1
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Zhang M, Lui KO, Zhou B. Application of New Lineage Tracing Techniques in Cardiovascular Development and Physiology. Circ Res 2024; 134:445-458. [PMID: 38359092 DOI: 10.1161/circresaha.123.323179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cardiovascular disease has been the leading cause of mortality and morbidity worldwide in the past 3 decades. Multiple cell lineages undergo dynamic alternations in gene expression, cell state determination, and cell fate conversion to contribute, adapt, and even modulate the pathophysiological processes during disease progression. There is an urgent need to understand the intricate cellular and molecular underpinnings of cardiovascular cell development in homeostasis and pathogenesis. Recent strides in lineage tracing methodologies have revolutionized our understanding of cardiovascular biology with the identification of new cellular origins, fates, plasticity, and heterogeneity within the cardiomyocyte, endothelial, and mesenchymal cell populations. In this review, we introduce the new technologies for lineage tracing of cardiovascular cells and summarize their applications in studying cardiovascular development, diseases, repair, and regeneration.
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Affiliation(s)
- MingJun Zhang
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, China (M.J., B.Z.)
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, China (K.O.L.)
| | - Bin Zhou
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, China (M.J., B.Z.)
- School of Life Science and Technology, ShanghaiTech University, China (B.Z.)
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, China (B.Z.)
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2
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Cautereels C, Smets J, De Saeger J, Cool L, Zhu Y, Zimmermann A, Steensels J, Gorkovskiy A, Jacobs TB, Verstrepen KJ. Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts. Nat Commun 2024; 15:1113. [PMID: 38326330 PMCID: PMC10850332 DOI: 10.1038/s41467-024-44996-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Lloyd Cool
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Yanmei Zhu
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium.
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3
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Zhong Y, Tan X, Wang X, Jiang J, Song K, Chen H, Zhang H, Wang Z, Zhang L, Guo C, Liang H, Yu W. Generation of Vgll4-DreER transgenic mouse for visualizing and manipulating VGLL4-expressing cells in vivo. J Biochem Mol Toxicol 2023; 37:e23435. [PMID: 37352117 DOI: 10.1002/jbt.23435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
Vestigial like family member 4 (VGLL4), a member of the Hippo pathway, is a transcriptional cofactor involved in many biological processes, such as tumor progression, postnatal heart growth, and muscle regeneration. However, the VGLL4 expression pattern in vivo remains unclear. To detect and trace Vgll4-expressing cells and their progeny, we generated and characterized a new tamoxifen-inducible Dre knock-in mouse line, Vgll4-DreER. This mouse line expressed DreER (Dre recombinase fused to the estrogen receptor) under the control of the endogenous Vgll4 promoter. After crossing the Vgll4-DreER mouse line with the Dre-responsive reporter H11-rRFP, Dre-mediated recombination in the tissue was monitored on the basis of red fluorescent protein (RFP) signals, which indicated the distribution of VGLL4-positive cells in vivo. Our data revealed that VGLL4 is widely expressed in various cell types at embryonic and neonatal stages. After comparison with our previously reported Vgll4-GFP mouse, we found that the RFP signal profile was wider than the green fluorescent protein (GFP) pattern, indicating that Vgll4-DreER is more sensitive for labeling VGLL4-expressing cells. We next used a dual-recombination system to simultaneously label VGLL4- and keratin 5 (KRT5)-positive cell populations, and no crosstalk was observed in the Krt5-CreER;Vgll4-DreER;R26-rGlR mice. Taken together, the Vgll4-DreER mouse line is a valuable new tool for examining the precise VGLL4 expression profile and conditional manipulating of VGLL4-expressing cells and their progeny.
