepted: 11/22/2024] [Indexed: 11/27/2024] Open
Abstract
The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of rare dominantly inherited neurodegenerative diseases characterized by progressive ataxia. The most common mutation seen across the SCAs is a CAG repeat expansion, causative for SCA1, 2, 3, 6, 7, 12 and 17. We recently identified dysregulation of alternative splicing as a novel, presymptomatic transcriptomic hallmark in mouse models of SCAs 1, 3 and 7. In order to understand if dysregulation of alternative splicing is a transcriptomic feature of patient-derived cell models of CAG SCAs, we performed RNA sequencing and transcriptomic analysis in patient-derived fibroblast cell lines of SCAs 1, 3 and 7. We identified widespread and robust dysregulation of alternative splicing across all CAG expansion SCA lines investigated, with disease relevant pathways affected, such as microtubule-based processes, transcriptional regulation, and DNA damage and repair. Novel disease-relevant alternative splicing events were validated across patient-derived fibroblast lines from multiple CAG SCAs and CAG containing reporter cell lines. Together this study demonstrates that dysregulation of alternative splicing represents a novel and shared pathogenic process in CAG expansion SCA1, 3 and 7 and can potentially be used as a biomarker across patient models of this group of devastating neurodegenerative diseases.
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Affiliation(s)
- Asmer Aliyeva
- RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, State University of New York, Albany, NY 12222, United States
| | - Claudia D Lennon
- RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - John D Cleary
- RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Hannah K Shorrock
- RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, State University of New York, Albany, NY 12222, United States
| | - J Andrew Berglund
- RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, State University of New York, Albany, NY 12222, United States
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4
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Ng BW, Kaukonen MK, McClements ME, Shamsnajafabadi H, MacLaren RE, Cehajic-Kapetanovic J. Genetic therapies and potential therapeutic applications of CRISPR activators in the eye. Prog Retin Eye Res 2024; 102:101289. [PMID: 39127142 DOI: 10.1016/j.preteyeres.2024.101289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Conventional gene therapy involving supplementation only treats loss-of-function diseases and is limited by viral packaging sizes, precluding therapy of large genes. The discovery of CRISPR/Cas has led to a paradigm shift in the field of genetic therapy, with the promise of precise gene editing, thus broadening the range of diseases that can be treated. The initial uses of CRISPR/Cas have focused mainly on gene editing or silencing of abnormal variants via utilising Cas endonuclease to trigger the target cell endogenous non-homologous end joining. Subsequently, the technology has evolved to modify the Cas enzyme and even its guide RNA, leading to more efficient editing tools in the form of base and prime editing. Further advancements of this CRISPR/Cas technology itself have expanded its functional repertoire from targeted editing to programmable transactivation, shifting the therapeutic focus to precise endogenous gene activation or upregulation with the potential for epigenetic modifications. In vivo experiments using this platform have demonstrated the potential of CRISPR-activators (CRISPRa) to treat various loss-of-function diseases, as well as in regenerative medicine, highlighting their versatility to overcome limitations associated with conventional strategies. This review summarises the molecular mechanisms of CRISPRa platforms, the current applications of this technology in vivo, and discusses potential solutions to translational hurdles for this therapy, with a focus on ophthalmic diseases.
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Affiliation(s)
- Benjamin Wj Ng
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maria K Kaukonen
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Hoda Shamsnajafabadi
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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5
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Bartelt LC, Fakhri M, Adamek G, Trybus M, Samelak-Czajka A, Jackowiak P, Fiszer A, Lowe CB, La Spada AR, Switonski PM. Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue. CELL REPORTS METHODS 2024; 4:100816. [PMID: 38981474 PMCID: PMC11294835 DOI: 10.1016/j.crmeth.2024.100816] [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: 12/19/2023] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
We developed a method that utilizes fluorescent labeling of nuclear envelopes alongside cytometry sorting for the selective isolation of Purkinje cell (PC) nuclei. Beginning with SUN1 reporter mice, we GFP-tagged envelopes to confirm that PC nuclei could be accurately separated from other cell types. We then developed an antibody-based protocol to make PC nuclear isolation more robust and adaptable to cerebellar tissues of any genotypic background. Immunofluorescent labeling of the nuclear membrane protein RanBP2 enabled the isolation of PC nuclei from C57BL/6 cerebellum. By analyzing the expression of PC markers, nuclear size, and nucleoli number, we confirmed that our method delivers a pure fraction of PC nuclei. To demonstrate its applicability, we isolated PC nuclei from spinocerebellar ataxia type 7 (SCA7) mice and identified transcriptional changes in known and new disease-associated genes. Access to pure PC nuclei offers insights into PC biology and pathology, including the nature of selective neuronal vulnerability.
