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Xiong K, Wang X, Feng C, Zhang K, Chen D, Yang S. Vectors in CRISPR Gene Editing for Neurological Disorders: Challenges and Opportunities. Adv Biol (Weinh) 2025; 9:e2400374. [PMID: 39950370 DOI: 10.1002/adbi.202400374] [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: 06/29/2024] [Revised: 01/13/2025] [Indexed: 03/18/2025]
Abstract
Diseases of the nervous system are recognized as the second leading cause of death worldwide. The global prevalence of neurological diseases, such as Huntington's disease, Alzheimer's disease, and Parkinson's disease has seen a significant rise due to the increasing proportion of the aging population. The discovery of the clustered regularly interspaced short palindromic repeats (CRISPR) genome editing technique has paved way for universal neurological diseases treatment. However, finding a safe and effective method to deliver CRISPR gene-editing tools remains a main challenge for genome editing therapies in vivo. Adeno-associated virus (AAV) is currently one of the most commonly used vector systems, but some issues remain unresolved, including capsid immunogenicity, off-target mutations, and potential genotoxicity. To address these concerns, researchers are actively encouraging the development of new delivery systems, like virus-like particles and nanoparticles. These novel systems have the potential to enhance targeting efficiency, thereby offering possible solutions to the current challenges. This article reviews CRISPR delivery vectors for neurological disorders treatment and explores potential solutions to overcome limitations in vector systems. Additionally, the delivery strategies of CRISPR systems are highlighted as valuable tools for studying neurological diseases, and the challenges and opportunities that these vectors present.
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Affiliation(s)
- Kexin Xiong
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Xiaxia Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Caicai Feng
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Di Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Sen Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
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2
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Guo Y, Zhao X. CRISPR-based genetic screens in human pluripotent stem cells derived neurons and brain organoids. Cell Tissue Res 2025; 399:1-8. [PMID: 39585363 DOI: 10.1007/s00441-024-03934-2] [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: 05/18/2024] [Accepted: 11/12/2024] [Indexed: 11/26/2024]
Abstract
Recent large-scale genome-wide association and single-cell RNA sequencing (scRNA-seq) studies have uncovered disease-associated genetic risk factors and cell type-specific genetic alterations. However, our understanding of how these genetic variants cause diseases and the underlying mechanisms remains largely unknown. Functional genomics screens using CRISPR-based technologies offer an effective tool for studying genes relevant to disease phenotypes. Here, we summarize recent CRISPR-based functional genomics screen approaches applied to human pluripotent stem cell (hPSC)-derived neurons and brain organoids. These screens have identified genes crucial for neurogenesis, neuronal survival, morphological development, and migration. Combining CRISPR-based genetic screens with scRNA-seq, researchers have revealed downstream genes and cellular pathways impacted by these genetic variants in human neural cells, providing new insights into the pathogenesis of neurodevelopmental disorders, such as microcephaly and autism spectrum disorders. Finally, we discuss current challenges and future directions for using CRISPR-based screens in furthering our understanding of neurological diseases and developing potential therapeutic strategies. Despite challenges, CRISPR-based screens have enormous potential for advancing the therapeutic development of many diseases.
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Affiliation(s)
- Yu Guo
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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3
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Moffa JC, Bland IN, Tooley JR, Kalyanaraman V, Heitmeier M, Creed MC, Copits BA. Cell-Specific Single Viral Vector CRISPR/Cas9 Editing and Genetically Encoded Tool Delivery in the Central and Peripheral Nervous Systems. eNeuro 2024; 11:ENEURO.0438-23.2024. [PMID: 38871457 PMCID: PMC11228695 DOI: 10.1523/eneuro.0438-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/20/2024] [Accepted: 04/18/2024] [Indexed: 06/15/2024] Open
Abstract
CRISPR/Cas9 gene editing represents an exciting avenue to study genes of unknown function and can be combined with genetically encoded tools such as fluorescent proteins, channelrhodopsins, DREADDs, and various biosensors to more deeply probe the function of these genes in different cell types. However, current strategies to also manipulate or visualize edited cells are challenging due to the large size of Cas9 proteins and the limited packaging capacity of adeno-associated viruses (AAVs). To overcome these constraints, we developed an alternative gene editing strategy using a single AAV vector and mouse lines that express Cre-dependent Cas9 to achieve efficient cell-type specific editing across the nervous system. Expressing Cre-dependent Cas9 from a genomic locus affords space to package guide RNAs for gene editing together with Cre-dependent, genetically encoded tools to manipulate, map, or monitor neurons using a single virus. We validated this strategy with three common tools in neuroscience: ChRonos, a channelrhodopsin, for studying synaptic transmission using optogenetics, GCaMP8f for recording Ca2+ transients using photometry, and mCherry for tracing axonal projections. We tested these tools in multiple brain regions and cell types, including GABAergic neurons in the nucleus accumbens, glutamatergic neurons projecting from the ventral pallidum to the lateral habenula, dopaminergic neurons in the ventral tegmental area, and proprioceptive neurons in the periphery. This flexible approach could help identify and test the function of novel genes affecting synaptic transmission, circuit activity, or morphology with a single viral injection.