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Affiliation(s)
- Yazhu Zhong
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Xixi Tan
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Xiaodong Wang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Jun Jiang
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Kai Song
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Haiyuan Chen
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Hao Zhang
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Zuoyun Wang
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Zhang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- 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, China
| | - Chunming Guo
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Hongfeng Liang
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Wei Yu
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
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4
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Mahmoudian RA, Farshchian M, Golyan FF, Mahmoudian P, Alasti A, Moghimi V, Maftooh M, Khazaei M, Hassanian SM, Ferns GA, Mahaki H, Shahidsales S, Avan A. Preclinical tumor mouse models for studying esophageal cancer. Crit Rev Oncol Hematol 2023; 189:104068. [PMID: 37468084 DOI: 10.1016/j.critrevonc.2023.104068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Preclinical models are extensively employed in cancer research because they can be manipulated in terms of their environment, genome, molecular biology, organ systems, and physical activity to mimic human behavior and conditions. The progress made in in vivo cancer research has resulted in significant advancements, enabling the creation of spontaneous, metastatic, and humanized mouse models. Most recently, the remarkable and extensive developments in genetic engineering, particularly the utilization of CRISPR/Cas9, transposable elements, epigenome modifications, and liquid biopsies, have further facilitated the design and development of numerous mouse models for studying cancer. In this review, we have elucidated the production and usage of current mouse models, such as xenografts, chemical-induced models, and genetically engineered mouse models (GEMMs), for studying esophageal cancer. Additionally, we have briefly discussed various gene-editing tools that could potentially be employed in the future to create mouse models specifically for esophageal cancer research.
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Affiliation(s)
- Reihaneh Alsadat Mahmoudian
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Moein Farshchian
- Division of Oncology, Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Fatemeh Fardi Golyan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvaneh Mahmoudian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Alasti
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Moghimi
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Department of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Hanie Mahaki
- Vascular & Endovascular Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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5
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Cassidy A, Onal M, Pelletier S. Novel methods for the generation of genetically engineered animal models. Bone 2023; 167:116612. [PMID: 36379415 PMCID: PMC9936561 DOI: 10.1016/j.bone.2022.116612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022]
Abstract
Genetically modified mouse models have shaped our understanding of biological systems in both physiological and pathological conditions. For decades, mouse genome engineering has relied on transgenesis and spontaneous gene replacement in embryonic stem (ES) cells. While these technologies provided a wealth of knowledge, they remain imprecise and expensive to use. Recent advances in genome editing technologies such as the development of targetable nucleases, the improvement of delivery systems, and the simplification of targeting strategies now allow for the rapid, precise manipulation of the mouse genome. In this review article, we discuss novel methods and targeting strategies for the generation of mouse models for the study of bone and skeletal muscle biology.
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Affiliation(s)
- Annelise Cassidy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Melda Onal
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Stephane Pelletier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
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6
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Nakayama M. VCre/VloxP and SCre/SloxP as Reliable Site-Specific Recombination Systems for Genome Engineering. Methods Mol Biol 2023; 2637:161-180. [PMID: 36773146 DOI: 10.1007/978-1-0716-3016-7_13] [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: 04/27/2023]
Abstract
The Cre/loxP system is a versatile and powerful tool that has been used to develop many kinds of genetically modified mice, such as conditional knockout mice and mutant protein-expressing mice through the excision of a STOP cassette. However, while numerous in vivo and in vitro applications of the Cre/loxP system have been reported, it remains difficult to target at one time more than one set of recognition sites in an identical single cell in mice using the Cre/loxP system. To overcome this barrier, we developed two novel site-specific recombination systems called VCre/VloxP and SCre/SloxP. These systems allow multiple independent site-specific recombination, for example, multiple targeted deletions in the same cell at different times. In this chapter, I describe the features of VCre/VloxP and SCre/SloxP, practical protocols and tips on how to use them in genomic engineering applications, potential problems in their use, and how problems can be identified and solved.
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Affiliation(s)
- Manabu Nakayama
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.