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Affiliation(s)
- Luke C Bartelt
- University Program in Genetics & Genomics, Duke University Medical Center, Durham, NC 27710, USA; Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mouad Fakhri
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Grazyna Adamek
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Trybus
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Samelak-Czajka
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
| | - Pawel M Switonski
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
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6
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Mannens CCA, Hu L, Lönnerberg P, Schipper M, Reagor CC, Li X, He X, Barker RA, Sundström E, Posthuma D, Linnarsson S. Chromatin accessibility during human first-trimester neurodevelopment. Nature 2024:10.1038/s41586-024-07234-1. [PMID: 38693260 DOI: 10.1038/s41586-024-07234-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/02/2024] [Indexed: 05/03/2024]
Abstract
The human brain develops through a tightly organized cascade of patterning events, induced by transcription factor expression and changes in chromatin accessibility. Although gene expression across the developing brain has been described at single-cell resolution1, similar atlases of chromatin accessibility have been primarily focused on the forebrain2-4. Here we describe chromatin accessibility and paired gene expression across the entire developing human brain during the first trimester (6-13 weeks after conception). We defined 135 clusters and used multiomic measurements to link candidate cis-regulatory elements to gene expression. The number of accessible regions increased both with age and along neuronal differentiation. Using a convolutional neural network, we identified putative functional transcription factor-binding sites in enhancers characterizing neuronal subtypes. We applied this model to cis-regulatory elements linked to ESRRB to elucidate its activation mechanism in the Purkinje cell lineage. Finally, by linking disease-associated single nucleotide polymorphisms to cis-regulatory elements, we validated putative pathogenic mechanisms in several diseases and identified midbrain-derived GABAergic neurons as being the most vulnerable to major depressive disorder-related mutations. Our findings provide a more detailed view of key gene regulatory mechanisms underlying the emergence of brain cell types during the first trimester and a comprehensive reference for future studies related to human neurodevelopment.
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Affiliation(s)
- Camiel C A Mannens
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Lijuan Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Peter Lönnerberg
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Marijn Schipper
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Caleb C Reagor
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY, USA
| | - Xiaofei Li
- Division of Neurodegeneration, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Erik Sundström
- Division of Neurodegeneration, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden.
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Kopp J, Koch LA, Lyubenova H, Küchler O, Holtgrewe M, Ivanov A, Dubourg C, Launay E, Brachs S, Mundlos S, Ehmke N, Seelow D, Fradin M, Kornak U, Fischer-Zirnsak B. Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy. Hum Genet 2024; 143:683-694. [PMID: 38592547 PMCID: PMC11098864 DOI: 10.1007/s00439-024-02669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Generalized lipodystrophy is a feature of various hereditary disorders, often leading to a progeroid appearance. In the present study we identified a missense and a frameshift variant in a compound heterozygous state in SUPT7L in a boy with intrauterine growth retardation, generalized lipodystrophy, and additional progeroid features. SUPT7L encodes a component of the transcriptional coactivator complex STAGA. By transcriptome sequencing, we showed the predicted missense variant to cause aberrant splicing, leading to exon truncation and thereby to a complete absence of SUPT7L in dermal fibroblasts. In addition, we found altered expression of genes encoding DNA repair pathway components. This pathway was further investigated and an increased rate of DNA damage was detected in proband-derived fibroblasts and genome-edited HeLa cells. Finally, we performed transient overexpression of wildtype SUPT7L in both cellular systems, which normalizes the number of DNA damage events. Our findings suggest SUPT7L as a novel disease gene and underline the link between genome instability and progeroid phenotypes.
