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Bendixen L, Jensen TI, Bak RO. CRISPR-Cas-mediated transcriptional modulation: The therapeutic promises of CRISPRa and CRISPRi. Mol Ther 2023; 31:1920-1937. [PMID: 36964659 PMCID: PMC10362391 DOI: 10.1016/j.ymthe.2023.03.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
The CRISPR-Cas system is commonly known for its ability to cleave DNA in a programmable manner, which has democratized gene editing and facilitated recent breakthroughs in gene therapy. However, newer iterations of the technology using nuclease-disabled Cas enzymes have spurred a variety of different types of genetic engineering platforms such as transcriptional modulation using the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) systems. This review introduces the creation of these programmable transcriptional modulators, various methods of delivery utilized for these systems, and recent technological developments. CRISPRa and CRISPRi have also been implemented in genetic screens for interrogating gene function and discovering genes involved in various biological pathways. We describe recent compelling examples of how these tools have become powerful means to unravel genetic networks and uncovering important information about devastating diseases. Finally, we provide an overview of preclinical studies in which transcriptional modulation has been used therapeutically, and we discuss potential future directions of these novel modalities.
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Affiliation(s)
- Louise Bendixen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Trine I Jensen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark.
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52
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Ramani B, Rose IVL, Pan A, Tian R, Ma K, Palop JJ, Kampmann M. Scalable, cell type-selective, AAV-based in vivo CRISPR screening in the mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544831. [PMID: 37398301 PMCID: PMC10312723 DOI: 10.1101/2023.06.13.544831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
CRISPR-based genetic screening directly in mammalian tissues in vivo is challenging due to the need for scalable, cell-type selective delivery and recovery of guide RNA libraries. We developed an in vivo adeno-associated virus-based and Cre recombinase-dependent workflow for cell type-selective CRISPR interference screening in mouse tissues. We demonstrate the power of this approach by identifying neuron-essential genes in the mouse brain using a library targeting over 2000 genes.
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Affiliation(s)
- Biswarathan Ramani
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew Pan
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Keran Ma
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Jorge J Palop
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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53
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Yan YW, Qian ES, Woodard LE, Bejoy J. Neural lineage differentiation of human pluripotent stem cells: Advances in disease modeling. World J Stem Cells 2023; 15:530-547. [PMID: 37424945 PMCID: PMC10324500 DOI: 10.4252/wjsc.v15.i6.530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/14/2023] [Accepted: 04/27/2023] [Indexed: 06/20/2023] Open
Abstract
Brain diseases affect 1 in 6 people worldwide. These diseases range from acute neurological conditions such as stroke to chronic neurodegenerative disorders such as Alzheimer’s disease. Recent advancements in tissue-engineered brain disease models have overcome many of the different shortcomings associated with the various animal models, tissue culture models, and epidemiologic patient data that are commonly used to study brain disease. One innovative method by which to model human neurological disease is via the directed differentiation of human pluripotent stem cells (hPSCs) to neural lineages including neurons, astrocytes, and oligodendrocytes. Three-dimensional models such as brain organoids have also been derived from hPSCs, offering more physiological relevance due to their incorporation of various cell types. As such, brain organoids can better model the pathophysiology of neural diseases observed in patients. In this review, we will emphasize recent developments in hPSC-based tissue culture models of neurological disorders and how they are being used to create neural disease models.
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Affiliation(s)
- Yuan-Wei Yan
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Eddie S Qian
- Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Lauren E Woodard
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37232, United States
- Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, United States
| | - Julie Bejoy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
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54
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Nott A, Holtman IR. Genetic insights into immune mechanisms of Alzheimer's and Parkinson's disease. Front Immunol 2023; 14:1168539. [PMID: 37359515 PMCID: PMC10285485 DOI: 10.3389/fimmu.2023.1168539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 06/28/2023] Open
Abstract
Microglia, the macrophages of the brain, are vital for brain homeostasis and have been implicated in a broad range of brain disorders. Neuroinflammation has gained traction as a possible therapeutic target for neurodegeneration, however, the precise function of microglia in specific neurodegenerative disorders is an ongoing area of research. Genetic studies offer valuable insights into understanding causality, rather than merely observing a correlation. Genome-wide association studies (GWAS) have identified many genetic loci that are linked to susceptibility to neurodegenerative disorders. (Post)-GWAS studies have determined that microglia likely play an important role in the development of Alzheimer's disease (AD) and Parkinson's disease (PD). The process of understanding how individual GWAS risk loci affect microglia function and mediate susceptibility is complex. A rapidly growing number of publications with genomic datasets and computational tools have formulated new hypotheses that guide the biological interpretation of AD and PD genetic risk. In this review, we discuss the key concepts and challenges in the post-GWAS interpretation of AD and PD GWAS risk alleles. Post-GWAS challenges include the identification of target cell (sub)type(s), causal variants, and target genes. Crucially, the prediction of GWAS-identified disease-risk cell types, variants and genes require validation and functional testing to understand the biological consequences within the pathology of the disorders. Many AD and PD risk genes are highly pleiotropic and perform multiple important functions that might not be equally relevant for the mechanisms by which GWAS risk alleles exert their effect(s). Ultimately, many GWAS risk alleles exert their effect by changing microglia function, thereby altering the pathophysiology of these disorders, and hence, we believe that modelling this context is crucial for a deepened understanding of these disorders.
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Affiliation(s)
- Alexi Nott
- Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Inge R. Holtman
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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55
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Funes S, Gadd DH, Mosqueda M, Zhong J, Jung J, Shankaracharya, Unger M, Cameron D, Dawes P, Keagle PJ, McDonough JA, Boopathy S, Sena-Esteves M, Lutz C, Skarnes WC, Lim ET, Schafer DP, Massi F, Landers JE, Bosco DA. Expression of ALS-PFN1 impairs vesicular degradation in iPSC-derived microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.541136. [PMID: 37398081 PMCID: PMC10312575 DOI: 10.1101/2023.06.01.541136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microglia play a pivotal role in neurodegenerative disease pathogenesis, but the mechanisms underlying microglia dysfunction and toxicity remain to be fully elucidated. To investigate the effect of neurodegenerative disease-linked genes on the intrinsic properties of microglia, we studied microglia-like cells derived from human induced pluripotent stem cells (iPSCs), termed iMGs, harboring mutations in profilin-1 (PFN1) that are causative for amyotrophic lateral sclerosis (ALS). ALS-PFN1 iMGs exhibited lipid dysmetabolism and deficits in phagocytosis, a critical microglia function. Our cumulative data implicate an effect of ALS-linked PFN1 on the autophagy pathway, including enhanced binding of mutant PFN1 to the autophagy signaling molecule PI3P, as an underlying cause of defective phagocytosis in ALS-PFN1 iMGs. Indeed, phagocytic processing was restored in ALS-PFN1 iMGs with Rapamycin, an inducer of autophagic flux. These outcomes demonstrate the utility of iMGs for neurodegenerative disease research and highlight microglia vesicular degradation pathways as potential therapeutic targets for these disorders.