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7
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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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8
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Phillips S, Ramos PV, Veeraraghavan P, Young SM. VikAD, a Vika site-specific recombinase-based system for efficient and scalable helper-dependent adenovirus production. Mol Ther Methods Clin Dev 2022; 24:117-126. [PMID: 35024378 PMCID: PMC8718833 DOI: 10.1016/j.omtm.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/04/2021] [Indexed: 11/09/2022]
Abstract
Recombinant viral vectors have become integral tools for basic in vivo research applications. Helper-dependent adenoviral (HdAd) vectors have a large packaging capacity of ∼36 kb of DNA that mediate long-term transgene expression in vitro and in vivo. The large carrying capacity of HdAd enables basic research or clinical applications requiring the delivery of large genes or multiple transgenes, which cannot be packaged into other widely used viral vectors. Currently, common HdAd production systems use an Ad helper virus (HV) with a packaging signal (Ψ) that is flanked by either loxP or FRT sites, which is excised in producer cells expressing Cre or Flp recombinases to prevent HV packaging. However, these production systems prevent the use of HdAd vectors for genetic strategies that rely on Cre or Flp recombination for cell-type-specific expression. To overcome these limitations, we developed the VikAD production system, which is based on producer cells expressing the Vika recombinase and an HV that contains a Ψ flanked by vox sites. The availability of this production system will greatly expand the utility and flexibility of HdAd vectors for use in research applications to monitor and manipulate cellular activity with increased specificity.
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Affiliation(s)
- Stacia Phillips
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Paula Valino Ramos
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Priyadharishini Veeraraghavan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Samuel M. Young
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
- Department of Otolaryngology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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9
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Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases. Comput Struct Biotechnol J 2022; 20:989-1001. [PMID: 35242289 PMCID: PMC8860914 DOI: 10.1016/j.csbj.2022.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
New functional regions emerging in evolution of DNA site-specific recombinase tails. Transient structural nucleation promotes function-dispensable regions to essential. Molecular dynamics reveals conformational diversity and its functional implications. Evolved disordered molecular mechanisms of N-term tails for protein stability. Structural disorder-based link between protein evolution, stability and function.
Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structural disorder-to-function relationships need to be deciphered. The DNA site-specific recombinase system Cre/loxP represents an attractive model to investigate functional molecular mechanisms of IDRs. Cre contains a functionally dispensable disordered N-terminal tail, which becomes indispensable in the evolved Tre/loxLTR recombinase system. The difficulty to experimentally obtain structural information about this tail has so far precluded any mechanistic study on its involvement in DNA recombination. Here, we use in vitro and in silico evolution data, conformational dynamics, AI-based folding simulations, thermodynamic stability calculations, mutagenesis and DNA recombination assays to investigate how evolution and the dynamic behavior of this IDR may determine distinct functional properties. Our studies suggest that partial conformational order in the N-terminal tail of Tre recombinase and its packing to a conserved hydrophobic surface on the protein provide thermodynamic stability. Based on our results, we propose a link between protein stability and function, offering new plausible atom-detailed mechanistic insights into disorder-function relationships. Our work highlights the potential of N-terminal tails to be exploited for regulation of the activity of Cre-like tyrosine-type SSRs, which merits future investigations and could be of relevance in future rational engineering for their use in biotechnology and genomic medicine.
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10
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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: 78] [Impact Index Per Article: 26.0] [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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11
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Tian X, Zhou B. Strategies for site-specific recombination with high efficiency and precise spatiotemporal resolution. J Biol Chem 2021; 296:100509. [PMID: 33676891 PMCID: PMC8050033 DOI: 10.1016/j.jbc.2021.100509] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
Site-specific recombinases (SSRs) are invaluable genome engineering tools that have enormously boosted our understanding of gene functions and cell lineage relationships in developmental biology, stem cell biology, regenerative medicine, and multiple diseases. However, the ever-increasing complexity of biomedical research requires the development of novel site-specific genetic recombination technologies that can manipulate genomic DNA with high efficiency and fine spatiotemporal control. Here, we review the latest innovative strategies of the commonly used Cre-loxP recombination system and its combinatorial strategies with other site-specific recombinase systems. We also highlight recent progress with a focus on the new generation of chemical- and light-inducible genetic systems and discuss the merits and limitations of each new and established system. Finally, we provide the future perspectives of combining various recombination systems or improving well-established site-specific genetic tools to achieve more efficient and precise spatiotemporal genetic manipulation.