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Affiliation(s)
- Jamie C Moffa
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Washington University Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri 63110
| | - India N Bland
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jessica R Tooley
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Washington University Division of Biological and Behavioral Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Vani Kalyanaraman
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Monique Heitmeier
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Meaghan C Creed
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Departments of Neuroscience, Psychiatry, and Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Bryan A Copits
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
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4
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z, Tong L, Wang Q, Rajamani KT, Muñoz-Castañeda R, Mu S, Qi T, Zhang Y, Ngiam ZC, Ohte N, Hanashima C, Wu Z, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. Cell 2024; 187:3236-3248.e21. [PMID: 38772369 PMCID: PMC11193654 DOI: 10.1016/j.cell.2024.04.050] [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: 09/08/2023] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Leveraging AAVs' versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screening with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 vectors across AAV serotypes combined with a transposon system, we substantially amplified labeling efficacy and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace S Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Jiwen Li
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Keerthi T Rajamani
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Rodrigo Muñoz-Castañeda
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Shang Mu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tianbo Qi
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yunxiao Zhang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zi Chao Ngiam
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Naoto Ohte
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Carina Hanashima
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Zhuhao Wu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA.
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Déglon N. Gene editing as a therapeutic strategy for spinocerebellar ataxia type-3. Rev Neurol (Paris) 2024; 180:378-382. [PMID: 38580500 DOI: 10.1016/j.neurol.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease, is a neurodegenerative disease caused by expanded polyglutamine repeats in exon 10 of the ataxin-3 gene, ATXN3. The accumulation of mutant ATXN3 protein leads to severe clinical manifestations and premature death. Clinically, SCA3 pathology is characterized by progressive ataxia leading to motor incoordination that may affect balance, gait and speech, and neuropathologically by a progressive degeneration of the spinal cord and cerebellum, as well as the cerebral cortex and basal ganglia. Although SCA3 is a rare disease, it is the most common autosomal dominant spinocerebellar ataxia worldwide. Its geographical distribution varies worldwide, with peak prevalence in certain regions of Brazil, Portugal and China. In 1994, the identification of the polyglutamine expansion in the ATXN3 gene made it possible not only to diagnose this pathology but also to dissect the mechanisms leading to cellular degeneration. As a monogenic disease for which only symptomatic treatment is available, the ATXN3 gene represents an attractive therapeutic target for gene editing strategies.
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Affiliation(s)
- N Déglon
- Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Pavillon 3, Avenue de Beaumont, 1011 Lausanne, Switzerland; Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN), Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
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Podolsky MJ, Kheyfets B, Pandey M, Beigh AH, Yang CD, Lizama CO, Datta R, Lin LL, Wang Z, Wolters PJ, McManus MT, Qi L, Atabai K. Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover. Nat Commun 2024; 15:1531. [PMID: 38378719 PMCID: PMC10879544 DOI: 10.1038/s41467-024-45817-8] [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: 01/14/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
Accumulating evidence has implicated impaired extracellular matrix (ECM) clearance as a key factor in fibrotic disease. Despite decades of research elucidating the effectors of ECM clearance, relatively little is understood regarding the upstream regulation of this process. Collagen is the most abundant constituent of normal and fibrotic ECM in mammalian tissues. Its catabolism occurs through extracellular proteolysis and cell-mediated uptake of collagen fragments for intracellular degradation. Given the paucity of information regarding the regulation of this latter process, here we execute unbiased genome-wide screens to understand the molecular underpinnings of cell-mediated collagen clearance. Using this approach, we discover a mechanism through which collagen biosynthesis is sensed by cells internally and directly regulates clearance of extracellular collagen. The sensing mechanism appears to be dependent on endoplasmic reticulum-resident protein SEL1L and occurs via a noncanonical function of this protein. This pathway functions as a homeostatic negative feedback loop that limits collagen accumulation in tissues. In human fibrotic lung disease, the induction of this collagen clearance pathway by collagen synthesis is impaired, thereby contributing to the pathological accumulation of collagen in lung tissue. Thus, we describe cell-autonomous, rheostatic collagen clearance as an important pathway of tissue homeostasis.
