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Ben-Simon Y, Hooper M, Narayan S, Daigle T, Dwivedi D, Way SW, Oster A, Stafford DA, Mich JK, Taormina MJ, Martinez RA, Opitz-Araya X, Roth JR, Allen S, Ayala A, Bakken TE, Barcelli T, Barta S, Bendrick J, Bertagnolli D, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, Chakka AB, Chakrabarty R, Chance RK, Chavan S, Departee M, Donadio N, Dotson N, Egdorf T, Gabitto M, Gary A, Gasperini M, Goldy J, Gore BB, Graybuck L, Greisman N, Haeseleer F, Halterman C, Helback O, Hockemeyer D, Huang C, Huff S, Hunker A, Johansen N, Juneau Z, Kalmbach B, Khem S, Kutsal R, Larsen R, Lee C, Lee AY, Leibly M, Lenz GH, Liang E, Lusk N, Malone J, Mollenkopf T, Morin E, Newman D, Ng L, Ngo K, Omstead V, Oyama A, Pham T, Pom CA, Potekhina L, Ransford S, Rette D, Rimorin C, Rocha D, Ruiz A, Sanchez RE, Sedeno-Cortes A, Sevigny JP, Shapovalova N, Shulga L, Sigler AR, Siverts LA, Somasundaram S, Stewart K, Tieu M, Trader C, van Velthoven CT, Walker M, Weed N, Wirthlin M, Wood T, Wynalda B, Yao Z, Zhou T, Ariza J, Dee N, Reding M, Ronellenfitch K, Mufti S, Sunkin SM, Smith KA, Esposito L, Waters J, Thyagarajan B, Yao S, Lein ES, Zeng H, Levi BP, Ngai J, Ting J, Tasic B. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597244. [PMID: 38915722 PMCID: PMC11195086 DOI: 10.1101/2024.06.10.597244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The mammalian cortex is comprised of cells with different morphological, physiological, and molecular properties that can be classified according to shared properties into cell types. Defining the contribution of each cell type to the computational and cognitive processes that are guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell type taxonomies from mice and humans to define marker genes and enhancers, and to build genetic tools for cortical cell types. Here, we present a large toolkit for selective targeting of cortical populations, including mouse transgenic lines and recombinant adeno-associated virus (AAV) vectors containing genomic enhancers. We report evaluation of fifteen new transgenic driver lines and over 680 different enhancer AAVs covering all major subclasses of cortical cells, with many achieving a high degree of specificity, comparable with existing transgenic lines. We find that the transgenic lines based on marker genes can provide exceptional specificity and completeness of cell type labeling, but frequently require generation of a triple-transgenic cross for best usability/specificity. On the other hand, enhancer AAVs are easy to screen and use, and can be easily modified to express diverse cargo, such as recombinases. However, their use depends on many factors, such as viral titer and route of administration. The tools reported here as well as the scaled process of tool creation provide an unprecedented resource that should enable diverse experimental strategies towards understanding mammalian cortex and brain function.
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Affiliation(s)
- Yoav Ben-Simon
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Marcus Hooper
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Sujatha Narayan
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Tanya Daigle
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | | | - Sharon W. Way
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Aaron Oster
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - John K. Mich
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Jada R. Roth
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Shona Allen
- University of California, Berkeley, Berkeley, CA 94720
| | - Angela Ayala
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Stuard Barta
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Sakshi Chavan
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Bryan B. Gore
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Noah Greisman
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | - Cindy Huang
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Sydney Huff
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Avery Hunker
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zoe Juneau
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shannon Khem
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Rana Kutsal
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Angus Y. Lee
- University of California, Berkeley, Berkeley, CA 94720
| | | | | | | | - Nicholas Lusk
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Elyse Morin
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Alana Oyama
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Shea Ransford
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dean Rette
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Dana Rocha
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | - Ana R. Sigler
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Kaiya Stewart
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Toren Wood
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Boaz P. Levi
- Allen Institute for Brain Science, Seattle, WA 98109
| | - John Ngai
- University of California, Berkeley, Berkeley, CA 94720
- Present affiliation: National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, WA 98109
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2
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Xu X, Han N, Zhao F, Fan R, Guo Q, Han X, Liu Y, Luo G. Inefficacy of anti-VEGF therapy reflected in VEGF-mediated photoreceptor degeneration. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102176. [PMID: 38689803 PMCID: PMC11059333 DOI: 10.1016/j.omtn.2024.102176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Abstract
Retinal neovascularization (RNV) is primarily driven by vascular endothelial growth factor (VEGF). However, current anti-VEGF therapies are limited by short half-lives and repeated injections, which reduce patient quality of life and increase medical risks. Additionally, not all patients benefit from anti-VEGF monotherapy, and some problems, such as unsatisfactory vision recovery, persist after long-term treatment. In this study, we constructed a recombinant adeno-associated virus (AAV), AAV2-SPLTH, which encodes an anti-VEGF antibody similar to bevacizumab, and assessed its effects in a doxycycline-induced Tet-opsin-VEGFA mouse model of RNV. AAV2-SPLTH effectively inhibited retinal leakage, RNV progression, and photoreceptor apoptosis in a Tet-opsin-VEGF mouse model. However, proteomic sequencing showed that AAV2-SPLTH failed to rescue the expression of phototransduction-related genes, which corresponded to reduced photoreceptor cell numbers. This study suggests that anti-VEGF monotherapy can significantly inhibit RNV to some extent but may not be enough to save visual function in the long term.
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Affiliation(s)
- Xin Xu
- Institute of Health Sciences, China Medical University, Shenyang 110122, China
| | - Ni Han
- Institute of Health Sciences, China Medical University, Shenyang 110122, China
| | - Fangkun Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110005, China
| | - Ruoyue Fan
- Bionce Biotechnology, Co., Ltd, Nanjing 210061, China
| | - Qingguo Guo
- Institute of Health Sciences, China Medical University, Shenyang 110122, China
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Xuefei Han
- Bionce Biotechnology, Co., Ltd, Nanjing 210061, China
| | - Ying Liu
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Guangzuo Luo
- Institute of Health Sciences, China Medical University, Shenyang 110122, China
- Bionce Biotechnology, Co., Ltd, Nanjing 210061, China
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3
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Jin L, Sullivan HA, Zhu M, Lavin TK, Matsuyama M, Fu X, Lea NE, Xu R, Hou Y, Rutigliani L, Pruner M, Babcock KR, Ip JPK, Hu M, Daigle TL, Zeng H, Sur M, Feng G, Wickersham IR. Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses. Nat Neurosci 2024; 27:373-383. [PMID: 38212587 PMCID: PMC10849964 DOI: 10.1038/s41593-023-01545-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Rabies-virus-based monosynaptic tracing is a widely used technique for mapping neural circuitry, but its cytotoxicity has confined it primarily to anatomical applications. Here we present a second-generation system for labeling direct inputs to targeted neuronal populations with minimal toxicity, using double-deletion-mutant rabies viruses. Viral spread requires expression of both deleted viral genes in trans in postsynaptic source cells. Suppressing this expression with doxycycline following an initial period of viral replication reduces toxicity to postsynaptic cells. Longitudinal two-photon imaging in vivo indicated that over 90% of both presynaptic and source cells survived for the full 12-week course of imaging. Ex vivo whole-cell recordings at 5 weeks postinfection showed that the second-generation system perturbs input and source cells much less than the first-generation system. Finally, two-photon calcium imaging of labeled networks of visual cortex neurons showed that their visual response properties appeared normal for 10 weeks, the longest we followed them.
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Affiliation(s)
- Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Lingang Laboratory, Shanghai, China
| | - Heather A Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mulangma Zhu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas K Lavin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Fu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas E Lea
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ran Xu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - YuanYuan Hou
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luca Rutigliani
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Maxwell Pruner
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey R Babcock
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacque Pak Kan Ip
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ming Hu
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Mriganka Sur
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Zhang Q, Liu X, Gong L, He M. Combinatorial genetic strategies for dissecting cell lineages, cell types, and gene function in the mouse brain. Dev Growth Differ 2023; 65:546-553. [PMID: 37963088 DOI: 10.1111/dgd.12902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Research in neuroscience has greatly benefited from the development of genetic approaches that enable lineage tracing, cell type targeting, and conditional gene regulation. Recent advances in combinatorial strategies, which integrate multiple cellular features, have significantly enhanced the spatiotemporal precision and flexibility of these manipulations. In this minireview, we introduce the concept and design of these strategies and provide a few examples of their application in genetic fate mapping, cell type targeting, and reversible conditional gene regulation. These advancements have facilitated in-depth investigation into the developmental principles underlying the assembly of brain circuits, granting experimental access to highly specific cell lineages and subtypes, as well as offering valuable new tools for modeling and studying neurological diseases. Additionally, we discuss future directions aimed at expanding and improving the existing genetic toolkit for a better understanding of the development, structure, and function of healthy and diseased brains.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xue Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Gong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao He
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
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5
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Xie L, Liu H, You Z, Wang L, Li Y, Zhang X, Ji X, He H, Yuan T, Zheng W, Wu Z, Xiong M, Wei W, Chen Y. Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding. Nat Methods 2023; 20:1244-1255. [PMID: 37460718 DOI: 10.1038/s41592-023-01947-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/06/2023] [Indexed: 08/09/2023]
Abstract
A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.