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Affiliation(s)
- Xueying Tian
- Key Laboratory of Regenerative Medicine of Ministry of Education, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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12
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Fenno LE, Ramakrishnan C, Kim YS, Evans KE, Lo M, Vesuna S, Inoue M, Cheung KYM, Yuen E, Pichamoorthy N, Hong ASO, Deisseroth K. Comprehensive Dual- and Triple-Feature Intersectional Single-Vector Delivery of Diverse Functional Payloads to Cells of Behaving Mammals. Neuron 2020; 107:836-853.e11. [PMID: 32574559 PMCID: PMC7687746 DOI: 10.1016/j.neuron.2020.06.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/29/2020] [Indexed: 01/12/2023]
Abstract
The resolution and dimensionality with which biologists can characterize cell types have expanded dramatically in recent years, and intersectional consideration of such features (e.g., multiple gene expression and anatomical parameters) is increasingly understood to be essential. At the same time, genetically targeted technology for writing in and reading out activity patterns for cells in living organisms has enabled causal investigation in physiology and behavior; however, cell-type-specific delivery of these tools (including microbial opsins for optogenetics and genetically encoded Ca2+ indicators) has thus far fallen short of versatile targeting to cells jointly defined by many individually selected features. Here, we develop a comprehensive intersectional targeting toolbox including 39 novel vectors for joint-feature-targeted delivery of 13 molecular payloads (including opsins, indicators, and fluorophores), systematic approaches for development and optimization of new intersectional tools, hardware for in vivo monitoring of expression dynamics, and the first versatile single-virus tools (Triplesect) that enable targeting of triply defined cell types.
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Affiliation(s)
- Lief E Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Evans
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathy Y M Cheung
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Elle Yuen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Alice S O Hong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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13
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Soni A, Augsburg M, Buchholz F, Pisabarro MT. Nearest-neighbor amino acids of specificity-determining residues influence the activity of engineered Cre-type recombinases. Sci Rep 2020; 10:13985. [PMID: 32814809 PMCID: PMC7438526 DOI: 10.1038/s41598-020-70867-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 08/03/2020] [Indexed: 11/29/2022] Open
Abstract
The tyrosine-type site-specific DNA recombinase Cre recombines its target site, loxP, with high activity and specificity without cross-recombining the target sites of highly related recombinases. Understanding how Cre achieves this precision is key to be able to rationally engineer site-specific recombinases (SSRs) for genome editing applications. Previous work has revealed key residues for target site selectivity in the Cre/loxP and the related Dre/rox recombinase systems. However, enzymes in which these residues were changed to the respective counterpart only showed weak activity on the foreign target site. Here, we use molecular modeling and dynamics simulation techniques to comprehensively explore the mechanisms by which these residues determine target recognition in the context of their flanking regions in the protein-DNA interface, and we establish a structure-based rationale for the design of improved recombination activities. Our theoretical models reveal that nearest-neighbors to the specificity-determining residues are important players for enhancing SSR activity on the foreign target site. Based on the established rationale, we design new Cre variants with improved rox recombination activities, which we validate experimentally. Our work provides new insights into the target recognition mechanisms of Cre-like recombinases and represents an important step towards the rational design of SSRs for applied genome engineering.
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Affiliation(s)
- Anjali Soni
- Structural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307, Dresden, Germany
| | - Martina Augsburg
- University Carl Gustav Carus and Medical Faculty, UCC, Medical Systems Biology, TU Dresden, Fetscherstrasse 74, Dresden, Germany
| | - Frank Buchholz
- University Carl Gustav Carus and Medical Faculty, UCC, Medical Systems Biology, TU Dresden, Fetscherstrasse 74, Dresden, Germany
| | - M Teresa Pisabarro
- Structural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307, Dresden, Germany.