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Vilca SJ, Margetts AV, Pollock TA, Tuesta LM. Transcriptional and epigenetic regulation of microglia in substance use disorders. Mol Cell Neurosci 2023; 125:103838. [PMID: 36893849 PMCID: PMC10247513 DOI: 10.1016/j.mcn.2023.103838] [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: 11/16/2022] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Microglia are widely known for their role in immune surveillance and for their ability to refine neurocircuitry during development, but a growing body of evidence suggests that microglia may also play a complementary role to neurons in regulating the behavioral aspects of substance use disorders. While many of these efforts have focused on changes in microglial gene expression associated with drug-taking, epigenetic regulation of these changes has yet to be fully understood. This review provides recent evidence supporting the role of microglia in various aspects of substance use disorder, with particular focus on changes to the microglial transcriptome and the potential epigenetic mechanisms driving these changes. Further, this review discusses the latest technical advances in low-input chromatin profiling and highlights the current challenges for studying these novel molecular mechanisms in microglia.
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Affiliation(s)
- Samara J Vilca
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America; Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America
| | - Alexander V Margetts
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America; Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America
| | - Tate A Pollock
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America; Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America
| | - Luis M Tuesta
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America; Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America.
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57
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Castranio EL, Hasel P, Haure-Mirande JV, Ramirez Jimenez AV, Hamilton BW, Kim RD, Glabe CG, Wang M, Zhang B, Gandy S, Liddelow SA, Ehrlich ME. Microglial INPP5D limits plaque formation and glial reactivity in the PSAPP mouse model of Alzheimer's disease. Alzheimers Dement 2023; 19:2239-2252. [PMID: 36448627 PMCID: PMC10481344 DOI: 10.1002/alz.12821] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022]
Abstract
INTRODUCTION The inositol polyphosphate-5-phosphatase D (INPP5D) gene encodes a dual-specificity phosphatase that can dephosphorylate both phospholipids and phosphoproteins. Single nucleotide polymorphisms in INPP5D impact risk for developing late onset sporadic Alzheimer's disease (LOAD). METHODS To assess the consequences of inducible Inpp5d knockdown in microglia of APPKM670/671NL /PSEN1Δexon9 (PSAPP) mice, we injected 3-month-old Inpp5dfl/fl /Cx3cr1CreER/+ and PSAPP/Inpp5dfl/fl /Cx3cr1CreER/+ mice with either tamoxifen (TAM) or corn oil (CO) to induce recombination. RESULTS At age 6 months, we found that the percent area of 6E10+ deposits and plaque-associated microglia in Inpp5d knockdown mice were increased compared to controls. Spatial transcriptomics identified a plaque-specific expression profile that was extensively altered by Inpp5d knockdown. DISCUSSION These results demonstrate that conditional Inpp5d downregulation in the PSAPP mouse increases plaque burden and recruitment of microglia to plaques. Spatial transcriptomics highlighted an extended gene expression signature associated with plaques and identified CST7 (cystatin F) as a novel marker of plaques. HIGHLIGHTS Inpp5d knockdown increases plaque burden and plaque-associated microglia number. Spatial transcriptomics identifies an expanded plaque-specific gene expression profile. Plaque-induced gene expression is altered by Inpp5d knockdown in microglia. Our plaque-associated gene signature overlaps with human Alzheimer's disease gene networks.
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Affiliation(s)
- Emilie L. Castranio
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
| | - Philip Hasel
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
| | | | | | - B. Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
| | - Rachel D. Kim
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
| | - Charles G. Glabe
- Department of Molecular Biology and Biochemistry,
University of California, Irvine, Irvine, California, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
- Department of Psychiatry and Alzheimer’s Disease
Research Center, Icahn School of Medicine at Mount Sinai, New York, New York,
USA
- James J. Peters VA Medical Center, Bronx, New York,
USA
| | - Shane A. Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
- Department of Neuroscience & Physiology, NYU Grossman
School of Medicine, New York, New York, USA
- Department of Ophthalmology, NYU Grossman School of
Medicine, New York, New York, USA
- Parekh Center for Interdisciplinary Neurology, NYU Grossman
School of Medicine, New York, New York, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
- Department of Pediatrics, Icahn School of Medicine at
Mount Sinai, New York, New York, USA
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58
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Watson LA, Meharena HS. From neurodevelopment to neurodegeneration: utilizing human stem cell models to gain insight into Down syndrome. Front Genet 2023; 14:1198129. [PMID: 37323671 PMCID: PMC10267712 DOI: 10.3389/fgene.2023.1198129] [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: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Down syndrome (DS), caused by triplication of chromosome 21, is the most frequent aneuploidy observed in the human population and represents the most common genetic form of intellectual disability and early-onset Alzheimer's disease (AD). Individuals with DS exhibit a wide spectrum of clinical presentation, with a number of organs implicated including the neurological, immune, musculoskeletal, cardiac, and gastrointestinal systems. Decades of DS research have illuminated our understanding of the disorder, however many of the features that limit quality of life and independence of individuals with DS, including intellectual disability and early-onset dementia, remain poorly understood. This lack of knowledge of the cellular and molecular mechanisms leading to neurological features of DS has caused significant roadblocks in developing effective therapeutic strategies to improve quality of life for individuals with DS. Recent technological advances in human stem cell culture methods, genome editing approaches, and single-cell transcriptomics have provided paradigm-shifting insights into complex neurological diseases such as DS. Here, we review novel neurological disease modeling approaches, how they have been used to study DS, and what questions might be addressed in the future using these innovative tools.