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Affiliation(s)
- Michael J Podolsky
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Benjamin Kheyfets
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Monika Pandey
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Afaq H Beigh
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher D Yang
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Carlos O Lizama
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Ritwik Datta
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Liangguang L Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhihong Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Paul J Wolters
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael T McManus
- Department of Microbiology and Immunology and UCSF Diabetes Center, University of California, San Francisco, CA, USA
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kamran Atabai
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Lung Biology Center, University of California, San Francisco, CA, USA.
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7
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Anselmi L, Ducrocq GP, Ruiz-Velasco V, Stocker SD, Higgins SP, Kaufman MP. Functional knockout of the TRPV1 channel has no effect on the exercise pressor reflex in rats. J Physiol 2023; 601:5241-5256. [PMID: 37878364 PMCID: PMC12042824 DOI: 10.1113/jp285267] [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: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
The role played by the transient receptor potential vanilloid 1 (TRPV1) channel on the thin fibre afferents evoking the exercise pressor reflex is controversial. To shed light on this controversy, we compared the exercise pressor reflex between newly developed TRPV1+/+ , TRPV1+/- and TRPV1-/- rats. Carotid arterial injection of capsaicin (0.5 μg), evoked significant pressor responses in TRPV1+/+ and TRPV1+/- rats, but not in TRPV1-/- rats. In acutely isolated dorsal root ganglion neurons innervating the gastrocnemius muscles, capsaicin evoked inward currents in neurons isolated from TRPV1+/+ and TRPV1+/- rats but not in neurons isolated from TRPV1-/- rats. The reflex was evoked by stimulating the tibial nerve in decerebrated rats whose femoral artery was either freely perfused or occluded. We found no difference between the reflex in the three groups of rats regardless of the patency of the femoral artery. For example, the peak pressor responses to contraction in TRPV1+/+ , TRPV1+/- and TRPV1-/- rats with patent femoral arteries averaged 17.1 ± 7.2, 18.9 ± 12.4 and 18.4 ± 8.6 mmHg, respectively. Stimulation of the tibial nerve after paralysis with pancuronium had no effect on arterial pressure, findings which indicated that the pressor responses to contraction were not caused by electrical stimulation of afferent tibial nerve axons. We also found that expression levels of acid-sensing ion channel 1 and endoperoxide 4 receptor in the L4 and 5 dorsal root ganglia were not upregulated in the TRPV1-/- rats. We conclude that TRPV1 is not needed to evoke the exercise pressor reflex in rats whose contracting muscles have either a patent or an occluded arterial blood supply. KEY POINTS: A reflex arising in contracting skeletal muscle contributes to the increases in arterial blood pressure, cardiac output and breathing evoked by exercise. The sensory arm of the reflex comprises both mechanoreceptors and metaboreceptors, of which the latter signals that blood flow to exercising muscle is not meeting its metabolic demand. The nature of the channel on the metaboreceptor sensing a mismatch between supply and demand is controversial; some believe that it is the transient receptor potential vanilloid 1 (TRPV1) channel. Using genetically engineered rats in which the TRPV1 channel is rendered non-functional, we have shown that it is not needed to evoke the metaboreflex.