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14
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Serizawa T, Isotani A, Matsumura T, Nakanishi K, Nonaka S, Shibata S, Ikawa M, Okano H. Developmental analyses of mouse embryos and adults using a non-overlapping tracing system for all three germ layers. Development 2019; 146:dev.174938. [PMID: 31597657 DOI: 10.1242/dev.174938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 09/30/2019] [Indexed: 12/24/2022]
Abstract
Genetic lineage-tracing techniques are powerful tools for studying specific cell populations in development and pathogenesis. Previous techniques have mainly involved systems for tracing a single gene, which are limited in their ability to facilitate direct comparisons of the contributions of different cell lineages. We have developed a new combinatorial system for tracing all three germ layers using self-cleaving 2A peptides and multiple site-specific recombinases (SSRs). In the resulting TRiCK (TRiple Coloured germ layer Knock-in) mice, the three germ layers are conditionally and simultaneously labelled with distinct fluorescent proteins via embryogenesis. We show that previously reported ectopic expressions of lineage markers are the outcome of secondary gene expression. The results presented here also indicate that the commitment of caudal axial stem cells to neural or mesodermal fate proceeds without lineage fluctuations, contrary to the notion of their bi-potency. Moreover, we developed IMES, an optimized tissue clearing method that is highly compatible with a variety of fluorescent proteins and immunostaining, and the combined use of TRiCK mice and IMES can facilitate comprehensive analyses of dynamic contributions of all three germ layers.
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Affiliation(s)
- Takashi Serizawa
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ayako Isotani
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.,Organ developmental engineering, Division of Biomedical Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takafumi Matsumura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Katsuyuki Nakanishi
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Shigenori Nonaka
- Spatiotemporal Regulations Group, Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Aichi 444-8585, Japan.,Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shinsuke Shibata
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
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15
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Abstract
Vascular smooth muscle cells (SMC) play a critical role in controlling blood pressure and blood distribution, as well as maintaining the structural integrity of the blood vessel. SMC also participate in physiological and pathological vascular remodeling due to their remarkable ability to dynamically modulate their phenotype. During the past decade, the development of in vivo fate mapping systems for unbiased identification and tracking of SMC and their progeny has led to major discoveries as well as the reevaluation of well-established concepts about the contribution of vascular SMC in major vascular diseases including atherosclerosis. Lineage tracing studies revealed that SMC undergoes multiple phenotypic transitions characterized by the expression of markers of alternative cell types (eg, macrophage-like and mesenchymal-stem cell-like) and populate injured or diseased vessels by oligoclonal expansion of a limited number of medial SMC. With the development of high-throughput transcriptomics and single-cell RNA sequencing (scRNAseq), the field is moving forward towards in-depth SMC phenotypic characterization. Herein, we review the major observations put forth by lineage and clonality tracing studies and the evidence in support for SMC phenotypic diversity in healthy and diseased vascular tissue. We will also discuss the opportunities and remaining challenges of combining lineage tracing and single-cell transcriptomics technologies, as well as studying the functional relevance of SMC phenotypic transitions and identifying the mechanisms controlling them.
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Affiliation(s)
- Mingjun Liu
- From the Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, PA (M.L., D.G.).,Division of Cardiology, University of Pittsburgh School of Medicine, PA (M.L., D.G.)
| | - Delphine Gomez
- From the Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, PA (M.L., D.G.).,Division of Cardiology, University of Pittsburgh School of Medicine, PA (M.L., D.G.)
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16
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Volobueva AS, Orekhov AN, Deykin AV. An update on the tools for creating transgenic animal models of human diseases - focus on atherosclerosis. ACTA ACUST UNITED AC 2019; 52:e8108. [PMID: 31038578 PMCID: PMC6487744 DOI: 10.1590/1414-431x20198108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
Abstract
Animal models of diseases are invaluable tools of modern medicine. More than forty years have passed since the first successful experiments and the spectrum of available models, as well as the list of methods for creating them, have expanded dramatically. The major step forward in creating specific disease models was the development of gene editing techniques, which allowed for targeted modification of the animal's genome. In this review, we discuss the available tools for creating transgenic animal models, such as transgenesis methods, recombinases, and nucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and CRISPR/Cas9 systems. We then focus specifically on the models of atherosclerosis, especially mouse models that greatly contributed to improving our understanding of the disease pathogenesis and we outline their characteristics and limitations.