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Affiliation(s)
- Lianshun Xie
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hengxin Liu
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Zhiwen You
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyue Wang
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yiwen Li
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyue Zhang
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoshan Ji
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Hui He
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Tingli Yuan
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Wenping Zheng
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Ziyan Wu
- UniXell Biotechnology, Shanghai, China
| | - Man Xiong
- State Key Laboratory of Medical Neurobiology-Ministry of Education Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
- Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.
- Lingang Laboratory, Shanghai, China.
| | - Yuejun Chen
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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Pearl PL, Tokatly Latzer I, Lee HHC, Rotenberg A. New Therapeutic Approaches to Inherited Metabolic Pediatric Epilepsies. Neurology 2023; 101:124-133. [PMID: 36878704 PMCID: PMC10382274 DOI: 10.1212/wnl.0000000000207133] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/17/2023] [Indexed: 03/08/2023] Open
Abstract
Treatment options for inherited metabolic epilepsies are rapidly expanding with advances in molecular biology and the genomic revolution. Traditional dietary and nutrient modification and inhibitors or enhancers of protein and enzyme function, the mainstays of therapy, are undergoing continuous revisions to increase biological activity and reduce toxicity. Enzyme replacement and gene replacement and editing hold promise for genetically targeted treatment and cures. Molecular, imaging, and neurophysiologic biomarkers are emerging as key indicators of disease pathophysiology, severity, and response to therapy.
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Affiliation(s)
- Phillip L Pearl
- From the Department of Neurology (P.L.P., I.T.L., H.H.C.L., A.R.), Boston Children's Hospital, Harvard Medical School, Boston, MA.
| | - Itay Tokatly Latzer
- From the Department of Neurology (P.L.P., I.T.L., H.H.C.L., A.R.), Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Henry H C Lee
- From the Department of Neurology (P.L.P., I.T.L., H.H.C.L., A.R.), Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Alexander Rotenberg
- From the Department of Neurology (P.L.P., I.T.L., H.H.C.L., A.R.), Boston Children's Hospital, Harvard Medical School, Boston, MA
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7
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Vanderhaeghen T, Timmermans S, Eggermont M, Watts D, Vandewalle J, Wallaeys C, Nuyttens L, De Temmerman J, Hochepied T, Dewaele S, Berghe JV, Sanders N, Wielockx B, Beyaert R, Libert C. The impact of hepatocyte-specific deletion of hypoxia-inducible factors on the development of polymicrobial sepsis with focus on GR and PPARα function. Front Immunol 2023; 14:1124011. [PMID: 37006237 PMCID: PMC10060827 DOI: 10.3389/fimmu.2023.1124011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionPolymicrobial sepsis causes acute anorexia (loss of appetite), leading to lipolysis in white adipose tissue and proteolysis in muscle, and thus release of free fatty acids (FFAs), glycerol and gluconeogenic amino acids. Since hepatic peroxisome proliferator-activated receptor alpha (PPARα) and glucocorticoid receptor (GR) quickly lose function in sepsis, these metabolites accumulate (causing toxicity) and fail to yield energy-rich molecules such as ketone bodies (KBs) and glucose. The mechanism of PPARα and GR dysfunction is not known.Methods & resultsWe investigated the hypothesis that hypoxia and/or activation of hypoxia inducible factors (HIFs) might play a role in these issues with PPARα and GR. After cecal ligation and puncture (CLP) in mice, leading to lethal polymicrobial sepsis, bulk liver RNA sequencing illustrated the induction of the genes encoding HIF1α and HIF2α, and an enrichment of HIF-dependent gene signatures. Therefore, we generated hepatocyte-specific knock-out mice for HIF1α, HIF2α or both, and a new HRE-luciferase reporter mouse line. After CLP, these HRE-luciferase reporter mice show signals in several tissues, including the liver. Hydrodynamic injection of an HRE-luciferase reporter plasmid also led to (liver-specific) signals in hypoxia and CLP. Despite these encouraging data, however, hepatocyte-specific HIF1α and/or HIF2α knock-out mice suggest that survival after CLP was not dependent on the hepatocyte-specific presence of HIF proteins, which was supported by measuring blood levels of glucose, FFAs, and KBs. The HIF proteins were also irrelevant in the CLP-induced glucocorticoid resistance, but we found indications that the absence of HIF1α in hepatocytes causes less inactivation of PPARα transcriptional function.ConclusionWe conclude that HIF1α and HIF2α are activated in hepatocytes in sepsis, but their contribution to the mechanisms leading to lethality are minimal.
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Affiliation(s)
- Tineke Vanderhaeghen
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Steven Timmermans
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Melanie Eggermont
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Deepika Watts
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany
- Deutsche Forschungsgemeinschaft (DFG) Research Centre and Cluster of Excellence for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Jolien Vandewalle
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Charlotte Wallaeys
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Louise Nuyttens
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Joyca De Temmerman
- Department of Nutrition, Genetics, and Ethology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
- Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Tino Hochepied
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sylviane Dewaele
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Joke Vanden Berghe
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Niek Sanders
- Department of Nutrition, Genetics, and Ethology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
- Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Ben Wielockx
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany
- Deutsche Forschungsgemeinschaft (DFG) Research Centre and Cluster of Excellence for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Rudi Beyaert
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Claude Libert
- Flanders Institute for Biotechnology (VIB) Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- *Correspondence: Claude Libert,
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8
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Gödecke N, Herrmann S, Weichelt V, Wirth D. A Ubiquitous Chromatin Opening Element and DNA Demethylation Facilitate Doxycycline-Controlled Expression during Differentiation and in Transgenic Mice. ACS Synth Biol 2023; 12:482-491. [PMID: 36755406 PMCID: PMC9942253 DOI: 10.1021/acssynbio.2c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Synthetic expression cassettes provide the ability to control transgene expression in experimental animal models through external triggers, enabling the study of gene function and the modulation of endogenous regulatory networks in vivo. The performance of synthetic expression cassettes in transgenic animals critically depends on the regulatory properties of the respective chromosomal integration sites, which are affected by the remodeling of the chromatin structure during development. The epigenetic status may affect the transcriptional activity of the synthetic cassettes and even lead to transcriptional silencing, depending on the chromosomal sites and the tissue. In this study, we investigated the influence of the ubiquitous chromosome opening element (UCOE) HNRPA2B1-CBX3 and its subfragments A2UCOE and CBX3 on doxycycline-controlled expression modules within the chromosomal Rosa26 locus. While HNRPA2B1-CBX3 and A2UCOE reduced the expression of the synthetic cassettes in mouse embryonic stem cells, CBX3 stabilized the expression and facilitated doxycycline-controlled expression after in vitro differentiation. In transgenic mice, the CBX3 element protected the cassettes from overt silencing although the expression was moderate and only partially controlled by doxycycline. We demonstrate that CBX3-flanked synthetic cassettes can be activated by decitabine-mediated blockade of DNA methylation or by specific recruitment of the catalytic demethylation domain of the ten-eleven translocation protein TET1 to the synthetic promoter. This suggests that CBX3 renders the synthetic cassettes permissive for subsequent epigenetic activation, thereby supporting doxycycline-controlled expression. Together, this study reveals a strategy for overcoming epigenetic constraints of synthetic expression cassettes, facilitating externally controlled transgene expression in mice.
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Affiliation(s)
- Natascha Gödecke
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sabrina Herrmann
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Viola Weichelt
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dagmar Wirth
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany,Institute
of Experimental Hematology, Medical University
Hannover (MHH), 30625 Hannover, Germany,
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9
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Liu J, Lu F. Visualization of in vivo cell-cell contact in the present and in the past. SCIENCE CHINA. LIFE SCIENCES 2023; 66:889-891. [PMID: 36622577 DOI: 10.1007/s11427-022-2262-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 01/10/2023]
Affiliation(s)
- Jingwen Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Lintott LG, Nutter LMJ. Genetic and Molecular Quality Control of Genetically Engineered Mice. Methods Mol Biol 2023; 2631:53-101. [PMID: 36995664 DOI: 10.1007/978-1-0716-2990-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genetically engineered mice are used as avatars to understand mammalian gene function and develop therapies for human disease. During genetic modification, unintended changes can occur, and these changes may result in misassigned gene-phenotype relationships leading to incorrect or incomplete experimental interpretations. The types of unintended changes that may occur depend on the allele type being made and the genetic engineering approach used. Here we broadly categorize allele types as deletions, insertions, base changes, and transgenes derived from engineered embryonic stem (ES) cells or edited mouse embryos. However, the methods we describe can be adapted to other allele types and engineering strategies. We describe the sources and consequ ences of common unintended changes and best practices for detecting both intended and unintended changes by screening and genetic and molecular quality control (QC) of chimeras, founders, and their progeny. Employing these practices, along with careful allele design and good colony management, will increase the chance that investigations using genetically engineered mice will produce high-quality reproducible results, to enable a robust understanding of gene function, human disease etiology, and therapeutic development.
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Affiliation(s)
- Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada.
- The Hospital for Sick Children, Toronto, ON, Canada.