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Affiliation(s)
- Laura Anselmi
- Heart and Vascular Institute Penn State College of Medicine, Hershey, PA, USA
| | - Guillaume P Ducrocq
- Heart and Vascular Institute Penn State College of Medicine, Hershey, PA, USA
- Mitochondria, Oxidative Stress and Muscular Protection Laboratory (UR 3072), Faculty of Medicine, University of Strasbourg, Strasbourg, France
| | - Victor Ruiz-Velasco
- Heart and Vascular Institute Penn State College of Medicine, Hershey, PA, USA
- Department of Anesthesiology and Perioperative Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Sean D Stocker
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shannon P Higgins
- Heart and Vascular Institute Penn State College of Medicine, Hershey, PA, USA
| | - Marc P Kaufman
- Heart and Vascular Institute Penn State College of Medicine, Hershey, PA, USA
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Zhang Q, Liu X, Gong L, He M. Combinatorial genetic strategies for dissecting cell lineages, cell types, and gene function in the mouse brain. Dev Growth Differ 2023; 65:546-553. [PMID: 37963088 DOI: 10.1111/dgd.12902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Research in neuroscience has greatly benefited from the development of genetic approaches that enable lineage tracing, cell type targeting, and conditional gene regulation. Recent advances in combinatorial strategies, which integrate multiple cellular features, have significantly enhanced the spatiotemporal precision and flexibility of these manipulations. In this minireview, we introduce the concept and design of these strategies and provide a few examples of their application in genetic fate mapping, cell type targeting, and reversible conditional gene regulation. These advancements have facilitated in-depth investigation into the developmental principles underlying the assembly of brain circuits, granting experimental access to highly specific cell lineages and subtypes, as well as offering valuable new tools for modeling and studying neurological diseases. Additionally, we discuss future directions aimed at expanding and improving the existing genetic toolkit for a better understanding of the development, structure, and function of healthy and diseased brains.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xue Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Gong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao He
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
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9
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Davis-Anderson K, Micheva-Viteva S, Solomon E, Hovde B, Cirigliano E, Harris J, Twary S, Iyer R. CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function. Int J Mol Sci 2023; 24:16161. [PMID: 38003351 PMCID: PMC10671572 DOI: 10.3390/ijms242216161] [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: 09/08/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Neurodegeneration causes a significant disease burden and there are few therapeutic interventions available for reversing or slowing the disease progression. Induced pluripotent stem cells (iPSCs) hold significant potential since they are sourced from adult tissue and have the capacity to be differentiated into numerous cell lineages, including motor neurons. This differentiation process traditionally relies on cell lineage patterning factors to be supplied in the differentiation media. Genetic engineering of iPSC with the introduction of recombinant master regulators of motor neuron (MN) differentiation has the potential to shorten and streamline cell developmental programs. We have established stable iPSC cell lines with transient induction of exogenous LHX3 and ISL1 from the Tet-activator regulatory region and have demonstrated that induction of the transgenes is not sufficient for the development of mature MNs in the absence of neuron patterning factors. Comparative global transcriptome analysis of MN development from native and Lhx-ISL1 modified iPSC cultures demonstrated that the genetic manipulation helped to streamline the neuronal patterning process. However, leaky gene expression of the exogenous MN master regulators in iPSC resulted in the premature activation of genetic pathways characteristic of the mature MN function. Dysregulation of metabolic and regulatory pathways within the developmental process affected the MN electrophysiological responses.
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Affiliation(s)
- Katie Davis-Anderson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Sofiya Micheva-Viteva
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Emilia Solomon
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Blake Hovde
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Elisa Cirigliano
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer Harris
- Information Systems and Modeling Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Scott Twary
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Rashi Iyer
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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10
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Berndt A, Cai D, Cohen A, Juarez B, Iglesias JT, Xiong H, Qin Z, Tian L, Slesinger PA. Current Status and Future Strategies for Advancing Functional Circuit Mapping In Vivo. J Neurosci 2023; 43:7587-7598. [PMID: 37940594 PMCID: PMC10634581 DOI: 10.1523/jneurosci.1391-23.2023] [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: 07/21/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 11/10/2023] Open
Abstract
The human brain represents one of the most complex biological systems, containing billions of neurons interconnected through trillions of synapses. Inherent to the brain is a biochemical complexity involving ions, signaling molecules, and peptides that regulate neuronal activity and allow for short- and long-term adaptations. Large-scale and noninvasive imaging techniques, such as fMRI and EEG, have highlighted brain regions involved in specific functions and visualized connections between different brain areas. A major shortcoming, however, is the need for more information on specific cell types and neurotransmitters involved, as well as poor spatial and temporal resolution. Recent technologies have been advanced for neuronal circuit mapping and implemented in behaving model organisms to address this. Here, we highlight strategies for targeting specific neuronal subtypes, identifying, and releasing signaling molecules, controlling gene expression, and monitoring neuronal circuits in real-time in vivo Combined, these approaches allow us to establish direct causal links from genes and molecules to the systems level and ultimately to cognitive processes.