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Affiliation(s)
- A S Volobueva
- Laboratory of Gene Therapy, Biocad Biotechnology Company, Strelnya, Russia
| | - A N Orekhov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow, Russia.,Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow, Russia
| | - A V Deykin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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17
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A single reporter mouse line for Vika, Flp, Dre, and Cre-recombination. Sci Rep 2018; 8:14453. [PMID: 30262904 PMCID: PMC6160450 DOI: 10.1038/s41598-018-32802-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/13/2018] [Indexed: 11/28/2022] Open
Abstract
Site-specific recombinases (SSR) are utilized as important genome engineering tools to precisely modify the genome of mice and other model organisms. Reporter mice that mark cells that at any given time had expressed the enzyme are frequently used for lineage tracing and to characterize newly generated mice expressing a recombinase from a chosen promoter. With increasing sophistication of genome alteration strategies, the demand for novel SSR systems that efficiently and specifically recombine their targets is rising and several SSR-systems are now used in combination to address complex biological questions in vivo. Generation of reporter mice for each one of these recombinases is cumbersome and increases the number of mouse lines that need to be maintained in animal facilities. Here we present a multi-reporter mouse line for loci-of-recombination (X) (MuX) that streamlines the characterization of mice expressing prominent recombinases. MuX mice constitutively express nuclear green fluorescent protein after recombination by either Cre, Flp, Dre or Vika recombinase, rationalizing the number of animal lines that need to be maintained. We also pioneer the use of the Vika/vox system in mice, illustrating its high efficacy and specificity, thereby facilitating future designs of sophisticated recombinase-based in vivo genome engineering strategies.
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18
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Liu K, Yu W, Tang M, Tang J, Liu X, Liu Q, Li Y, He L, Zhang L, Evans SM, Tian X, Lui KO, Zhou B. A dual genetic tracing system identifies diverse and dynamic origins of cardiac valve mesenchyme. Development 2018; 145:dev.167775. [PMID: 30111655 DOI: 10.1242/dev.167775] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/27/2018] [Indexed: 12/24/2022]
Abstract
In vivo genomic engineering is instrumental for studying developmental biology and regenerative medicine. Development of novel systems with more site-specific recombinases (SSRs) that complement with the commonly used Cre-loxP would be valuable for more precise lineage tracing and genome editing. Here, we introduce a new SSR system via Nigri-nox. By generating tissue-specific Nigri knock-in and its responding nox reporter mice, we show that the Nigri-nox system works efficiently in vivo by targeting specific tissues. As a new orthogonal system to Cre-loxP, Nigri-nox provides an additional control of genetic manipulation. We also demonstrate how the two orthogonal systems Nigri-nox and Cre-loxP could be used simultaneously to map the cell fate of two distinct developmental origins of cardiac valve mesenchyme in the mouse heart, providing dynamics of cellular contribution from different origins for cardiac valve mesenchyme during development. This work provides a proof-of-principle application of the Nigri-nox system for in vivo mouse genomic engineering. Coupled with other SSR systems, Nigri-nox would be valuable for more precise delineation of origins and cell fates during development, diseases and regeneration.