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11
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Zhang S, Zhao H, Liu Z, Liu K, Zhu H, Pu W, He L, Wang RA, Zhou B. Monitoring of cell-cell communication and contact history in mammals. Science 2022; 378:eabo5503. [PMID: 36454848 DOI: 10.1126/science.abo5503] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Monitoring of cell-cell communication in multicellular organisms is fundamental to understanding diverse biological processes such as embryogenesis and tumorigenesis. To track cell-cell contacts in vivo, we developed an intercellular genetic technology to monitor cell-cell contact and to trace cell contact histories by permanently marking contacts between cells. In mice, we engineered an artificial Notch ligand into one cell (the sender cell) and an artificial receptor into another cell (the receiver cell). Contact between the sender and receiver cells triggered a synthetic Notch signaling that activated downstream transcriptional programs in the receiver cell, thereby transiently or permanently labeling it. In vivo cell-cell contact was observed during development, tissue homeostasis, and tumor growth. This technology may be useful for studying dynamic in vivo cell-cell contacts and cell fate plasticity.
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Affiliation(s)
- Shaohua Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zixin Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Kuo Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Huan Zhu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenjuan Pu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lingjuan He
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Rong A Wang
- Laboratory for Accelerated Vascular Research, Department of Surgery, Division of Vascular Surgery, University of California, San Francisco, CA 94143, USA
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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12
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Arias A, Manubens-Gil L, Dierssen M. Fluorescent transgenic mouse models for whole-brain imaging in health and disease. Front Mol Neurosci 2022; 15:958222. [PMID: 36211979 PMCID: PMC9538927 DOI: 10.3389/fnmol.2022.958222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.
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Affiliation(s)
- Adrian Arias
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Mara Dierssen
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- *Correspondence: Mara Dierssen,
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13
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Yoshiki A, Ballard G, Perez AV. Genetic quality: a complex issue for experimental study reproducibility. Transgenic Res 2022; 31:413-430. [PMID: 35751794 PMCID: PMC9489590 DOI: 10.1007/s11248-022-00314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.
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Affiliation(s)
- Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, 3050074, Japan.
| | - Gregory Ballard
- Comparative Medicine and Quality, The Jackson Laboratory, Bar Harbor, ME 04609, USA
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14
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Rang FJ, de Luca KL, de Vries SS, Valdes-Quezada C, Boele E, Nguyen PD, Guerreiro I, Sato Y, Kimura H, Bakkers J, Kind J. Single-cell profiling of transcriptome and histone modifications with EpiDamID. Mol Cell 2022; 82:1956-1970.e14. [PMID: 35366395 PMCID: PMC9153956 DOI: 10.1016/j.molcel.2022.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/24/2021] [Accepted: 03/02/2022] [Indexed: 12/25/2022]
Abstract
Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.
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Affiliation(s)
- Franka J Rang
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Sandra S de Vries
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Christian Valdes-Quezada
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Ellen Boele
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Phong D Nguyen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Isabel Guerreiro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Jeroen Bakkers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Department of Pediatric Cardiology, Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands.
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15
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Márta K, Booth D, Csordás G, Hajnóczky G. Fluorescent protein transgenic mice for the study of Ca 2+ and redox signaling. Free Radic Biol Med 2022; 181:241-250. [PMID: 35158029 PMCID: PMC8988923 DOI: 10.1016/j.freeradbiomed.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/10/2022] [Indexed: 01/29/2023]
Abstract
Many unanswered questions of physiology and medicine require in vivo studies of cellular processes in murine models. These processes commonly depend on intracellular Ca2+ and redox alterations. Fluorescent dyes have succeeded in real-time intracellular monitoring of Ca2+, redox and the different Reactive Oxygen Species (ROS) in single cells, but have seldomly been applied in vivo. The advance in Fluorescent Protein (FP) technology has created alternative tools for the same task, which can be delivered with viruses or genomic integration strategies into mice. With the availability of several color options for both Ca2+ and redox reporting FP, multiparameter measurements have also become feasible: measuring different species, and the same parameter at different locations using organelle-specific targeting sequences at the same time. We, here, focus on mice with genomic integration of Ca2+ and redox reporters, provide a list of the available models and summarize the strategies of their generation and utilization. We also describe a novel Calcium DoubleSpy mouse model that conditionally expresses both RCaMP in the cytoplasm and GEM-GECO1 in the mitochondrial matrix, allowing the study of mitochondrial Ca2+ related physiology and pathogenesis simultaneously in two distinct intracellular compartments.
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Affiliation(s)
- Katalin Márta
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - David Booth
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - György Csordás
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - György Hajnóczky
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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16
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Voltage imaging in the olfactory bulb using transgenic mouse lines expressing the genetically encoded voltage indicator ArcLight. Sci Rep 2022; 12:1875. [PMID: 35115567 PMCID: PMC8813909 DOI: 10.1038/s41598-021-04482-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs) allow optical recordings of membrane potential changes in defined cell populations. Transgenic reporter animals that facilitate precise and repeatable targeting with high expression levels would further the use of GEVIs in the in vivo mammalian brain. However, the literature on developing and applying transgenic mouse lines as vehicles for GEVI expression is limited. Here we report the first in vivo experiments using a transgenic reporter mouse for the GEVI ArcLight, which utilizes a Cre/tTA dependent expression system (TIGRE 1.0). We developed two mouse lines with ArcLight expression restricted to either olfactory receptor neurons, or a subpopulation of interneurons located in the granule and glomerular layers in the olfactory bulb. The ArcLight expression in these lines was sufficient for in vivo imaging of odorant responses in single trials using epifluorescence and 2-photon imaging. The voltage responses were odor-specific and concentration-dependent, which supported earlier studies about perceptual transformations carried out by the bulb that used calcium sensors of neural activity. This study demonstrates that the ArcLight transgenic line is a flexible genetic tool that can be used to record the neuronal electrical activity of different cell types with a signal-to-noise ratio that is comparable to previous reports using viral transduction.
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17
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Delerue F, Ittner LM. Microinjection of Zygotes for CRISPR/Cas9-Mediated Insertion of Transgenes into the Murine Rosa26 Safe Harbor. Methods Mol Biol 2022; 2495:115-128. [PMID: 35696031 DOI: 10.1007/978-1-0716-2301-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genetically modified (GM) mice are widely used in biomedical research because they can address complex questions in an in-vivo setting that could not otherwise be addressed in-vitro. Microinjection of zygotes remains the most common technique to generate GM animals to date. Here, we describe the targeted insertion (knock-in) of transgenes by microinjection of 1-cell or 2-cell stage embryos into the murine Rosa26 safe harbor.
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Affiliation(s)
- Fabien Delerue
- Genome Editing at Macquarie (GEM), Dementia Research Centre, Macquarie University, Sydney, NSW, Australia.
| | - Lars M Ittner
- Genome Editing at Macquarie (GEM), Dementia Research Centre, Macquarie University, Sydney, NSW, Australia
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18
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Redolfi N, García-Casas P, Fornetto C, Sonda S, Pizzo P, Pendin D. Lighting Up Ca 2+ Dynamics in Animal Models. Cells 2021; 10:2133. [PMID: 34440902 PMCID: PMC8392631 DOI: 10.3390/cells10082133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/08/2021] [Accepted: 08/16/2021] [Indexed: 12/11/2022] Open
Abstract
Calcium (Ca2+) signaling coordinates are crucial processes in brain physiology. Particularly, fundamental aspects of neuronal function such as synaptic transmission and neuronal plasticity are regulated by Ca2+, and neuronal survival itself relies on Ca2+-dependent cascades. Indeed, impaired Ca2+ homeostasis has been reported in aging as well as in the onset and progression of neurodegeneration. Understanding the physiology of brain function and the key processes leading to its derangement is a core challenge for neuroscience. In this context, Ca2+ imaging represents a powerful tool, effectively fostered by the continuous amelioration of Ca2+ sensors in parallel with the improvement of imaging instrumentation. In this review, we explore the potentiality of the most used animal models employed for Ca2+ imaging, highlighting their application in brain research to explore the pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Nelly Redolfi
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Paloma García-Casas
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Chiara Fornetto
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Sonia Sonda
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
| | - Diana Pendin
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
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19
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Petracovici A, Bonasio R. Distinct PRC2 subunits regulate maintenance and establishment of Polycomb repression during differentiation. Mol Cell 2021; 81:2625-2639.e5. [PMID: 33887196 PMCID: PMC8217195 DOI: 10.1016/j.molcel.2021.03.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3. PRC2 subunits form two holocomplexes-PRC2.1 and PRC2.2-but the roles of these two PRC2 assemblies during differentiation are unclear. We employed auxin-inducible degradation to deplete PRC2.1 subunit MTF2 or PRC2.2 subunit JARID2 during differentiation of embryonic stem cells (ESCs) to neural progenitors (NPCs). Depletion of either MTF2 or JARID2 resulted in incomplete differentiation due to defects in gene regulation. Distinct sets of Polycomb target genes were derepressed in the absence of MTF2 or JARID2. MTF2-sensitive genes were marked by H3K27me3 in ESCs and remained silent during differentiation, whereas JARID2-sensitive genes were preferentially active in ESCs and became newly repressed in NPCs. Thus, MTF2 and JARID2 contribute non-redundantly to Polycomb silencing, suggesting that PRC2.1 and PRC2.2 have distinct functions in maintaining and establishing, respectively, Polycomb repression during differentiation.