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59
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Li K, Ouyang M, Zhan J, Tian R. CRISPR-based functional genomics screening in human-pluripotent-stem-cell-derived cell types. CELL GENOMICS 2023; 3:100300. [PMID: 37228745 PMCID: PMC10203043 DOI: 10.1016/j.xgen.2023.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
While our knowledge of gene expression in different human cell types is rapidly expanding with advances in transcriptomic profiling technologies, the next challenge is to understand gene function in each cell type. CRISPR-Cas9-based functional genomics screening offers a powerful approach to determine gene function in a high-throughput manner. With the maturation of stem cell technology, a variety of human cell types can be derived from human pluripotent stem cells (hPSCs). Recently, the integration of CRISPR screening with hPSC differentiation technologies opens up unprecedented opportunities to systematically examine gene function in different human cell types and identify mechanisms and therapeutic targets for human diseases. This review highlights recent progress in the development and applications of CRISPR-Cas9-based functional genomics screening in hPSC-derived cell types, discusses current challenges and limitations, and outlines future directions for this emerging field.
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Affiliation(s)
- Kun Li
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Miao Ouyang
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Jiangshan Zhan
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
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60
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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61
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Temple S. Advancing cell therapy for neurodegenerative diseases. Cell Stem Cell 2023; 30:512-529. [PMID: 37084729 PMCID: PMC10201979 DOI: 10.1016/j.stem.2023.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/20/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Cell-based therapies are being developed for various neurodegenerative diseases that affect the central nervous system (CNS). Concomitantly, the roles of individual cell types in neurodegenerative pathology are being uncovered by genetic and single-cell studies. With a greater understanding of cellular contributions to health and disease and with the arrival of promising approaches to modulate them, effective therapeutic cell products are now emerging. This review examines how the ability to generate diverse CNS cell types from stem cells, along with a deeper understanding of cell-type-specific functions and pathology, is advancing preclinical development of cell products for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Sally Temple
- Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
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62
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McMillan RE, Wang E, Carlin AF, Coufal NG. Human microglial models to study host-virus interactions. Exp Neurol 2023; 363:114375. [PMID: 36907350 PMCID: PMC10521930 DOI: 10.1016/j.expneurol.2023.114375] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 03/14/2023]
Abstract
Microglia, the resident macrophage of the central nervous system, are increasingly recognized as contributing to diverse aspects of human development, health, and disease. In recent years, numerous studies in both mouse and human models have identified microglia as a "double edged sword" in the progression of neurotropic viral infections: protecting against viral replication and cell death in some contexts, while acting as viral reservoirs and promoting excess cellular stress and cytotoxicity in others. It is imperative to understand the diversity of human microglial responses in order to therapeutically modulate them; however, modeling human microglia has been historically challenging due to significant interspecies differences in innate immunity and rapid transformation upon in vitro culture. In this review, we discuss the contribution of microglia to the neuropathogenesis of key neurotropic viral infections: human immunodeficiency virus 1 (HIV-1), Zika virus (ZIKV), Japanese encephalitis virus (JEV), West Nile virus (WNV), Herpes simplex virus (HSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We pay special attention to recent work with human stem cell-derived microglia and propose strategies to leverage these powerful models to further uncover species- and disease-specific microglial responses and novel therapeutic interventions for neurotropic viral infections.
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Affiliation(s)
- Rachel E McMillan
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, United States of America; Department of Pathology and Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America
| | - Ellen Wang
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92093, United States of America
| | - Aaron F Carlin
- Department of Pathology and Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America.
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92093, United States of America.
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63
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Li E, Benitez C, Boggess SC, Koontz M, Rose IV, Draeger N, Teter OM, Samelson AJ, Ullian EM, Kampmann M. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538498. [PMID: 37163077 PMCID: PMC10168378 DOI: 10.1101/2023.04.26.538498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The sheer complexity of the brain has complicated our ability to understand its cellular mechanisms in health and disease. Genome-wide association studies have uncovered genetic variants associated with specific neurological phenotypes and diseases. In addition, single-cell transcriptomics have provided molecular descriptions of specific brain cell types and the changes they undergo during disease. Although these approaches provide a giant leap forward towards understanding how genetic variation can lead to functional changes in the brain, they do not establish molecular mechanisms. To address this need, we developed a 3D co-culture system termed iAssembloids (induced multi-lineage assembloids) that enables the rapid generation of homogenous neuron-glia spheroids. We characterize these iAssembloids with immunohistochemistry and single-cell transcriptomics and combine them with large-scale CRISPRi-based screens. In our first application, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response in the presence of reactive oxygen species elicited by high neuronal activity, which was not previously found in 2D monoculture neuron screens. We also apply the platform to investigate the role of APOE-ε4, a risk variant for Alzheimer's Disease, in its effect on neuronal survival. This platform expands the toolbox for the unbiased identification of mechanisms of cell-cell interactions in brain health and disease.
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Affiliation(s)
- Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Camila Benitez
- TETRAD Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Steven C. Boggess
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Koontz
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Indigo V.L. Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nina Draeger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Olivia M. Teter
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Avi J. Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Erik M. Ullian
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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64
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Antignano I, Liu Y, Offermann N, Capasso M. Aging microglia. Cell Mol Life Sci 2023; 80:126. [PMID: 37081238 PMCID: PMC10119228 DOI: 10.1007/s00018-023-04775-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
Microglia are the tissue-resident macrophage population of the brain, specialized in supporting the CNS environment and protecting it from endogenous and exogenous insults. Nonetheless, their function declines with age, in ways that remain to be fully elucidated. Given the critical role played by microglia in neurodegenerative diseases, a better understanding of the aging microglia phenotype is an essential prerequisite in designing better preventive and therapeutic strategies. In this review, we discuss the most recent literature on microglia in aging, comparing findings in rodent models and human subjects.