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Affiliation(s)
- Kuo Liu
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Yu
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muxue Tang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Juan Tang
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiuxiu Liu
- The 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
| | - Qiaozhen Liu
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Li
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lingjuan He
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libo Zhang
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sylvia M Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Xueying Tian
- Key Laboratory of Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Kathy O Lui
- Department of Chemical Pathology; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Bin Zhou
- The 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 Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Key Laboratory of Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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19
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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20
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Pu W, He L, Han X, Tian X, Li Y, Zhang H, Liu Q, Huang X, Zhang L, Wang QD, Yu Z, Yang X, Smart N, Zhou B. Genetic Targeting of Organ-Specific Blood Vessels. Circ Res 2018; 123:86-99. [PMID: 29764841 DOI: 10.1161/circresaha.118.312981] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/20/2023]
Abstract
RATIONALE Organs of the body require vascular networks to supply oxygen and nutrients and maintain physiological function. The blood vessels of different organs are structurally and functionally heterogeneous in nature. To more precisely dissect their distinct in vivo function in individual organs, without potential interference from off-site targets, it is necessary to genetically target them in an organ-specific manner. OBJECTIVE The objective of this study was to generate a genetic system that targets vascular endothelial cells in an organ- or tissue-specific manner and to exemplify the potential application of intersectional genetics for precise, target-specific gene manipulation in vivo. METHODS AND RESULTS We took advantage of 2 orthogonal recombination systems, Dre-rox and Cre-loxP, to create a genetic targeting system based on intersectional genetics. Using this approach, Cre activity was only detectable in cells that had expressed both Dre and Cre. Applying this new system, we generated a coronary endothelial cell-specific Cre (CoEC-Cre) and a brain endothelial cell-specific Cre (BEC-Cre). Through lineage tracing, gene knockout and overexpression experiments, we demonstrated that CoEC-Cre and BEC-Cre efficiently and specifically target blood vessels in the heart and brain, respectively. By deletion of vascular endothelial growth factor receptor 2 using BEC-Cre, we showed that vascular endothelial growth factor signaling regulates angiogenesis in the central nervous system and also controls the integrity of the blood-brain barrier. CONCLUSIONS We provide 2 examples to illustrate the use of intersectional genetics for more precise gene targeting in vivo, namely manipulation of genes in blood vessels of the heart and brain. More broadly, this system provides a valuable strategy for tissue-specific gene manipulation that can be widely applied to other fields of biomedical research.
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Affiliation(s)
- Wenjuan Pu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Lingjuan He
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Ximeng Han
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; School of Life Science and Technology, Shanghai Tech University, China (X. Han, H.Z., B.Z.)
| | - Xueying Tian
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Yan Li
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Hui Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; School of Life Science and Technology, Shanghai Tech University, China (X. Han, H.Z., B.Z.)
| | - Qiaozhen Liu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Xiuzhen Huang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Libo Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Qing-Dong Wang
- Bioscience Heart Failure, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden (Q.-D.W.)
| | - Zhenyang Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Laboratory of Proteomics, Institute of Biotechnology, China (Z.Y., X.Y.)
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Laboratory of Proteomics, Institute of Biotechnology, China (Z.Y., X.Y.)
| | - Nicola Smart
- British Heart Foundation Centre of Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom (N.S.)
| | - Bin Zhou
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.) .,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.).,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; School of Life Science and Technology, Shanghai Tech University, China (X. Han, H.Z., B.Z.).,Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China (B.Z.)
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21
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Gengenbacher N, Singhal M, Augustin HG. Preclinical mouse solid tumour models: status quo, challenges and perspectives. Nat Rev Cancer 2017; 17:751-765. [PMID: 29077691 DOI: 10.1038/nrc.2017.92] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oncology research in humans is limited to analytical and observational studies for obvious ethical reasons, with therapy-focused clinical trials being the one exception to this rule. Preclinical mouse tumour models therefore serve as an indispensable intermediate experimental model system bridging more reductionist in vitro research with human studies. Based on a systematic survey of preclinical mouse tumour studies published in eight scientific journals in 2016, this Analysis provides an overview of how contemporary preclinical mouse tumour biology research is pursued. It thereby identifies some of the most important challenges in this field and discusses potential ways in which preclinical mouse tumour models could be improved for better relevance, reproducibility and translatability.