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Affiliation(s)
- Ana Petracovici
- Graduate Group in Cell and Molecular Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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20
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Gonzalez-Estevez A, Verrico A, Orniacki C, Reina-San-Martin B, Doye V. Integrity of the short arm of the nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation. J Cell Sci 2021; 134:268378. [PMID: 34037234 DOI: 10.1242/jcs.258340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Many cellular processes, ranging from cell division to differentiation, are controlled by nuclear pore complexes (NPCs). However, studying the contributions of individual NPC subunits to these processes in vertebrates has long been impeded by their complexity and the lack of efficient genetic tools. Here, we use genome editing in mouse embryonic stem cells (mESCs) to characterize the role of NPC structural components, focusing on the short arm of the Y-complex that comprises Nup85, Seh1 and Nup43. We show that Seh1 and Nup43, although dispensable in pluripotent mESCs, are required for their normal cell growth rates, their viability upon differentiation and for the maintenance of proper NPC density. mESCs with an N-terminally truncated Nup85 mutation (in which interaction with Seh1 is greatly impaired) feature a similar reduction of NPC density. However, their proliferation and differentiation are unaltered, indicating that it is the integrity of the Y-complex, rather than the number of NPCs, that is critical to ensure these processes.
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Affiliation(s)
- Alba Gonzalez-Estevez
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| | - Annalisa Verrico
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France
| | - Clarisse Orniacki
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.,Inserm U 1258, Illkirch 67404, France.,Centre National de la Recherche Scientifique UMR (Unité Mixte de Recherche) 7104, Illkirch 67404, France.,Université de Strasbourg, Illkirch 67404, France
| | - Valérie Doye
- Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75006 Paris, France.,Ecole Doctorale BioSPC, Université de Paris, Paris, France
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21
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Enhancer viruses for combinatorial cell-subclass-specific labeling. Neuron 2021; 109:1449-1464.e13. [PMID: 33789083 DOI: 10.1016/j.neuron.2021.03.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022]
Abstract
Rapid cell type identification by new genomic single-cell analysis methods has not been met with efficient experimental access to these cell types. To facilitate access to specific neural populations in mouse cortex, we collected chromatin accessibility data from individual cells and identified enhancers specific for cell subclasses and types. When cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, these enhancers drive transgene expression in specific cortical cell subclasses. We extensively characterized several enhancer AAVs to show that they label different projection neuron subclasses as well as a homologous neuron subclass in human cortical slices. We also show how coupling enhancer viruses expressing recombinases to a newly generated transgenic mouse, Ai213, enables strong labeling of three different neuronal classes/subclasses in the brain of a single transgenic animal. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.
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22
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Lee HHC, Pearl PL, Rotenberg A. Enzyme Replacement Therapy for Succinic Semialdehyde Dehydrogenase Deficiency: Relevance in γ-Aminobutyric Acid Plasticity. J Child Neurol 2021; 36:1200-1209. [PMID: 33624531 PMCID: PMC8382780 DOI: 10.1177/0883073821993000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Succinic semialdehyde dehydrogenase deficiency (SSADHD) is a rare inborn metabolic disorder caused by the functional impairment of SSADH (encoded by the ALDH5A1 gene), an enzyme essential for metabolism of the inhibitory neurotransmitter γ-aminobutyric acid (GABA). In SSADHD, pathologic accumulation of GABA and its metabolite γ-hydroxybutyrate (GHB) results in broad spectrum encephalopathy including developmental delay, ataxia, seizures, and a heightened risk of sudden unexpected death in epilepsy (SUDEP). Proof-of-concept systemic SSADH restoration via enzyme replacement therapy increased survival of SSADH knockout mice, suggesting that SSADH restoration might be a viable intervention for SSADHD. However, before testing enzyme replacement therapy or gene therapy in patients, we must consider its safety and feasibility in the context of early brain development and unique SSADHD pathophysiology. Specifically, a profound use-dependent downregulation of GABAA receptors in SSADHD indicates a risk that any sudden SSADH restoration might diminish GABAergic tone and provoke seizures. In addition, the tight developmental regulation of GABA circuit plasticity might limit the age window when SSADH restoration is accomplished safely. Moreover, given SSADH expressions are cell type-specific, targeted instead of global restoration might be necessary. We therefore describe 3 key parameters for the clinical readiness of SSADH restoration: (1) rate, (2) timing, and (3) cell type specificity. Our work focuses on the construction of a novel SSADHD mouse model that allows "on-demand" SSADH restoration for the systematic investigation of these key parameters. We aim to understand the impacts of specific SSADH restoration protocols on brain physiology, accelerating bench-to-bedside development of enzyme replacement therapy or gene therapy for SSADHD patients.
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Affiliation(s)
- Henry Hing Cheong Lee
- FM Kirby Neurobiology Center, Boston Children’s Hospital,Correspondence: Henry Lee () and Alexander Rotenberg ()
| | | | - Alexander Rotenberg
- FM Kirby Neurobiology Center, Boston Children’s Hospital,Department of Neurology, Boston Children’s Hospital,Correspondence: Henry Lee () and Alexander Rotenberg ()
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23
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Huseyin MK, Klose RJ. Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy. Nat Commun 2021; 12:887. [PMID: 33563969 PMCID: PMC7873255 DOI: 10.1038/s41467-021-21130-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. How PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here, we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We observe that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, suggesting that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.
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Affiliation(s)
- Miles K Huseyin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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24
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Mollinedo-Gajate I, Song C, Knöpfel T. Genetically Encoded Voltage Indicators. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:209-224. [PMID: 33398815 DOI: 10.1007/978-981-15-8763-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Optogenetic approaches combine the power to allocate optogenetic tools (proteins) to specific cell populations (defined genetically or functionally) and the use of light-based interfaces between biological wetware (cells and tissues) and hardware (controllers and recorders). The optogenetic toolbox contains two main compartments: tools to interfere with cellular processes and tools to monitor cellular events. Among the latter are genetically encoded voltage indicators (GEVIs). This chapter outlines the development, current state of the art and prospects of emerging optical GEVI imaging technologies.
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Affiliation(s)
| | - Chenchen Song
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London, UK
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London, UK.
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25
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Nishizono H, Yasuda R, Laviv T. Methodologies and Challenges for CRISPR/Cas9 Mediated Genome Editing of the Mammalian Brain. Front Genome Ed 2020; 2:602970. [PMID: 34713226 PMCID: PMC8525404 DOI: 10.3389/fgeed.2020.602970] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
Neurons and glia are highly polarized cells with extensive subcellular structures extending over large distances from their cell bodies. Previous research has revealed elaborate protein signaling complexes localized within intracellular compartments. Thus, exploring the function and the localization of endogenous proteins is vital to understanding the precise molecular mechanisms underlying the synapse, cellular, and circuit function. Recent advances in CRISPR/Cas9-based genome editing techniques have allowed researchers to rapidly develop transgenic animal models and perform single-cell level genome editing in the mammalian brain. Here, we introduce and comprehensively review the latest techniques for genome-editing in whole animals using fertilized eggs and methods for gene editing in specific neuronal populations in the adult or developing mammalian brain. Finally, we describe the advantages and disadvantages of each technique, as well as the challenges that lie ahead to advance the generation of methodologies for genome editing in the brain using the current CRISPR/Cas9 system.
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Affiliation(s)
- Hirofumi Nishizono
- Department of Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, FL, United States
| | - Ryohei Yasuda
- Department of Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, FL, United States
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26
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Pryzhkova MV, Xu MJ, Jordan PW. Adaptation of the AID system for stem cell and transgenic mouse research. Stem Cell Res 2020; 49:102078. [PMID: 33202307 PMCID: PMC7784532 DOI: 10.1016/j.scr.2020.102078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022] Open
Abstract
The auxin-inducible degron (AID) system is becoming a widely used method for rapid and reversible degradation of target proteins. This system has been successfully used to study gene and protein functions in eukaryotic cells and common model organisms, such as nematode and fruit fly. To date, applications of the AID system in mammalian stem cell research are limited. Furthermore, standard mouse models harboring the AID system have not been established. Here we have explored the utility of the H11 safe-harbor locus for integration of the TIR1 transgene, an essential component of auxin-based protein degradation system. We have shown that the H11 locus can support constitutive and conditional TIR1 expression in mouse and human embryonic stem cells, as well as in mice. We demonstrate that the AID system can be successfully employed for rapid degradation of stable proteins in embryonic stem cells, which is crucial for investigation of protein functions in quickly changing environments, such as stem cell proliferation and differentiation. As embryonic stem cells possess unlimited proliferative capacity, differentiation potential, and can mimic organ development, we believe that these research tools will be an applicable resource to a broad scientific audience.
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Affiliation(s)
- Marina V Pryzhkova
- Biochemistry and Molecular Biology Department, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Michelle J Xu
- Biochemistry and Molecular Biology Department, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Philip W Jordan
- Biochemistry and Molecular Biology Department, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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27
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Lake EMR, Ge X, Shen X, Herman P, Hyder F, Cardin JA, Higley MJ, Scheinost D, Papademetris X, Crair MC, Constable RT. Simultaneous cortex-wide fluorescence Ca 2+ imaging and whole-brain fMRI. Nat Methods 2020; 17:1262-1271. [PMID: 33139894 PMCID: PMC7704940 DOI: 10.1038/s41592-020-00984-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/21/2020] [Indexed: 12/31/2022]
Abstract
Achieving a comprehensive understanding of brain function requires multiple imaging modalities with complementary strengths. We present an approach for concurrent widefield optical and functional magnetic resonance imaging. By merging these modalities, we can simultaneously acquire whole-brain blood-oxygen-level-dependent (BOLD) and whole-cortex calcium-sensitive fluorescent measures of brain activity. In a transgenic murine model, we show that calcium predicts the BOLD signal, using a model that optimizes a gamma-variant transfer function. We find consistent predictions across the cortex, which are best at low frequency (0.009-0.08 Hz). Furthermore, we show that the relationship between modality connectivity strengths varies by region. Our approach links cell-type-specific optical measurements of activity to the most widely used method for assessing human brain function.