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Affiliation(s)
| | - Denise Cai
- Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | | | | | | | - Zhenpeng Qin
- University of Texas-Dallas, Richardson, TX 75080
| | - Lin Tian
- University of California-Davis, Davis, CA 95616
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Moffa JC, Bland IN, Tooley JR, Kalyanaraman V, Heitmeier M, Creed MC, Copits BA. Cell specific single viral vector CRISPR/Cas9 editing and genetically encoded tool delivery in the central and peripheral nervous systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561249. [PMID: 37873336 PMCID: PMC10592710 DOI: 10.1101/2023.10.10.561249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gene manipulation strategies using germline knockout, conditional knockout, and more recently CRISPR/Cas9 are crucial tools for advancing our understanding of the nervous system. However, traditional gene knockout approaches can be costly and time consuming, may lack cell-type specificity, and can induce germline recombination. Viral gene editing presents and an exciting alternative to more rapidly study genes of unknown function; however, current strategies to also manipulate or visualize edited cells are challenging due to the large size of Cas9 proteins and the limited packaging capacity of adeno-associated viruses (AAVs). To overcome these constraints, we have developed an alternative gene editing strategy using a single AAV vector and mouse lines that express Cre-dependent Cas9 to achieve efficient cell-type specific editing across the nervous system. Expressing Cre-dependent Cas9 in specific cell types in transgenic mouse lines affords more space to package guide RNAs for gene editing together with Cre-dependent, genetically encoded tools to manipulate, map, or monitor neurons using a single virus. We validated this strategy with three commonly used tools in neuroscience: ChRonos, a channelrhodopsin, for manipulating synaptic transmission using optogenetics; GCaMP8f for recording Ca2+ transients using fiber photometry, and mCherry for anatomical tracing of axonal projections. We tested these tools in multiple brain regions and cell types, including GABAergic neurons in the nucleus accumbens (NAc), glutamatergic neurons projecting from the ventral pallidum (VP) to the lateral habenula (LHb), dopaminergic neurons in the ventral tegmental area (VTA), and parvalbumin (PV)-positive proprioceptive neurons in the periphery. This flexible approach should be useful to identify novel genes that affect synaptic transmission, circuit activity, or morphology with a single viral injection.
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Affiliation(s)
- Jamie C. Moffa
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
- Washington University Medical Scientist Training Program, Washington University School of Medicine; St. Louis, MO
| | - India N. Bland
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| | - Jessica R. Tooley
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
- Washington University Division of Biological and Behavioral Sciences, Washington University School of Medicine; St. Louis, MO
| | - Vani Kalyanaraman
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| | - Monique Heitmeier
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| | - Meaghan C. Creed
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
- Departments of Neuroscience, Psychiatry, and Biomedical Engineering, Washington University School of Medicine, St. Louis, MO
| | - Bryan A. Copits
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Wang Z, Tong L, Wang Q, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558077. [PMID: 37790302 PMCID: PMC10542124 DOI: 10.1101/2023.09.18.558077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Systematic analysis of gene function across diverse cell types in vivo is hindered by two challenges: obtaining sufficient cells from live tissues and accurately identifying each cell's perturbation in high-throughput single-cell assays. Leveraging AAV's versatile cell type tropism and high labeling capacity, we expanded the resolution and scale of in vivo CRISPR screens: allowing phenotypic analysis at single-cell resolution across a multitude of cell types in the embryonic brain, adult brain, and peripheral nervous system. We undertook extensive tests of 86 AAV serotypes, combined with a transposon system, to substantially amplify labeling and accelerate in vivo gene delivery from weeks to days. Using this platform, we performed an in utero genetic screen as proof-of-principle and identified pleiotropic regulatory networks of Foxg1 in cortical development, including Layer 6 corticothalamic neurons where it tightly controls distinct networks essential for cell fate specification. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% (mediated by lentivirus), and achieve analysis of over 30,000 cells in one experiment, thus enabling massively parallel in vivo Perturb-seq. Compatible with various perturbation techniques (CRISPRa/i) and phenotypic measurements (single-cell or spatial multi-omics), our platform presents a flexible, modular approach to interrogate gene function across diverse cell types in vivo, connecting gene variants to their causal functions.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Sean K. Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace S. Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Joshua Z. Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
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