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Affiliation(s)
- Ignazio Antignano
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Yingxiao Liu
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Nina Offermann
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Melania Capasso
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
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Bhatti JS, Khullar N, Mishra J, Kaur S, Sehrawat A, Sharma E, Bhatti GK, Selman A, Reddy PH. Stem cells in the treatment of Alzheimer's disease - Promises and pitfalls. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166712. [PMID: 37030521 DOI: 10.1016/j.bbadis.2023.166712] [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: 02/25/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
Alzheimer's disease (AD) is the most widespread form of neurodegenerative disorder that causes memory loss and multiple cognitive issues. The underlying mechanisms of AD include the build-up of amyloid-β and phosphorylated tau, synaptic damage, elevated levels of microglia and astrocytes, abnormal microRNAs, mitochondrial dysfunction, hormonal imbalance, and age-related neuronal loss. However, the etiology of AD is complex and involves a multitude of environmental and genetic factors. Currently, available AD medications only alleviate symptoms and do not provide a permanent cure. Therefore, there is a need for therapies that can prevent or reverse cognitive decline, brain tissue loss, and neural instability. Stem cell therapy is a promising treatment for AD because stem cells possess the unique ability to differentiate into any type of cell and maintain their self-renewal. This article provides an overview of the pathophysiology of AD and existing pharmacological treatments. This review article focuses on the role of various types of stem cells in neuroregeneration, the potential challenges, and the future of stem cell-based therapies for AD, including nano delivery and gaps in stem cell technology.
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Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Jayapriya Mishra
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Satinder Kaur
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Abhishek Sehrawat
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Eva Sharma
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Ashley Selman
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
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66
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Boal AM, McGrady NR, Chamling X, Kagitapalli BS, Zack DJ, Calkins DJ, Risner ML. Microfluidic Platforms Promote Polarization of Human-Derived Retinal Ganglion Cells That Model Axonopathy. Transl Vis Sci Technol 2023; 12:1. [PMID: 37010860 PMCID: PMC10080917 DOI: 10.1167/tvst.12.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/09/2023] [Indexed: 04/04/2023] Open
Abstract
Purpose Axons depend on long-range transport of proteins and organelles which increases susceptibility to metabolic stress in disease. The axon initial segment (AIS) is particularly vulnerable due to the high bioenergetic demand of action potential generation. Here, we prepared retinal ganglion cells derived from human embryonic stem cells (hRGCs) to probe how axonal stress alters AIS morphology. Methods hRGCs were cultured on coverslips or microfluidic platforms. We assayed AIS specification and morphology by immunolabeling against ankyrin G (ankG), an axon-specific protein, and postsynaptic density 95 (PSD-95), a dendrite-specific protein. Using microfluidic platforms that enable fluidic isolation, we added colchicine to the axon compartment to lesion axons. We verified axonopathy by measuring the anterograde axon transport of cholera toxin subunit B and immunolabeling against cleaved caspase 3 (CC3) and phosphorylated neurofilament H (SMI-34). We determined the influence of axon injury on AIS morphology by immunolabeling samples against ankG and measuring AIS distance from soma and length. Results Based on measurements of ankG and PSD-95 immunolabeling, microfluidic platforms promote the formation and separation of distinct somatic-dendritic versus axonal compartments in hRGCs compared to coverslip cultures. Chemical lesioning of axons by colchicine reduced hRGC anterograde axon transport, increased varicosity density, and enhanced expression of CC3 and SMI-34. Interestingly, we found that colchicine selectively affected hRGCs with axon-carrying dendrites by reducing AIS distance from somas and increasing length, thus suggesting reduced capacity to maintain excitability. Conclusions Thus, microfluidic platforms promote polarized hRGCs that enable modeling of axonopathy. Translational Relevance Microfluidic platforms may be used to assay compartmentalized degeneration that occurs during glaucoma.
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Affiliation(s)
- Andrew M. Boal
- Vanderbilt Eye Institute, Department of Ophthalmology & Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nolan R. McGrady
- Vanderbilt Eye Institute, Department of Ophthalmology & Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xitiz Chamling
- Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bhanu S. Kagitapalli
- Vanderbilt Eye Institute, Department of Ophthalmology & Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Donald J. Zack
- Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David J. Calkins
- Vanderbilt Eye Institute, Department of Ophthalmology & Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael L. Risner
- Vanderbilt Eye Institute, Department of Ophthalmology & Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
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Hong Y, Yang Q, Song H, Ming GL. Opportunities and limitations for studying neuropsychiatric disorders using patient-derived induced pluripotent stem cells. Mol Psychiatry 2023; 28:1430-1439. [PMID: 36782062 PMCID: PMC10213114 DOI: 10.1038/s41380-023-01990-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Neuropsychiatric disorders affect a large proportion of the global population and there is an urgent need to understand the pathogenesis and to develop novel and improved treatments of these devastating disorders. However, the diverse symptomatology combined with complex polygenic etiology, and the limited access to disorder-relevant cell types in human brains represent a major obstacle for mechanistic disease research. Conventional animal models, such as rodents, are limited by inherent species differences in brain development, architecture, and function. Advances in human induced pluripotent stem cells (hiPSCs) technologies have provided platforms for new discoveries in neuropsychiatric disorders. First, hiPSC-based disease models enable unprecedented investigation of psychiatric disorders at the molecular, cellular, and structural levels. Second, hiPSCs derived from patients with known genetics, symptoms, and drug response profiles offer an opportunity to recapitulate pathogenesis in relevant cell types and provide novel approaches for understanding disease mechanisms and for developing effective treatments. Third, genome-editing technologies have extended the potential of hiPSCs for generating models to elucidate the genetic basis of rare monogenetic and complex polygenic psychiatric disorders and to establish the causality between genotype and phenotype. Here we review opportunities and limitations for studying psychiatric disorders using various hiPSC-derived model systems.
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Affiliation(s)
- Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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68
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de Majo M, Koontz M, Marsan E, Salinas N, Ramsey A, Kuo YM, Seo K, Li H, Dräger N, Leng K, Gonzales SL, Kurnellas M, Miyaoka Y, Klim JR, Kampmann M, Ward ME, Huang EJ, Ullian EM. Granulin loss of function in human mature brain organoids implicates astrocytes in TDP-43 pathology. Stem Cell Reports 2023; 18:706-719. [PMID: 36827976 PMCID: PMC10031303 DOI: 10.1016/j.stemcr.2023.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/25/2023] Open
Abstract
Loss of function (LoF) of TAR-DNA binding protein 43 (TDP-43) and mis-localization, together with TDP-43-positive and hyperphosphorylated inclusions, are found in post-mortem tissue of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients, including those carrying LoF variants in the progranulin gene (GRN). Modeling TDP-43 pathology has been challenging in vivo and in vitro. We present a three-dimensional induced pluripotent stem cell (iPSC)-derived paradigm-mature brain organoids (mbOrg)-composed of cortical-like-astrocytes (iA) and neurons. When devoid of GRN, mbOrgs spontaneously recapitulate TDP-43 mis-localization, hyperphosphorylation, and LoF phenotypes. Mixing and matching genotypes in mbOrgs showed that GRN-/- iA are drivers for TDP-43 pathology. Finally, we rescued TDP-43 LoF by adding exogenous progranulin, demonstrating a link between TDP-43 LoF and progranulin expression. In conclusion, we present an iPSC-derived platform that shows striking features of human TDP-43 proteinopathy and provides a tool for the mechanistic modeling of TDP-43 pathology and patient-tailored therapeutic screening for FTD and ALS.