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Affiliation(s)
- Johannes Kopp
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Leonard A Koch
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
| | - Hristiana Lyubenova
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Oliver Küchler
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christele Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, F-35033, France
- Univercity Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, F-35000, France
| | - Erika Launay
- Service de Cytogénétique et Biologie cellulaire, Hôpital Pontchaillou - CHU Rennes, 2 rue Henri Le Guilloux - Rennes cedex 9, France, Rennes, F-35033, France
| | - Sebastian Brachs
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre Référence Déficiences Intellectuelles CRDI, Hôpital Sud - CHU Rennes, 16 boulevard de Bulgarie - BP 90347, Rennes cedex 2, Rennes, F-35203, France
- Service de Génétique, CH Saint Brieuc, St Brieuc, 22000, France
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany.
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Lubachowski M, VanGenderen C, Valentine S, Belak Z, Davies GF, Arnason TG, Harkness TAA. Activation of the Anaphase Promoting Complex Restores Impaired Mitotic Progression and Chemosensitivity in Multiple Drug-Resistant Human Breast Cancer. Cancers (Basel) 2024; 16:1755. [PMID: 38730707 PMCID: PMC11083742 DOI: 10.3390/cancers16091755] [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: 03/22/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
The development of multiple-drug-resistant (MDR) cancer all too often signals the need for toxic alternative therapy or palliative care. Our recent in vivo and in vitro studies using canine MDR lymphoma cancer cells demonstrate that the Anaphase Promoting Complex (APC) is impaired in MDR cells compared to normal canine control and drug-sensitive cancer cells. Here, we sought to establish whether this phenomena is a generalizable mechanism independent of species, malignancy type, or chemotherapy regime. To test the association of blunted APC activity with MDR cancer behavior, we used matched parental and MDR MCF7 human breast cancer cells, and a patient-derived xenograft (PDX) model of human triple-negative breast cancer. We show that APC activating mechanisms, such as APC subunit 1 (APC1) phosphorylation and CDC27/CDC20 protein associations, are reduced in MCF7 MDR cells when compared to chemo-sensitive matched cell lines. Consistent with impaired APC function in MDR cells, APC substrate proteins failed to be effectively degraded. Similar to our previous observations in canine MDR lymphoma cells, chemical activation of the APC using Mad2 Inhibitor-1 (M2I-1) in MCF7 MDR cells enhanced APC substrate degradation and resensitized MDR cells in vitro to the cytotoxic effects of the alkylating chemotherapeutic agent, doxorubicin (DOX). Using cell cycle arrest/release experiments, we show that mitosis is delayed in MDR cells with elevated substrate levels. When pretreated with M2I-1, MDR cells progress through mitosis at a faster rate that coincides with reduced levels of APC substrates. In our PDX model, mice growing a clinically MDR human triple-negative breast cancer tumor show significantly reduced tumor growth when treated with M2I-1, with evidence of increased DNA damage and apoptosis. Thus, our results strongly support the hypothesis that APC impairment is a driver of aggressive tumor development and that targeting the APC for activation has the potential for meaningful clinical benefits in treating recurrent cases of MDR malignancy.
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Affiliation(s)
- Mathew Lubachowski
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
- Division of Geriatrics, Department of Medicine, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Cordell VanGenderen
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (C.V.); (S.V.); (T.G.A.)
| | - Sarah Valentine
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (C.V.); (S.V.); (T.G.A.)
| | - Zach Belak
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
| | - Gerald Floyd Davies
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
| | - Terra Gayle Arnason
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (C.V.); (S.V.); (T.G.A.)
