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Sachdev A, Gill K, Sckaff M, Birk AM, Aladesuyi Arogundade O, Brown KA, Chouhan RS, Issagholian-Lewin PO, Patel E, Watry HL, Bernardi MT, Keough KC, Tsai YC, Smith AST, Conklin BR, Clelland CD. Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision. Proc Natl Acad Sci U S A 2024; 121:e2307814121. [PMID: 38621131 PMCID: PMC11047104 DOI: 10.1073/pnas.2307814121] [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: 05/09/2023] [Accepted: 03/01/2024] [Indexed: 04/17/2024] Open
Abstract
Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding single nucleotide polymorphism in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using digital droplet PCR (ddPCR), we determined that transcription from the mutant allele is upregulated at least 10-fold, and that sense transcription is independently regulated from each allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat poly-GP expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production, and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all dipeptide repeat proteins, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including antisense oligonucleotides (ASOs) and CRISPR gene editing.
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Affiliation(s)
| | - Kamaljot Gill
- Gladstone Institutes, San Francisco, CA94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
| | - Maria Sckaff
- Gladstone Institutes, San Francisco, CA94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
| | | | - Olubankole Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Katherine A. Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Runvir S. Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Patrick Oliver Issagholian-Lewin
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Esha Patel
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | | | | | | | | | - Alec Simon Tulloch Smith
- Department of Physiology and Biophysics, University of Washington, Seattle, WA98195
- The Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98195
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA94158
- Department of Medicine, University of California San Francisco, San Francisco, CA94143
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA94143
- Department of Pharmacology, University of California San Francisco, San Francisco, CA94158
| | - Claire Dudley Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
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Feliciano CM, Wu K, Watry HL, Marley CBE, Ramadoss GN, Ghanim HY, Liu AZ, Zholudeva LV, McDevitt TC, Saporta MA, Conklin BR, Judge LM. Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E. Front Cell Dev Biol 2021; 9:723023. [PMID: 34485306 PMCID: PMC8415563 DOI: 10.3389/fcell.2021.723023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/22/2021] [Indexed: 12/26/2022] Open
Abstract
Many neuromuscular disorders are caused by dominant missense mutations that lead to dominant-negative or gain-of-function pathology. This category of disease is challenging to address via drug treatment or gene augmentation therapy because these strategies may not eliminate the effects of the mutant protein or RNA. Thus, effective treatments are severely lacking for these dominant diseases, which often cause severe disability or death. The targeted inactivation of dominant disease alleles by gene editing is a promising approach with the potential to completely remove the cause of pathology with a single treatment. Here, we demonstrate that allele-specific CRISPR gene editing in a human model of axonal Charcot-Marie-Tooth (CMT) disease rescues pathology caused by a dominant missense mutation in the neurofilament light chain gene (NEFL, CMT type 2E). We utilized a rapid and efficient method for generating spinal motor neurons from human induced pluripotent stem cells (iPSCs) derived from a patient with CMT2E. Diseased motor neurons recapitulated known pathologic phenotypes at early time points of differentiation, including aberrant accumulation of neurofilament light chain protein in neuronal cell bodies. We selectively inactivated the disease NEFL allele in patient iPSCs using Cas9 enzymes to introduce a frameshift at the pathogenic N98S mutation. Motor neurons carrying this allele-specific frameshift demonstrated an amelioration of the disease phenotype comparable to that seen in an isogenic control with precise correction of the mutation. Our results validate allele-specific gene editing as a therapeutic approach for CMT2E and as a promising strategy to silence dominant mutations in any gene for which heterozygous loss-of-function is well tolerated. This highlights the potential for gene editing as a therapy for currently untreatable dominant neurologic diseases.
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Affiliation(s)
- Carissa M. Feliciano
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
| | - Kenneth Wu
- Gladstone Institutes, San Francisco, CA, United States
| | | | - Chiara B. E. Marley
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
| | - Gokul N. Ramadoss
- Gladstone Institutes, San Francisco, CA, United States
- Biomedical Sciences Ph.D. Program, University of California, San Francisco, San Francisco, CA, United States
| | | | - Angela Z. Liu
- Gladstone Institutes, San Francisco, CA, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, United States
| | | | - Todd C. McDevitt
- Gladstone Institutes, San Francisco, CA, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Mario A. Saporta
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Innovative Genomics Institute, Berkeley, CA, United States
| | - Luke M. Judge
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
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Watry HL, Feliciano CM, Gjoni K, Takahashi G, Miyaoka Y, Conklin BR, Judge LM. Rapid, precise quantification of large DNA excisions and inversions by ddPCR. Sci Rep 2020; 10:14896. [PMID: 32913194 PMCID: PMC7483445 DOI: 10.1038/s41598-020-71742-z] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
The excision of genomic sequences using paired CRISPR-Cas nucleases is a powerful tool to study gene function, create disease models and holds promise for therapeutic gene editing. However, our understanding of the factors that favor efficient excision is limited by the lack of a rapid, accurate measurement of DNA excision outcomes that is free of amplification bias. Here, we introduce ddXR (droplet digital PCR eXcision Reporter), a method that enables the accurate and sensitive detection of excisions and inversions independent of length. The method can be completed in a few hours without the need for next-generation sequencing. The ddXR method uncovered unexpectedly high rates of large (> 20 kb) excisions and inversions, while also revealing a surprisingly low dependence on linear distance, up to 170 kb. We further modified the method to measure precise repair of excision junctions and allele-specific excision, with important implications for disease modeling and therapeutic gene editing.
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Affiliation(s)
- Hannah L Watry
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carissa M Feliciano
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA
| | - Gou Takahashi
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Bruce R Conklin
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Ophthalmology, UCSF, San Francisco, CA, USA.
- Department of Medicine, UCSF, San Francisco, CA, USA.
| | - Luke M Judge
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA.
- Department of Pediatrics, UCSF, San Francisco, CA, USA.
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Wienert B, Wyman SK, Richardson CD, Yeh CD, Akcakaya P, Porritt MJ, Morlock M, Vu JT, Kazane KR, Watry HL, Judge LM, Conklin BR, Maresca M, Corn JE. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 2019; 364:286-289. [PMID: 31000663 PMCID: PMC6589096 DOI: 10.1126/science.aav9023] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/23/2019] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas genome editing induces targeted DNA damage but can also affect off-target sites. Current off-target discovery methods work using purified DNA or specific cellular models but are incapable of direct detection in vivo. We developed DISCOVER-Seq (discovery of in situ Cas off-targets and verification by sequencing), a universally applicable approach for unbiased off-target identification that leverages the recruitment of DNA repair factors in cells and organisms. Tracking the precise recruitment of MRE11 uncovers the molecular nature of Cas activity in cells with single-base resolution. DISCOVER-Seq works with multiple guide RNA formats and types of Cas enzymes, allowing characterization of new editing tools. Off-targets can be identified in cell lines and patient-derived induced pluripotent stem cells and during adenoviral editing of mice, paving the way for in situ off-target discovery within individual patient genotypes during therapeutic genome editing.
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Affiliation(s)
- Beeke Wienert
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Christopher D Richardson
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Charles D Yeh
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Pinar Akcakaya
- Discovery Biology, AstraZeneca, 43150 Gothenburg, Sweden
| | | | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Katelynn R Kazane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hannah L Watry
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Luke M Judge
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA 94158, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California San Francisco, San Francisco, California 94143, USA
| | | | - Jacob E Corn
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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