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Affiliation(s)
- Martina de Majo
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA; Synapticure Inc, Chicago, IL 60612, USA.
| | - Mark Koontz
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA; Synapticure Inc, Chicago, IL 60612, USA
| | - Elise Marsan
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nir Salinas
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Arren Ramsey
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yien-Ming Kuo
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kyounghee Seo
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Huinan Li
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nina Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Kun Leng
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Santiago L Gonzales
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eric J Huang
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA; Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Erik M Ullian
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA; Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA.
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You SF, Brase L, Filipello F, Iyer AK, Del-Aguila J, He J, D’Oliveira Albanus R, Budde J, Norton J, Gentsch J, Dräger NM, Sattler SM, Kampmann M, Piccio L, Morris JC, Perrin RJ, McDade E, Paul SM, Cashikar AG, Benitez BA, Harari O, Karch CM. MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285545. [PMID: 36798226 PMCID: PMC9934804 DOI: 10.1101/2023.02.06.23285545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Genome-wide association studies (GWAS) have identified many modifiers of Alzheimer disease (AD) risk enriched in microglia. Two of these modifiers are common variants in the MS4A locus (rs1582763: protective and rs6591561: risk) and serve as major regulators of CSF sTREM2 levels. To understand their functional impact on AD, we used single nucleus transcriptomics to profile brains from carriers of these variants. We discovered a "chemokine" microglial subpopulation that is altered in MS4A variant carriers and for which MS4A4A is the major regulator. The protective variant increases MS4A4A expression and shifts the chemokine microglia subpopulation to an interferon state, while the risk variant suppresses MS4A4A expression and reduces this subpopulation of microglia. Our findings provide a mechanistic explanation for the AD variants in the MS4A locus. Further, they pave the way for future mechanistic studies of AD variants and potential therapeutic strategies for enhancing microglia resilience in AD pathogenesis.
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Affiliation(s)
- Shih-Feng You
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Logan Brase
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Fabia Filipello
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Abhirami K. Iyer
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Jorge Del-Aguila
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - June He
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | | | - John Budde
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Nina M. Dräger
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sydney M. Sattler
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Piccio
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- Charles Perkins Centre and Brain and Mind Centre, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - John C. Morris
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J. Perrin
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric McDade
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
| | | | - Steven M. Paul
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Anil G. Cashikar
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Bruno A. Benitez
- Department of Neurology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, USA
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Murdock MH, Tsai LH. Insights into Alzheimer's disease from single-cell genomic approaches. Nat Neurosci 2023; 26:181-195. [PMID: 36593328 PMCID: PMC10155598 DOI: 10.1038/s41593-022-01222-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/28/2022] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is an age-related disease pathologically defined by the deposition of amyloid plaques and neurofibrillary tangles in the brain parenchyma. Single-cell profiling has shown that Alzheimer's dementia involves the complex interplay of virtually every major brain cell type. Here, we highlight cell-type-specific molecular perturbations in AD. We discuss how genomic information from single cells expands existing paradigms of AD pathogenesis and highlight new opportunities for therapeutic interventions.
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Affiliation(s)
- Mitchell H Murdock
- Department of Brain and Cognitive Sciences, The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Cheng J, Lin G, Wang T, Wang Y, Guo W, Liao J, Yang P, Chen J, Shao X, Lu X, Zhu L, Wang Y, Fan X. Massively Parallel CRISPR-Based Genetic Perturbation Screening at Single-Cell Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204484. [PMID: 36504444 PMCID: PMC9896079 DOI: 10.1002/advs.202204484] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-based genetic screening has been demonstrated as a powerful approach for unbiased functional genomics research. Single-cell CRISPR screening (scCRISPR) techniques, which result from the combination of single-cell toolkits and CRISPR screening, allow dissecting regulatory networks in complex biological systems at unprecedented resolution. These methods allow cells to be perturbed en masse using a pooled CRISPR library, followed by high-content phenotyping. This is technically accomplished by annotating cells with sgRNA-specific barcodes or directly detectable sgRNAs. According to the integration of distinct single-cell technologies, these methods principally fall into four categories: scCRISPR with RNA-seq, scCRISPR with ATAC-seq, scCRISPR with proteome probing, and imaging-based scCRISPR. scCRISPR has deciphered genotype-phenotype relationships, genetic regulations, tumor biological issues, and neuropathological mechanisms. This review provides insight into the technical breakthrough of scCRISPR by systematically summarizing the advancements of various scCRISPR methodologies and analyzing their merits and limitations. In addition, an application-oriented approach guide is offered to meet researchers' individualized demands.