- Division of Endocrinology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2S2, Canada
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Troy Anthony Alan Harkness
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
- Division of Geriatrics, Department of Medicine, University of Alberta, Edmonton, AB T6G 2S2, Canada
- 320 Heritage Medical Research Centre, University of Alberta, 11207-87 Ave NW, Edmonton, AB T6G 2S2, Canada
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Delaney JR, La Spada AR. Protocol for mapping double-stranded DNA break sites across the genome with translocation capture sequencing. STAR Protoc 2023; 4:102205. [PMID: 37000621 PMCID: PMC10068614 DOI: 10.1016/j.xpro.2023.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/30/2023] [Accepted: 03/07/2023] [Indexed: 04/01/2023] Open
Abstract
Translocation sequencing can be used to assess mechanisms of DNA repair and identify genome-wide double-strand breaks (DSBs) accessible to DNA repair machinery. Here, we present a protocol for mapping double-strand DNA break sites across the genome with translocation capture sequencing. Bait DSBs are introduced using a Cas9 nuclease and repaired by the host cell, connecting bait DSBs to other DSBs. Repair sites are detected by isolating bait site DNA, cleaving normal sequence to enrich off-site repair, and next-generation sequencing. For complete details on the use and execution of this protocol, please refer to Switonski et al. (2021).1.
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Affiliation(s)
- Joe R Delaney
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurobiology & Behavior, School of Biosciences, University of California, Irvine, Irvine, CA 92697, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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Piwecka M, Fiszer A, Rolle K, Olejniczak M. RNA regulation in brain function and disease 2022 (NeuroRNA): A conference report. Front Mol Neurosci 2023; 16:1133209. [PMID: 36993784 PMCID: PMC10040806 DOI: 10.3389/fnmol.2023.1133209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023] Open
Abstract
Recent research integrates novel technologies and methods from the interface of RNA biology and neuroscience. This advancing integration of both fields creates new opportunities in neuroscience to deepen the understanding of gene expression programs and their regulation that underlies the cellular heterogeneity and physiology of the central nervous system. Currently, transcriptional heterogeneity can be studied in individual neural cell types in health and disease. Furthermore, there is an increasing interest in RNA technologies and their application in neurology. These aspects were discussed at an online conference that was shortly named NeuroRNA.
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Affiliation(s)
- Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Miller W, Pruett CLH, Stone W, Eide C, Riddle M, Popp C, Yousefzadeh M, Lees C, Seelig D, Thompson E, Orr H, Niedernhofer L, Tolar J. Accumulation of senescence observed in spinocerebellar ataxia type 7 mouse model. PLoS One 2022; 17:e0275580. [PMID: 36251631 PMCID: PMC9576077 DOI: 10.1371/journal.pone.0275580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease caused by a trinucleotide CAG repeat. SCA7 predominantly causes a loss of photoreceptors in the retina and Purkinje cells of the cerebellum. Severe infantile-onset SCA7 also causes renal and cardiac irregularities. Previous reports have shown that SCA7 results in increased susceptibility to DNA damage. Since DNA damage can lead to accumulation of senescent cells, we hypothesized that SCA7 causes an accumulation of senescent cells over the course of disease. A 140-CAG repeat SCA7 mouse model was evaluated for signs of disease-specific involvement in the kidney, heart, and cerebellum, tissues that are commonly affected in the infantile form. We found evidence of significant renal abnormality that coincided with an accumulation of senescent cells in the kidneys of SCA7140Q/5Q mice, based on histology findings in addition to RT-qPCR for the cell cycle inhibitors p16Ink4a and p21Cip1 and senescence-associated ß-galactosidase (SA-ßgal) staining, respectively. The Purkinje layer in the cerebellum of SCA7140Q/5Q mice also displayed SA-ßgal+ cells. These novel findings offer evidence that senescent cells accumulate in affected tissues and may possibly contribute to SCA7’s specific phenotype.
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Affiliation(s)
- William Miller
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | | | - William Stone
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | - Cindy Eide
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | - Megan Riddle
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | - Courtney Popp
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | - Matthew Yousefzadeh
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States of America
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Christopher Lees
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | - Davis Seelig
- Comparative Pathology Shared Resource, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Elizabeth Thompson
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States of America
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Harry Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, United States of America
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN, United States of America
| | - Laura Niedernhofer
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States of America
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Jakub Tolar
- Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States of America
- * E-mail:
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