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Affiliation(s)
- Evelyn M R Lake
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA.
| | - Xinxin Ge
- Department of Neurobiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Xilin Shen
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Peter Herman
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Fahmeed Hyder
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Jessica A Cardin
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Michael J Higley
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT, USA
| | - Dustin Scheinost
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Xenophon Papademetris
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Michael C Crair
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA.
| | - R Todd Constable
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA. .,Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA. .,Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
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28
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Cell-Type-Specific Gene Inactivation and In Situ Restoration via Recombinase-Based Flipping of Targeted Genomic Region. J Neurosci 2020; 40:7169-7186. [PMID: 32801153 DOI: 10.1523/jneurosci.1044-20.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/22/2020] [Accepted: 07/30/2020] [Indexed: 11/21/2022] Open
Abstract
Conditional gene inactivation and restoration are powerful tools for studying gene functions in the nervous system and for modeling neuropsychiatric diseases. The combination of the two is necessary to interrogate specific cell types within defined developmental stages. However, very few methods and animal models have been developed for such purpose. Here we present a versatile method for conditional gene inactivation and in situ restoration through reversibly inverting a critical part of its endogenous genomic sequence by Cre- and Flp-mediated recombinations. Using this method, we generated a mouse model to manipulate Mecp2, an X-linked dosage-sensitive gene whose mutations cause Rett syndrome. Combined with multiple Cre- and Flp-expressing drivers and viral tools, we achieved efficient and reliable Mecp2 inactivation and restoration in the germline and several neuronal cell types, and demonstrated phenotypic reversal and prevention on cellular and behavioral levels in male mice. This study not only provides valuable tools and critical insights for Mecp2 and Rett syndrome, but also offers a generally applicable strategy to decipher other neurologic disorders.SIGNIFICANCE STATEMENT Studying neurodevelopment and modeling neurologic disorders rely on genetic tools, such as conditional gene regulation. We developed a new method to combine conditional gene inactivation and restoration on a single allele without disturbing endogenous expression pattern or dosage. We applied it to manipulate Mecp2, a gene residing on X chromosome whose malfunction leads to neurologic disease, including Rett syndrome. Our results demonstrated the efficiency, specificity, and versatility of this new method, provided valuable tools and critical insights for Mecp2 function and Rett syndrome research, and offered a generally applicable strategy to investigate other genes and genetic disorders.
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29
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Ahmadzadeh E, Bayin NS, Qu X, Singh A, Madisen L, Stephen D, Zeng H, Joyner AL, Rosello-Diez A. A collection of genetic mouse lines and related tools for inducible and reversible intersectional mis-expression. Development 2020; 147:dev.186650. [PMID: 32366677 DOI: 10.1242/dev.186650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
Abstract
Thanks to many advances in genetic manipulation, mouse models have become very powerful in their ability to interrogate biological processes. In order to precisely target expression of a gene of interest to particular cell types, intersectional genetic approaches using two promoter/enhancers unique to a cell type are ideal. Within these methodologies, variants that add temporal control of gene expression are the most powerful. We describe the development, validation and application of an intersectional approach that involves three transgenes, requiring the intersection of two promoter/enhancers to target gene expression to precise cell types. Furthermore, the approach uses available lines expressing tTA/rTA to control the timing of gene expression based on whether doxycycline is absent or present, respectively. We also show that the approach can be extended to other animal models, using chicken embryos. We generated three mouse lines targeted at the Tigre (Igs7) locus with TRE-loxP-tdTomato-loxP upstream of three genes (p21, DTA and Ctgf), and combined them with Cre and tTA/rtTA lines that target expression to the cerebellum and limbs. Our tools will facilitate unraveling biological questions in multiple fields and organisms.
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Affiliation(s)
- Elham Ahmadzadeh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - N Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Xinli Qu
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - Aditi Singh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Daniel Stephen
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Alberto Rosello-Diez
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
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30
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Imayoshi I, Tabuchi S, Matsumoto M, Kitano S, Miyachi H, Kageyama R, Yamanaka A. Light-induced silencing of neural activity in Rosa26 knock-in and BAC transgenic mice conditionally expressing the microbial halorhodopsin eNpHR3. Sci Rep 2020; 10:3191. [PMID: 32081938 PMCID: PMC7035371 DOI: 10.1038/s41598-020-59984-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/06/2020] [Indexed: 12/25/2022] Open
Abstract
An engineered light-inducible chloride pump, Natronomonas pharaonis halorhodopsin 3 (eNpHR3) enables temporally and spatially precise inhibition of genetically defined cell populations in the intact nervous tissues. In this report, we show the generation of new mouse strains that express eNpHR3-EYFP fusion proteins after Cre- and/or Flp-mediated recombination to optically inhibit neuronal activity. In these mouse strains, Cre/Flp recombination induced high levels of opsin expression. We confirmed their light-induced activities by brain slice whole-cell patch clamp experiments. eNpHR3-expressing neurons were optically hyperpolarized and silenced from firing action potentials. In prolonged silencing of action potentials, eNpHR3 was superior to eNpHR2, a former version of the engineered pump. Thus, these eNpHR3 mouse strains offer reliable genetic tools for light-induced inhibiting of neuronal activity in defined sets of neurons.
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Affiliation(s)
- Itaru Imayoshi
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan. .,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan. .,World Premier International Research Initiative-Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan.
| | - Sawako Tabuchi
- Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
| | - Mami Matsumoto
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Satsuki Kitano
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Hitoshi Miyachi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Ryoichiro Kageyama
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan. .,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan. .,World Premier International Research Initiative-Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan.
| | - Akihiro Yamanaka
- Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
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31
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Peng H, Chau VQ, Phetsang W, Sebastian RM, Stone MRL, Datta S, Renwick M, Tamer YT, Toprak E, Koh AY, Blaskovich MA, Hulleman JD. Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo. Mol Ther Methods Clin Dev 2019; 15:27-39. [PMID: 31649953 PMCID: PMC6804886 DOI: 10.1016/j.omtm.2019.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
The E. coli dihydrofolate reductase (DHFR) destabilizing domain (DD), which shows promise as a biologic tool and potential gene therapy approach, can be utilized to achieve spatial and temporal control of protein abundance in vivo simply by administration of its stabilizing ligand, the routinely prescribed antibiotic trimethoprim (TMP). However, chronic TMP use drives development of antibiotic resistance (increasing likelihood of subsequent infections) and disrupts the gut microbiota (linked to autoimmune and neurodegenerative diseases), tempering translational excitement of this approach in model systems and for treating human diseases. Herein, we identified a TMP-based, non-antibiotic small molecule, termed 14a (MCC8529), and tested its ability to control multiple DHFR-based reporters and signaling proteins. We found that 14a is non-toxic and can effectively stabilize DHFR DDs expressed in mammalian cells. Furthermore, 14a crosses the blood-retinal barrier and stabilizes DHFR DDs expressed in the mouse eye with kinetics comparable to that of TMP (≤6 h). Surprisingly, 14a stabilized a DHFR DD in the liver significantly better than TMP did, while having no effect on the mouse gut microbiota. Our results suggest that alternative small-molecule DHFR DD stabilizers (such as 14a) may be ideal substitutes for TMP in instances when conditional, non-antibiotic control of protein abundance is desired in the eye and beyond.
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Affiliation(s)
- Hui Peng
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Viet Q. Chau
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Wanida Phetsang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Rebecca M. Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - M. Rhia L. Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Shyamtanu Datta
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Marian Renwick
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yusuf T. Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Andrew Y. Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Mark A.T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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32
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Browning J, Rooney M, Hams E, Takahashi S, Mizuno S, Sugiyama F, Fallon PG, Kelly VP. Highly efficient CRISPR-targeting of the murine Hipp11 intergenic region supports inducible human transgene expression. Mol Biol Rep 2019; 47:1491-1498. [PMID: 31811500 DOI: 10.1007/s11033-019-05204-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/21/2019] [Indexed: 01/21/2023]
Abstract
Safe harbor loci allow predicable integration of a transgene into the genome without perturbing endogenous gene activity and for decades have been exploited in the mouse to investigate gene function, generate humanised models and create tissue specific reporter and Cre recombinase expressing lines. Herein, we show that the murine Hipp11 intergenic region can facilitate highly efficient integration of a large transgene-the human CD1A promoter and coding region-by means of CRISPR-Cas9 mediated homology directed repair. The data shows that the single copy human CD1A transgene is faithfully expressed in an inducible manner in homozygous animals in both macrophage and dendritic cells. Our results validate the Hipp11 intergenic region as being a highly amenable target site for functional transgene integration in mouse.