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Affiliation(s)
- Junyun Cheng
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Gaole Lin
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Tianhao Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Yunzhu Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Wenbo Guo
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jie Liao
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Penghui Yang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jie Chen
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xin Shao
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiaoyan Lu
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Jinhua Institute of Zhejiang UniversityJinhua321016China
| | - Ling Zhu
- The Save Sight InstituteFaculty of Medicine and Healththe University of SydneySydneyNSW2000Australia
| | - Yi Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxing314100China
| | - Xiaohui Fan
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Jinhua Institute of Zhejiang UniversityJinhua321016China
- The Save Sight InstituteFaculty of Medicine and Healththe University of SydneySydneyNSW2000Australia
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxing314100China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
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Sahlgren Bendtsen KM, Hall VJ. The Breakthroughs and Caveats of Using Human Pluripotent Stem Cells in Modeling Alzheimer's Disease. Cells 2023; 12:cells12030420. [PMID: 36766763 PMCID: PMC9913971 DOI: 10.3390/cells12030420] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Modeling Alzheimer's disease (AD) using human-induced pluripotent stem cells (iPSCs) is a field now spanning 15 years. Developments in the field have shown a shift in using simple 2D cortical neuron models to more advanced tri-cultures and 3D cerebral organoids that recapitulate more features of the disease. This is largely due to development and optimization of new cell protocols. In this review, we highlight recent major breakthroughs in the AD field and the implications this has in modeling AD using iPSCs (AD-iPSCs). To date, AD-iPSCs have been largely used to recapitulate and study impaired amyloid precursor protein (APP) processing and tau phosphorylation in both familial and sporadic AD. AD-iPSCs have also been studied for varying neuronal and glial dysfunctions. Moreover, they have been useful for discovering new molecular mechanisms, such as identifying proteins that bridge APP processing with tau phosphorylation and for identifying molecular pathways that bridge APP processing dysfunction with impaired cholesterol biosynthesis. Perhaps the greatest use of AD-iPSCs has been in discovering compounds via drug screening, that reduce amyloid beta (Aβ) in neurons, such as the anti-inflammatory compound, cromolyn, and antiparasitic drugs, avermectins. In addition, high content screening using AD-iPSCs has led to the identification of statins that can reduce levels of phosphorylated tau (p-Tau) in neurons. Some of these compounds have made it through to testing in human clinical trials. Improvements in omic technologies including single cell RNA sequencing and proteomics as well as advances in production of iPSC-cerebral organoids and tri-cultures is likely to result in the further discovery of new drugs and treatments for AD. Some caveats remain in the field, including, long experimental conditions to create mature neurons, high costs of media that limit research capabilities, and a lack of reproducibility using current iPSC-cerebral organoid protocols. Despite these current limitations, AD-iPSCs remain an excellent cellular model for studying AD mechanisms and for drug discovery.
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The Interplay between α-Synuclein and Microglia in α-Synucleinopathies. Int J Mol Sci 2023; 24:ijms24032477. [PMID: 36768798 PMCID: PMC9916729 DOI: 10.3390/ijms24032477] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Synucleinopathies are a set of devastating neurodegenerative diseases that share a pathologic accumulation of the protein α-synuclein (α-syn). This accumulation causes neuronal death resulting in irreversible dementia, deteriorating motor symptoms, and devastating cognitive decline. While the etiology of these conditions remains largely unknown, microglia, the resident immune cells of the central nervous system (CNS), have been consistently implicated in the pathogenesis of synucleinopathies. Microglia are generally believed to be neuroprotective in the early stages of α-syn accumulation and contribute to further neurodegeneration in chronic disease states. While the molecular mechanisms by which microglia achieve this role are still being investigated, here we highlight the major findings to date. In this review, we describe how structural varieties of inherently disordered α-syn result in varied microglial receptor-mediated interactions. We also summarize which microglial receptors enable cellular recognition and uptake of α-syn. Lastly, we review the downstream effects of α-syn processing within microglia, including spread to other brain regions resulting in neuroinflammation and neurodegeneration in chronic disease states. Understanding the mechanism of microglial interactions with α-syn is vital to conceptualizing molecular targets for novel therapeutic interventions. In addition, given the significant diversity in the pathophysiology of synucleinopathies, such molecular interactions are vital in gauging all potential pathways of neurodegeneration in the disease state.
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74
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Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Front Cell Dev Biol 2023; 11:1158373. [PMID: 37101616 PMCID: PMC10123288 DOI: 10.3389/fcell.2023.1158373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The brain is arguably the most complex part of the human body in form and function. Much remains unclear about the molecular mechanisms that regulate its normal and pathological physiology. This lack of knowledge largely stems from the inaccessible nature of the human brain, and the limitation of animal models. As a result, brain disorders are difficult to understand and even more difficult to treat. Recent advances in generating human pluripotent stem cells (hPSCs)-derived 2-dimensional (2D) and 3-dimensional (3D) neural cultures have provided an accessible system to model the human brain. Breakthroughs in gene editing technologies such as CRISPR/Cas9 further elevate the hPSCs into a genetically tractable experimental system. Powerful genetic screens, previously reserved for model organisms and transformed cell lines, can now be performed in human neural cells. Combined with the rapidly expanding single-cell genomics toolkit, these technological advances culminate to create an unprecedented opportunity to study the human brain using functional genomics. This review will summarize the current progress of applying CRISPR-based genetic screens in hPSCs-derived 2D neural cultures and 3D brain organoids. We will also evaluate the key technologies involved and discuss their related experimental considerations and future applications.
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Affiliation(s)
- Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Yun Li,
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Var SR, Strell P, Johnson ST, Roman A, Vasilakos Z, Low WC. Transplanting Microglia for Treating CNS Injuries and Neurological Diseases and Disorders, and Prospects for Generating Exogenic Microglia. Cell Transplant 2023; 32:9636897231171001. [PMID: 37254858 PMCID: PMC10236244 DOI: 10.1177/09636897231171001] [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: 01/26/2023] [Revised: 03/18/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2023] Open
Abstract
Microglia are associated with a wide range of both neuroprotective and neuroinflammatory functions in the central nervous system (CNS) during development and throughout lifespan. Chronically activated and dysfunctional microglia are found in many diseases and disorders, such as Alzheimer's disease, Parkinson's disease, and CNS-related injuries, and can accelerate or worsen the condition. Transplantation studies designed to replace and supplement dysfunctional microglia with healthy microglia offer a promising strategy for addressing microglia-mediated neuroinflammation and pathologies. This review will cover microglial involvement in neurological diseases and disorders and CNS-related injuries, current microglial transplantation strategies, and different approaches and considerations for generating exogenic microglia.