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Affiliation(s)
- Nicolas Gengenbacher
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), 69120 Heidelberg, Germany
| | - Mahak Singhal
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), 69120 Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Hellmut G Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), 69120 Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- German Cancer Consortium, 69120 Heidelberg, Germany
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22
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Meinke G, Karpinski J, Buchholz F, Bohm A. Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA. Nucleic Acids Res 2017; 45:9726-9740. [PMID: 28934476 PMCID: PMC5766204 DOI: 10.1093/nar/gkx603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/06/2017] [Indexed: 01/07/2023] Open
Abstract
As part of the HIV infection cycle, viral DNA inserts into the genome of host cells such that the integrated DNA encoding the viral proteins is flanked by long terminal repeat (LTR) regions from the retrovirus. In an effort to develop novel genome editing techniques that safely excise HIV provirus from cells, Tre, an engineered version of Cre recombinase, was designed to target a 34-bp sequence within the HIV-1 LTR (loxLTR). The sequence targeted by Tre lacks the symmetry present in loxP, the natural DNA substrate for Cre. We report here the crystal structure of a catalytically inactive (Y324F) mutant of this engineered Tre recombinase in complex with the loxLTR DNA substrate. We also report that 17 of the 19 amino acid changes relative to Cre contribute to the altered specificity, even though many of these residues do not contact the DNA directly. We hypothesize that some mutations increase the flexibility of the Cre tetramer and that this, along with flexibility in the DNA, enable the engineered enzyme and DNA substrate to adopt complementary conformations.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Janet Karpinski
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Dresden, 01307 Dresden, Germany,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Andrew Bohm
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA,To whom correspondence should be addressed. Tel: +1 617 636 2994; Fax: +1 617 636 2409;
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23
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Beyond the canonical strategies of horizontal gene transfer in prokaryotes. Curr Opin Microbiol 2017; 38:95-105. [PMID: 28600959 DOI: 10.1016/j.mib.2017.04.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023]
Abstract
Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE. Among those strategies that require MGEs, there is a range of newly reported, hybrid and intermediate MGEs mobilizing only their own DNA, others that mobilize preferentially bacterial DNA, or both. Considering HGT strategies independent of MGE, a few are even not restricted to DNA transfer, but can also mobilize other molecules. This review considers those HGT strategies that are less commonly dealt with in the literature. The real impact of these elements could, in some conditions, be more relevant than previously thought.
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24
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Czapiński J, Kiełbus M, Kałafut J, Kos M, Stepulak A, Rivero-Müller A. How to Train a Cell-Cutting-Edge Molecular Tools. Front Chem 2017; 5:12. [PMID: 28344971 PMCID: PMC5344921 DOI: 10.3389/fchem.2017.00012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/20/2017] [Indexed: 12/28/2022] Open
Abstract
In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.
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Affiliation(s)
- Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Postgraduate School of Molecular Medicine, Medical University of WarsawWarsaw, Poland
| | - Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Michał Kos
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi UniversityTurku, Finland
- Department of Biosciences, Åbo Akademi UniversityTurku, Finland
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25
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Sakurai T, Shindo T, Sato M. Noninheritable Maternal Factors Useful for Genetic Manipulation in Mammals. Results Probl Cell Differ 2017; 63:495-510. [PMID: 28779331 DOI: 10.1007/978-3-319-60855-6_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mammalian early embryogenesis is supported by maternal factors, such as messenger RNA (mRNA) and proteins, produced and accumulated during oogenesis at least up to the stage when zygotic activation commences. These maternal factors are involved in biologically important events such as epigenetic activation, reprogramming, and mitochondrial growth. Most of these maternal mRNAs are degraded by the 2-cell to 4 ~ 8-cell stages. Maternal proteins, which are produced during oogenesis or by the maternal mRNAs, are degraded by the 4 ~ 8-cell stage. In other words, the maternal factors exist during specific stages of early embryogenesis. In this chapter, we will briefly summarize the property of these maternal factors and mention possible applications of these factors for developing new reproduction engineering-related technologies and producing genetically modified animals. More specifically, we will show the usefulness of maternally accumulated Cas9 protein as a promising tool for CRISPR-/Cas9-based simultaneous genetic modification of multiple loci in mammals.
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Affiliation(s)
- Takayuki Sakurai
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan. .,Basic Research Division for Next-Generation Disease Models and Fundamental Technology, Research Center for Next Generation Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
| | - Takayuki Shindo
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.,Basic Research Division for Next-Generation Disease Models and Fundamental Technology, Research Center for Next Generation Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8544, Japan
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