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Affiliation(s)
- Jill Browning
- School of Biochemistry& Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Michael Rooney
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Emily Hams
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Satoru Takahashi
- 1-1-1 Tennodai Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Seiya Mizuno
- 1-1-1 Tennodai Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Fumihiro Sugiyama
- 1-1-1 Tennodai Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Padraic G Fallon
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Vincent P Kelly
- School of Biochemistry& Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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33
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Nesterova TB, Wei G, Coker H, Pintacuda G, Bowness JS, Zhang T, Almeida M, Bloechl B, Moindrot B, Carter EJ, Alvarez Rodrigo I, Pan Q, Bi Y, Song CX, Brockdorff N. Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation. Nat Commun 2019; 10:3129. [PMID: 31311937 PMCID: PMC6635394 DOI: 10.1038/s41467-019-11171-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/19/2019] [Indexed: 01/05/2023] Open
Abstract
Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing.
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Affiliation(s)
- Tatyana B Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Heather Coker
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Joseph S Bowness
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mafalda Almeida
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Bianca Bloechl
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Benoit Moindrot
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- I2BC Paris-Sud University, Gif-Sur-Yvette, France
| | - Emma J Carter
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ines Alvarez Rodrigo
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Qi Pan
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ying Bi
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H. A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality. Cell 2019; 174:465-480.e22. [PMID: 30007418 DOI: 10.1016/j.cell.2018.06.035] [Citation(s) in RCA: 449] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/12/2018] [Accepted: 06/13/2018] [Indexed: 01/05/2023]
Abstract
Modern genetic approaches are powerful in providing access to diverse cell types in the brain and facilitating the study of their function. Here, we report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.
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Affiliation(s)
- Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Travis A Hage
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ulf Knoblich
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rylan S Larsen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Marc M Takeno
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lawrence Huang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachael Larsen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Maya Mills
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Miranda Walker
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garreck H Lenz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Mariya Chavarha
- Departments of Neurobiology and Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Medea J McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | | | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jérôme Lecoq
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Z Lin
- Departments of Neurobiology and Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Edward S Boyden
- MIT Media Lab and McGovern Institute, Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lu Li
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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Fan H, Liu X, Shen Y, Chen S, Huan Y, Shan J, Zhou C, Wu S, Zhang Z, Wang Y. In Vivo Genetic Strategies for the Specific Lineage Tracing of Stem Cells. Curr Stem Cell Res Ther 2019; 14:230-238. [PMID: 30047336 DOI: 10.2174/1574888x13666180726110138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/04/2018] [Accepted: 06/26/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Characterization of the fate changes of stem cells is essential to understand the roles of certain stem cells both during development and in diseases, such as cancer. In the past two decades, more and more importance has been paid to the studies of in vivo lineage tracing, because they could authentically reveal the differentiation, migration and even proliferation of stem cells. However, specific genetic tools have only been developed until recently. OBJECTIVE To summarize the progresses of genetic tools for specific lineage tracing with emphasis on their applications in investigating the stem cell niche signals. RESULTS Three major genetic strategies have been reviewed according to the development of technique, particularly the advantages and disadvantages of individual methods. CONCLUSION In vivo specific lineage tracing of stem cells could be achieved by comprehensive application of multiple genetic tools.
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Affiliation(s)
- Hong Fan
- Department of Neurobiology, Institute of Neurosciences, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an 710032, China
| | - Xinyu Liu
- Cadet team of undergraduate, School of Basic Medicine, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an, 710032, China
| | - Yahui Shen
- Cadet team of undergraduate, School of Basic Medicine, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an, 710032, China
| | - Siwei Chen
- Cadet team of undergraduate, School of Basic Medicine, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an, 710032, China
| | - Yu Huan
- Cadet team of undergraduate, School of Basic Medicine, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an, 710032, China
| | - Junjia Shan
- Cadet team of undergraduate, School of Basic Medicine, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an, 710032, China
| | - Chengji Zhou
- Department of Biochemistry and Molecular Medicine, Institute for Pediatric Regenerative Medicine, University of California-Davis, 2425 Stockton Blvd, Sacramento, CA 95817, United States
| | - Shengxi Wu
- Department of Neurobiology, Institute of Neurosciences, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an 710032, China
| | - Zifeng Zhang
- Department of Ophthalmology, Eye Institute of Chinese PLA, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Yazhou Wang
- Department of Neurobiology, Institute of Neurosciences, Fourth Military Medical University, 169 Chang Le Xi Road, Xi'an 710032, China
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Small Molecule-Based Inducible Gene Therapies for Retinal Degeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1185:65-69. [PMID: 31884590 DOI: 10.1007/978-3-030-27378-1_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The eye is an excellent target organ for gene therapy. It is physically isolated, easily accessible, immune-privileged, and postmitotic. Furthermore, potential gene therapies introduced into the eye can be evaluated by noninvasive methods such as fundoscopy, electroretinography, and optical coherence tomography. In the last two decades, great advances have been made in understanding the molecular underpinnings of retinal degenerative diseases. Building upon the development of modern techniques for gene delivery, many gene-based therapies have been effectively used to treat loss-of-function retinal diseases in mice and men. Significant effort has been invested into making gene delivery vehicles more efficient, less toxic, and non-immunogenic. However, one challenge for the treatment of more complex gain-of-function diseases, many of which might be benefited by the regulation of cellular stress-responsive signaling pathways, is the ability to control the strategy in a physiological (conditional) manner. This review is focused on promising retinal gene therapy strategies that rely on small molecule-based conditional regulation and the inherent limitations and challenges of these strategies that need to be addressed prior to their extensive use.
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Datta S, Renwick M, Chau VQ, Zhang F, Nettesheim ER, Lipinski DM, Hulleman JD. A Destabilizing Domain Allows for Fast, Noninvasive, Conditional Control of Protein Abundance in the Mouse Eye - Implications for Ocular Gene Therapy. Invest Ophthalmol Vis Sci 2018; 59:4909-4920. [PMID: 30347085 PMCID: PMC6181441 DOI: 10.1167/iovs.18-24987] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/30/2018] [Indexed: 01/23/2023] Open
Abstract
Purpose Temporal and reversible control of protein expression in vivo is a central goal for many gene therapies, especially for strategies involving proteins that are detrimental to physiology if constitutively expressed. Accordingly, we explored whether protein abundance in the mouse retina could be effectively controlled using a destabilizing Escherichia coli dihydrofolate reductase (DHFR) domain whose stability is dependent on the small molecule, trimethoprim (TMP). Methods We intravitreally injected wild-type C57BL6/J mice with an adeno-associated vector (rAAV2/2[MAX]) constitutively expressing separate fluorescent reporters: DHFR fused to yellow fluorescent protein (DHFR.YFP) and mCherry. TMP or vehicle was administered to mice via oral gavage, drinking water, or eye drops. Ocular TMP levels post treatment were quantified by LC-MS/MS. Protein abundance was measured by fundus fluorescence imaging and western blotting. Visual acuity, response to light stimulus, retinal structure, and gene expression were evaluated after long-term (3 months) TMP treatment. Results Without TMP, DHFR.YFP was efficiently degraded in the retina. TMP achieved ocular concentrations of ∼13.6 μM (oral gavage), ∼331 nM (drinking water), and ∼636 nM (eye drops). Oral gavage and TMP eye drops stabilized DHFR.YFP as quickly as 6 hours, whereas continuous TMP drinking water could stabilize DHFR.YFP for ≥3 months. Stabilization was completely and repeatedly reversible following removal/addition of TMP in all regimens. Long-term TMP treatment had no impact on retina function/structure and had no effect on >99.9% of tested genes. Conclusions This DHFR-based conditional system is a rapid, efficient, and reversible tool to effectively control protein expression in the retina.
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Affiliation(s)
- Shyamtanu Datta
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Marian Renwick
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Viet Q. Chau
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Fang Zhang
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Emily R. Nettesheim
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Daniel M. Lipinski
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neuroscience, University of Oxford, Oxford, United Kingdom
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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Seeman SC, Campagnola L, Davoudian PA, Hoggarth A, Hage TA, Bosma-Moody A, Baker CA, Lee JH, Mihalas S, Teeter C, Ko AL, Ojemann JG, Gwinn RP, Silbergeld DL, Cobbs C, Phillips J, Lein E, Murphy G, Koch C, Zeng H, Jarsky T. Sparse recurrent excitatory connectivity in the microcircuit of the adult mouse and human cortex. eLife 2018; 7:e37349. [PMID: 30256194 PMCID: PMC6158007 DOI: 10.7554/elife.37349] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/21/2018] [Indexed: 01/09/2023] Open
Abstract
Generating a comprehensive description of cortical networks requires a large-scale, systematic approach. To that end, we have begun a pipeline project using multipatch electrophysiology, supplemented with two-photon optogenetics, to characterize connectivity and synaptic signaling between classes of neurons in adult mouse primary visual cortex (V1) and human cortex. We focus on producing results detailed enough for the generation of computational models and enabling comparison with future studies. Here, we report our examination of intralaminar connectivity within each of several classes of excitatory neurons. We find that connections are sparse but present among all excitatory cell classes and layers we sampled, and that most mouse synapses exhibited short-term depression with similar dynamics. Synaptic signaling between a subset of layer 2/3 neurons, however, exhibited facilitation. These results contribute to a body of evidence describing recurrent excitatory connectivity as a conserved feature of cortical microcircuits.