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Affiliation(s)
- Susanna R. Var
- Department of Neurosurgery, Medical
School, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, Medical School,
University of Minnesota, Minneapolis, MN, USA
| | - Phoebe Strell
- Stem Cell Institute, Medical School,
University of Minnesota, Minneapolis, MN, USA
- Department of Veterinary and Biomedical
Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Sether T. Johnson
- Department of Neurosurgery, Medical
School, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, Medical School,
University of Minnesota, Minneapolis, MN, USA
| | - Alex Roman
- Department of Neuroscience, University
of Minnesota, Minneapolis, MN, USA
| | - Zoey Vasilakos
- Stem Cell Institute, Medical School,
University of Minnesota, Minneapolis, MN, USA
- Department of Neuroscience, University
of Minnesota, Minneapolis, MN, USA
| | - Walter C. Low
- Department of Neurosurgery, Medical
School, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, Medical School,
University of Minnesota, Minneapolis, MN, USA
- Department of Veterinary and Biomedical
Sciences, University of Minnesota, Minneapolis, MN, USA
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76
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Chu YN, Akahori A, Takatori S, Tomita T. Pathological Roles of INPP5D in Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:289-301. [PMID: 37525057 DOI: 10.1007/978-3-031-31978-5_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Current hypothesis of Alzheimer's disease (AD) postulates that amyloid β (Aβ) deposition in the brain causes tau inclusion in neurons and leads to cognitive decline. The discovery of the genetic association between triggering receptor expressed on myeloid cells 2 (TREM2) with increased AD risk points to a causal link between microglia and AD pathogenesis, and revealed a crucial role of TREM2-dependent clustering of microglia around amyloid plaques that prevents Aβ toxicity to facilitate tau deposition near the plaques. Here we review the physiological and pathological roles of another AD risk gene expressed in microglia, inositol polyphosphate-5-polyphosphatase D (INPP5D), which encodes a phosphoinositide phosphatase. Evidence suggests that its risk polymorphisms alter the expression level and/or function of INPP5D, while concomitantly affecting tau levels in cerebrospinal fluids. In β-amyloidosis mice, INPP5D was upregulated upon Aβ deposition and negatively regulated the microglial clustering toward amyloid plaques. INPP5D seems to exert its function by acting antagonistically at downstream of the TREM2 signaling pathway, suggesting that it is a novel regulator of the protective barrier by microglia. Further studies to elucidate INPP5D's role in AD may help in developing new therapeutic targets for AD treatment.
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Affiliation(s)
- Yung Ning Chu
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Aika Akahori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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77
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Warden AS, Han C, Hansen E, Trescott S, Nguyen C, Kim R, Schafer D, Johnson A, Wright M, Ramirez G, Lopez-Sanchez M, Coufal NG. Tools for studying human microglia: In vitro and in vivo strategies. Brain Behav Immun 2023; 107:369-382. [PMID: 36336207 PMCID: PMC9810377 DOI: 10.1016/j.bbi.2022.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Microglia may only represent 10% of central nervous system (CNS) cells but they perform critical roles in development, homeostasis and neurological disease. Microglia are also environmentally regulated, quickly losing their transcriptomic and epigenetic signature after leaving the CNS. This facet of microglia biology is both fascinating and technically challenging influencing the study of the genetics and function of human microglia in a manner that recapitulates the CNS environment. In this review we provide a comprehensive overview of existing in vitro and in vivo methodology to study human microglia, such as immortalized cells lines, stem cell-derived microglia, cerebral organoids and xenotransplantation. Since there is currently no single method that completely recapitulates all hallmarks of human ex vivo adult homeostatic microglia, we also discuss the advantages and limitations of each existing model as a practical guide for researchers.
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Affiliation(s)
- Anna S Warden
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Claudia Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Hansen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samantha Trescott
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Celina Nguyen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Roy Kim
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Avalon Johnson
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madison Wright
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gabriela Ramirez
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Lopez-Sanchez
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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Shi H, Doench JG, Chi H. CRISPR screens for functional interrogation of immunity. Nat Rev Immunol 2022:10.1038/s41577-022-00802-4. [DOI: 10.1038/s41577-022-00802-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
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79
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Towards elucidating disease-relevant states of neurons and glia by CRISPR-based functional genomics. Genome Med 2022; 14:130. [PMID: 36401300 PMCID: PMC9673433 DOI: 10.1186/s13073-022-01134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
Our understanding of neurological diseases has been tremendously enhanced over the past decade by the application of new technologies. Genome-wide association studies have highlighted glial cells as important players in diseases. Single-cell profiling technologies are providing descriptions of disease states of neurons and glia at unprecedented molecular resolution. However, significant gaps remain in our understanding of the mechanisms driving disease-associated cell states, and how these states contribute to disease. These gaps in our understanding can be bridged by CRISPR-based functional genomics, a powerful approach to systematically interrogate gene function. In this review, we will briefly review the current literature on neurological disease-associated cell states and introduce CRISPR-based functional genomics. We discuss how advances in CRISPR-based screens, especially when implemented in the relevant brain cell types or cellular environments, have paved the way towards uncovering mechanisms underlying neurological disease-associated cell states. Finally, we will delineate current challenges and future directions for CRISPR-based functional genomics to further our understanding of neurological diseases and potential therapeutic strategies.
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80
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Limone F, Klim JR, Mordes DA. Pluripotent stem cell strategies for rebuilding the human brain. Front Aging Neurosci 2022; 14:1017299. [PMID: 36408113 PMCID: PMC9667068 DOI: 10.3389/fnagi.2022.1017299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/27/2022] [Indexed: 01/03/2023] Open
Abstract
Neurodegenerative disorders have been extremely challenging to treat with traditional drug-based approaches and curative therapies are lacking. Given continued progress in stem cell technologies, cell replacement strategies have emerged as concrete and potentially viable therapeutic options. In this review, we cover advances in methods used to differentiate human pluripotent stem cells into several highly specialized types of neurons, including cholinergic, dopaminergic, and motor neurons, and the potential clinical applications of stem cell-derived neurons for common neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, ataxia, and amyotrophic lateral sclerosis. Additionally, we summarize cellular differentiation techniques for generating glial cell populations, including oligodendrocytes and microglia, and their conceivable translational roles in supporting neural function. Clinical trials of specific cell replacement therapies in the nervous system are already underway, and several attractive avenues in regenerative medicine warrant further investigation.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA, United States,Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, United States,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States,Leiden University Medical Center, Leiden, Netherlands
| | - Joseph R. Klim
- Faze Medicines, Cambridge, MA, United States,*Correspondence: Joseph R. Klim,
| | - Daniel A. Mordes
- Institute for Neurodegenerative Diseases, Department of Pathology, University of California, San Francisco, San Francisco, CA, United States,Daniel A. Mordes,
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81
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Cakir B, Kiral FR, Park IH. Advanced in vitro models: Microglia in action. Neuron 2022; 110:3444-3457. [PMID: 36327894 DOI: 10.1016/j.neuron.2022.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
Abstract
In the central nervous system (CNS), microglia carry out multiple tasks related to brain development, maintenance of brain homeostasis, and function of the CNS. Recent advanced in vitro model systems allow us to perform more detailed and specific analyses of microglial functions in the CNS. The development of human pluripotent stem cells (hPSCs)-based 2D and 3D cell culture methods, particularly advancements in brain organoid models, offers a better platform to dissect microglial function in various contexts. Despite the improvement of these methods, there are still definite restrictions. Understanding their drawbacks and benefits ensures their proper use. In this primer, we review current developments regarding in vitro microglial production and characterization and their use to address fundamental questions about microglial function in healthy and diseased states, and we discuss potential future improvements with a particular emphasis on brain organoid models.