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Affiliation(s)
| | | | | | - Alex Hoggarth
- Allen Institute for Brain ScienceSeattleUnited States
| | - Travis A Hage
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Jung Hoon Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Andrew L Ko
- Regional Epilepsy Center at Harborview Medical CenterSeattleUnited States
- Department of Neurological SurgeryUniversity of Washington School of MedicineSeattleUnited States
| | - Jeffrey G Ojemann
- Regional Epilepsy Center at Harborview Medical CenterSeattleUnited States
- Department of Neurological SurgeryUniversity of Washington School of MedicineSeattleUnited States
| | - Ryder P Gwinn
- Epilepsy Surgery and Functional NeurosurgerySwedish Neuroscience InstituteSeattleUnited States
| | - Daniel L Silbergeld
- Department of Neurological SurgeryUniversity of Washington School of MedicineSeattleUnited States
| | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor TreatmentSwedish Neuroscience InstituteSeattleUnited States
| | - John Phillips
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Gabe Murphy
- Allen Institute for Brain ScienceSeattleUnited States
| | - Christof Koch
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
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Gödecke N, Zha L, Spencer S, Behme S, Riemer P, Rehli M, Hauser H, Wirth D. Controlled re-activation of epigenetically silenced Tet promoter-driven transgene expression by targeted demethylation. Nucleic Acids Res 2017; 45:e147. [PMID: 28934472 PMCID: PMC5766184 DOI: 10.1093/nar/gkx601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/03/2017] [Indexed: 12/20/2022] Open
Abstract
Faithful expression of transgenes in cell cultures and mice is often challenged by locus dependent epigenetic silencing. We investigated silencing of Tet-controlled expression cassettes within the mouse ROSA26 locus. We observed pronounced DNA methylation of the Tet promoter concomitant with loss of expression in mES cells as well as in differentiated cells and transgenic animals. Strikingly, the ROSA26 promoter remains active and methylation free indicating that this silencing mechanism specifically affects the transgene, but does not spread to the host's chromosomal neighborhood. To reactivate Tet cassettes a synthetic fusion protein was constructed and expressed in silenced cells. This protein includes the enzymatic domains of ten eleven translocation methylcytosine dioxygenase 1 (TET-1) as well as the Tet repressor DNA binding domain. Expression of the synthetic fusion protein and Doxycycline treatment allowed targeted demethylation of the Tet promoter in the ROSA26 locus and in another genomic site, rescuing transgene expression in cells and transgenic mice. Thus, inducible, reversible and site-specific epigenetic modulation is a promising strategy for reactivation of silenced transgene expression, independent of the integration site.
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Affiliation(s)
- Natascha Gödecke
- Helmholtz Centre for Infection Research, RG Model Systems for Infection and Immunity (MSYS), Braunschweig, Germany
| | - Lisha Zha
- Helmholtz Centre for Infection Research, RG Model Systems for Infection and Immunity (MSYS), Braunschweig, Germany
| | - Shawal Spencer
- Helmholtz Centre for Infection Research, RG Model Systems for Infection and Immunity (MSYS), Braunschweig, Germany
| | - Sara Behme
- Helmholtz Centre for Infection Research, RG Model Systems for Infection and Immunity (MSYS), Braunschweig, Germany
| | - Pamela Riemer
- Helmholtz Centre for Infection Research, RG Model Systems for Infection and Immunity (MSYS), Braunschweig, Germany
| | - Michael Rehli
- University Hospital, Dept. Internal Medicine III, Regensburg, Germany
| | - Hansjörg Hauser
- Helmholtz Centre for Infection Research, Dept. of Scientific Strategy, Braunschweig, Germany
| | - Dagmar Wirth
- Helmholtz Centre for Infection Research, RG Model Systems for Infection and Immunity (MSYS), Braunschweig, Germany.,Hannover Medical School, Experimental Hematology, Hannover, Germany
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The CpG-sites of the CBX3 ubiquitous chromatin opening element are critical structural determinants for the anti-silencing function. Sci Rep 2017; 7:7919. [PMID: 28801671 PMCID: PMC5554207 DOI: 10.1038/s41598-017-04212-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/10/2017] [Indexed: 12/28/2022] Open
Abstract
Suppression of therapeutic transgene expression from retroviral gene therapy vectors by epigenetic defence mechanisms represents a problem that is particularly encountered in pluripotent stem cells (PSCs) and their differentiated progeny. Transgene expression in these cells, however, can be stabilised by CpG-rich ubiquitous chromatin opening elements (UCOEs). In this context we recently demonstrated profound anti-silencing properties for the small (679 bp) CBX3-UCO element and we now confirmed this observation in the context of the defined murine chromosomal loci ROSA26 and TIGRE. Moreover, since the structural basis for the anti-silencing activity of UCOEs has remained poorly defined, we interrogated various CBX3 subfragments in the context of lentiviral vectors and murine PSCs. We demonstrated marked though distinct anti-silencing activity in the pluripotent state and during PSC-differentiation for several of the CBX3 subfragments. This activity was significantly correlated with CpG content as well as endogenous transcriptional activity. Interestingly, also a scrambled CBX3 version with preserved CpG-sites retained the anti-silencing activity despite the lack of endogenous promoter activity. Our data therefore highlight the importance of CpG-sites and transcriptional activity for UCOE functionality and suggest contributions from different mechanisms to the overall anti-silencing function of the CBX3 element.
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Song C, Do QB, Antic SD, Knöpfel T. Transgenic Strategies for Sparse but Strong Expression of Genetically Encoded Voltage and Calcium Indicators. Int J Mol Sci 2017; 18:ijms18071461. [PMID: 28686207 PMCID: PMC5535952 DOI: 10.3390/ijms18071461] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 01/09/2023] Open
Abstract
Rapidly progressing development of optogenetic tools, particularly genetically encoded optical indicators, enables monitoring activities of neuronal circuits of identified cell populations in longitudinal in vivo studies. Recently developed advanced transgenic approaches achieve high levels of indicator expression. However, targeting non-sparse cell populations leads to dense expression patterns such that optical signals from neuronal processes cannot be allocated to individual neurons. This issue is particularly pertinent for the use of genetically encoded voltage indicators whose membrane-delimited signals arise largely from the neuropil where dendritic and axonal membranes of many cells intermingle. Here we address this need for sparse but strong expression of genetically encoded optical indicators using a titratable recombination-activated transgene transcription to achieve a Golgi staining-type indicator expression pattern in vivo. Using different transgenic strategies, we also illustrate that co-expression of genetically encoded voltage and calcium indicators can be achieved in vivo for studying neuronal circuit input–output relationships.
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Affiliation(s)
- Chenchen Song
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London W12 0NN, UK.
| | - Quyen B Do
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London W12 0NN, UK.
| | - Srdjan D Antic
- Institute for Systems Genomics, Stem Cell Institute, UConn Health, Farmington, CT 06030-3401, USA.
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London W12 0NN, UK.
- Centre for Neurotechnology, Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK.
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Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell 2017; 169:930-944.e22. [PMID: 28525758 PMCID: PMC5538188 DOI: 10.1016/j.cell.2017.05.004] [Citation(s) in RCA: 1037] [Impact Index Per Article: 148.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 01/17/2023]
Abstract
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Johan H Gibcus
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Alec Uebersohn
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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Wolf D, Zirlik A, Ley K. Beyond vascular inflammation--recent advances in understanding atherosclerosis. Cell Mol Life Sci 2015; 72:3853-69. [PMID: 26100516 PMCID: PMC4577451 DOI: 10.1007/s00018-015-1971-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 06/10/2015] [Accepted: 06/15/2015] [Indexed: 12/23/2022]
Abstract
Atherosclerosis is the most life-threatening pathology worldwide. Its major clinical complications, stroke, myocardial infarction, and heart failure, are on the rise in many regions of the world--despite considerable progress in understanding cause, progression, and consequences of atherosclerosis. Originally perceived as a lipid-storage disease of the arterial wall (Die cellularpathologie in ihrer begründung auf physiologische und pathologische gewebelehre. August Hirschwald Verlag Berlin, [1871]), atherosclerosis was recognized as a chronic inflammatory disease in 1986 (New Engl J Med 314:488-500, 1986). The presence of lymphocytes in atherosclerotic lesions suggested autoimmune processes in the vessel wall (Clin Exp Immunol 64:261-268, 1986). Since the advent of suitable mouse models of atherosclerosis (Science 258:468-471, 1992; Cell 71:343-353, 1992; J Clin Invest 92:883-893, 1993) and the development of flow cytometry to define the cellular infiltrate in atherosclerotic lesions (J Exp Med 203:1273-1282, 2006), the origin, lineage, phenotype, and function of distinct inflammatory cells that trigger or inhibit the inflammatory response in the atherosclerotic plaque have been studied. Multiphoton microscopy recently enabled direct visualization of antigen-specific interactions between T cells and antigen-presenting cells in the vessel wall (J Clin Invest 122:3114-3126, 2012). Vascular immunology is now emerging as a new field, providing evidence for protective as well as damaging autoimmune responses (Int Immunol 25:615-622, 2013). Manipulating inflammation and autoimmunity both hold promise for new therapeutic strategies in cardiovascular disease. Ongoing work (J Clin Invest 123:27-36, 2013; Front Immunol 2013; Semin Immunol 31:95-101, 2009) suggests that it may be possible to develop antigen-specific immunomodulatory prevention and therapy-a vaccine against atherosclerosis.