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Affiliation(s)
- Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA.
| | - Ferdi Ridvan Kiral
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA.
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82
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Shalita R, Amit I. The industrial genomic revolution: A new era in neuroimmunology. Neuron 2022; 110:3429-3443. [PMID: 36257321 DOI: 10.1016/j.neuron.2022.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Recent discoveries have highlighted the importance of understanding the complex interactions between the brain and immune systems in health and neurodegenerative disease. In this Primer, we outline single-cell multiomics approaches. Applied to patient samples with rich metadata, functional organoids, and animal models, single-cell studies will facilitate the next big leap in translational neuro-immune research. We believe this will pave the way for reshaping our understanding of the neuro-immune interplay: from descriptive to functional, from broad cell types to effective pathways, spatial organization, biomarkers, and targets, toward a comprehensive mechanistic understanding that will be the impetus for drug discovery and therapeutic breakthroughs. We envision that in the near future, single-cell multiomics technologies, along with the advances in immunotherapy development, will become a major driving force and fully integrated resource in the toolset for the development of therapeutic agents in neuroimmunology, which will revolutionize drug development for treating neurodegenerative diseases.
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Affiliation(s)
- Rotem Shalita
- Department of Systems Immunology, Weizmann Institute, Rehovot, 7610001, Israel.
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute, Rehovot, 7610001, Israel.
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83
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Maguire E, Connor-Robson N, Shaw B, O’Donoghue R, Stöberl N, Hall-Roberts H. Assaying Microglia Functions In Vitro. Cells 2022; 11:3414. [PMID: 36359810 PMCID: PMC9654693 DOI: 10.3390/cells11213414] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Microglia, the main immune modulators of the central nervous system, have key roles in both the developing and adult brain. These functions include shaping healthy neuronal networks, carrying out immune surveillance, mediating inflammatory responses, and disposing of unwanted material. A wide variety of pathological conditions present with microglia dysregulation, highlighting the importance of these cells in both normal brain function and disease. Studies into microglial function in the context of both health and disease thus have the potential to provide tremendous insight across a broad range of research areas. In vitro culture of microglia, using primary cells, cell lines, or induced pluripotent stem cell derived microglia, allows researchers to generate reproducible, robust, and quantifiable data regarding microglia function. A broad range of assays have been successfully developed and optimised for characterizing microglial morphology, mediation of inflammation, endocytosis, phagocytosis, chemotaxis and random motility, and mediation of immunometabolism. This review describes the main functions of microglia, compares existing protocols for measuring these functions in vitro, and highlights common pitfalls and future areas for development. We aim to provide a comprehensive methodological guide for researchers planning to characterise microglial functions within a range of contexts and in vitro models.
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Affiliation(s)
- Emily Maguire
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
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84
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Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells 2022; 11:2803. [PMID: 36139380 PMCID: PMC9496777 DOI: 10.3390/cells11182803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 01/25/2023] Open
Abstract
The cerebral cortex forms early in development according to a series of heritable neurodevelopmental instructions. Despite deep evolutionary conservation of the cerebral cortex and its foundational six-layered architecture, significant variations in cortical size and folding can be found across mammals, including a disproportionate expansion of the prefrontal cortex in humans. Yet our mechanistic understanding of neurodevelopmental processes is derived overwhelmingly from rodent models, which fail to capture many human-enriched features of cortical development. With the advent of pluripotent stem cells and technologies for differentiating three-dimensional cultures of neural tissue in vitro, cerebral organoids have emerged as an experimental platform that recapitulates several hallmarks of human brain development. In this review, we discuss the merits and limitations of cerebral organoids as experimental models of the developing human brain. We highlight innovations in technology development that seek to increase its fidelity to brain development in vivo and discuss recent efforts to use cerebral organoids to study regeneration and brain evolution as well as to develop neurological and neuropsychiatric disease models.
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Affiliation(s)
- Tomasz J. Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sofie R. Salama
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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85
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Cooper YA, Teyssier N, Dräger NM, Guo Q, Davis JE, Sattler SM, Yang Z, Patel A, Wu S, Kosuri S, Coppola G, Kampmann M, Geschwind DH. Functional regulatory variants implicate distinct transcriptional networks in dementia. Science 2022; 377:eabi8654. [PMID: 35981026 DOI: 10.1126/science.abi8654] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Predicting the function of noncoding variation is a major challenge in modern genetics. In this study, we used massively parallel reporter assays to screen 5706 variants identified from genome-wide association studies for both Alzheimer's disease (AD) and progressive supranuclear palsy (PSP), identifying 320 functional regulatory variants (frVars) across 27 loci, including the complex 17q21.31 region. We identified and validated multiple risk loci using CRISPR interference or excision, including complement 4 (C4A) and APOC1 in AD and PLEKHM1 and KANSL1 in PSP. Functional variants disrupt transcription factor binding sites converging on enhancers with cell type-specific activity in PSP and AD, implicating a neuronal SP1-driven regulatory network in PSP pathogenesis. These analyses suggest that noncoding genetic risk is driven by common genetic variants through their aggregate activity on specific transcriptional programs.
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Affiliation(s)
- Yonatan A Cooper
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Noam Teyssier
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Nina M Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Qiuyu Guo
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Sydney M Sattler
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Zhongan Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Abdulsamie Patel
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Sarah Wu
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
- Institute of Precision Health, University of California, Los Angeles, CA 90095, USA
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