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Affiliation(s)
- Dennis Wolf
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Andreas Zirlik
- Atherogenesis Research Group, Cardiology and Angiology I, Heart Center, University of Freiburg, Freiburg, Germany
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA.
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Natsubori A, Takata N, Tanaka KF. Observation and manipulation of glial cell function by virtue of sufficient probe expression. Front Cell Neurosci 2015; 9:176. [PMID: 26005405 PMCID: PMC4424858 DOI: 10.3389/fncel.2015.00176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/21/2015] [Indexed: 01/22/2023] Open
Abstract
The development of gene-encoded indicators and actuators to observe and manipulate cellular functions is being advanced and investigated. Expressing these probe molecules in glial cells is expected to enable observation and manipulation of glial cell activity, leading to elucidate the behaviors and causal roles of glial cells. The first step toward understanding glial cell functions is to express the probes in sufficient amounts, and the Knockin-mediated ENhanced Gene Expression (KENGE)-tet system provides a strategy for achieving this. In the present article, three examples of KENGE-tet system application are reviewed: depolarization of oligodendrocytes, intracellular acidification of astrocytes, and observation of intracellular calcium levels in the fine processes of astrocytes.
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Affiliation(s)
- Akiyo Natsubori
- Department of Neuropsychiatry, School of Medicine, Keio University Tokyo, Japan
| | - Norio Takata
- Department of Neuropsychiatry, School of Medicine, Keio University Tokyo, Japan
| | - Kenji F Tanaka
- Department of Neuropsychiatry, School of Medicine, Keio University Tokyo, Japan
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Madisen L, Garner AR, Shimaoka D, Chuong AS, Klapoetke NC, Li L, van der Bourg A, Niino Y, Egolf L, Monetti C, Gu H, Mills M, Cheng A, Tasic B, Nguyen TN, Sunkin SM, Benucci A, Nagy A, Miyawaki A, Helmchen F, Empson RM, Knöpfel T, Boyden ES, Reid RC, Carandini M, Zeng H. Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance. Neuron 2015; 85:942-58. [PMID: 25741722 PMCID: PMC4365051 DOI: 10.1016/j.neuron.2015.02.022] [Citation(s) in RCA: 720] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 01/08/2015] [Accepted: 02/11/2015] [Indexed: 12/25/2022]
Abstract
An increasingly powerful approach for studying brain circuits relies on targeting genetically encoded sensors and effectors to specific cell types. However, current approaches for this are still limited in functionality and specificity. Here we utilize several intersectional strategies to generate multiple transgenic mouse lines expressing high levels of novel genetic tools with high specificity. We developed driver and double reporter mouse lines and viral vectors using the Cre/Flp and Cre/Dre double recombinase systems and established a new, retargetable genomic locus, TIGRE, which allowed the generation of a large set of Cre/tTA-dependent reporter lines expressing fluorescent proteins, genetically encoded calcium, voltage, or glutamate indicators, and optogenetic effectors, all at substantially higher levels than before. High functionality was shown in example mouse lines for GCaMP6, YCX2.60, VSFP Butterfly 1.2, and Jaws. These novel transgenic lines greatly expand the ability to monitor and manipulate neuronal activities with increased specificity. VIDEO ABSTRACT
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Affiliation(s)
- Linda Madisen
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Aleena R Garner
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Daisuke Shimaoka
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Amy S Chuong
- MIT Media Lab and McGovern Institute, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA 02139, USA
| | - Nathan C Klapoetke
- MIT Media Lab and McGovern Institute, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA 02139, USA
| | - Lu Li
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Alexander van der Bourg
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Yusuke Niino
- Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Ladan Egolf
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Claudio Monetti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Hong Gu
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Maya Mills
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Adrian Cheng
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Thuc Nghi Nguyen
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Andrea Benucci
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK; Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Atsushi Miyawaki
- Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ruth M Empson
- Department of Physiology, Brain Health Research Centre, University of Otago, PO Box 913, Dunedin 9054, New Zealand
| | - Thomas Knöpfel
- The Division of Brain Sciences, Department of Medicine, Imperial College London, 160 DuCane Road, London, W12 0NN, UK
| | - Edward S Boyden
- MIT Media Lab and McGovern Institute, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA 02139, USA
| | - R Clay Reid
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Hongkui Zeng
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA.
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Abstract
In this issue of Neuron, Madisen et al. (2015) report the construction of several new transgenic mouse lines that apply intersectional genetic tools to achieve high levels of expression and cell-type specificity, providing a useful resource for future studies.
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Affiliation(s)
- William E Allen
- Neurosciences Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- Neurosciences Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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47
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A simple and highly efficient method to identify the integration site of a transgene in the animal genome. Neurosci Res 2014; 80:91-4. [DOI: 10.1016/j.neures.2013.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 11/22/2013] [Indexed: 11/17/2022]
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Affiliation(s)
- Z. Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724;
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington 98103;
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Wan M, Kaundal R, Huang H, Zhao J, Yang X, Chaiyachati BH, Li S, Chi T. A general approach for controlling transcription and probing epigenetic mechanisms: application to the CD4 locus. THE JOURNAL OF IMMUNOLOGY 2013; 190:737-47. [PMID: 23293358 DOI: 10.4049/jimmunol.1201278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Synthetic regulatory proteins such as tetracycline (tet)-controlled transcription factors are potentially useful for repression as well as ectopic activation of endogenous genes and also for probing their regulatory mechanisms, which would offer a versatile genetic tool advantageous over conventional gene targeting methods. In this study, we provide evidence supporting this concept using Cd4 as a model. CD4 is expressed in double-positive and CD4 cells but irreversibly silenced in CD8 cells. The silencing is mediated by heterochromatin established during CD8 lineage development via transient action of the Cd4 silencer; once established, the heterochromatin becomes self-perpetuating independently of the Cd4 silencer. Using a tet-sensitive Cd4 allele harboring a removable Cd4 silencer, we found that a tet-controlled repressor recapitulated the phenotype of Cd4-deficient mice, inhibited Cd4 expression in a reversible and dose-dependent manner, and could surprisingly replace the Cd4 silencer to induce irreversible Cd4 silencing in CD8 cells, thus suggesting the Cd4 silencer is not the (only) determinant of heterochromatin formation. In contrast, a tet-controlled activator reversibly disrupted Cd4 silencing in CD8 cells. The Cd4 silencer impeded this disruption but was not essential for its reversal, which revealed a continuous role of the silencer in mature CD8 cells while exposing a remarkable intrinsic self-regenerative ability of heterochromatin after forced disruption. These data demonstrate an effective approach for gene manipulation and provide insights into the epigenetic Cd4 regulatory mechanisms that are otherwise difficult to obtain.
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Affiliation(s)
- Mimi Wan
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
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Chaiyachati BH, Kaundal RK, Zhao J, Wu J, Flavell R, Chi T. LoxP-FRT Trap (LOFT): a simple and flexible system for conventional and reversible gene targeting. BMC Biol 2012. [PMID: 23198860 PMCID: PMC3529186 DOI: 10.1186/1741-7007-10-96] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Conditional gene knockout (cKO) mediated by the Cre/LoxP system is indispensable for exploring gene functions in mice. However, a major limitation of this method is that gene KO is not reversible. A number of methods have been developed to overcome this, but each method has its own limitations. Results We describe a simple method we have named LOFT [LoxP-flippase (FLP) recognition target (FRT) Trap], which is capable of reversible cKO and free of the limitations associated with existing techniques. This method involves two alleles of a target gene: a standard floxed allele, and a multi-functional allele bearing an FRT-flanked gene-trap cassette, which inactivates the target gene while reporting its expression with green fluorescent protein (GFP); the trapped allele is thus a null and GFP reporter by default, but is convertible into a wild-type allele. The floxed and trapped alleles can typically be generated using a single construct bearing a gene-trap cassette doubly flanked by LoxP and FRT sites, and can be used independently to achieve conditional and constitutive gene KO, respectively. More importantly, in mice bearing both alleles and also expressing the Cre and FLP recombinases, sequential function of the two enzymes should lead to deletion of the target gene, followed by restoration of its expression, thus achieving reversible cKO. LOFT should be generally applicable to mouse genes, including the growing numbers of genes already floxed; in the latter case, only the trapped alleles need to be generated to confer reversibility to the pre-existing cKO models. LOFT has other applications, including the creation and reversal of hypomorphic mutations. In this study we proved the principle of LOFT in the context of T-cell development, at a hypomorphic allele of Baf57/Smarce1 encoding a subunit of the chromatin-remodeling Brg/Brahma-associated factor (BAF) complex. Interestingly, the FLP used in the current work caused efficient reversal in peripheral T cells but not thymocytes, which is advantageous for studying developmental epigenetic programming of T-cell functions, a fundamental issue in immunology. Conclusions LOFT combines well-established basic genetic methods into a simple and reliable method for reversible gene targeting, with the flexibility of achieving traditional constitutive and conditional KO.
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Affiliation(s)
- Barbara H Chaiyachati
- Department of Immunobiology, Yale University Medical School, 300 Cedar Street, New Haven, CT 06520, USA
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