1
|
Liu J, Chen S, Huang G, Wen P, Zhou X, Wu Y. Trisomy 21-driven metabolite alterations are linked to cellular injuries in Down syndrome. Cell Mol Life Sci 2024; 81:112. [PMID: 38433139 PMCID: PMC10909777 DOI: 10.1007/s00018-024-05127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/10/2023] [Accepted: 01/14/2024] [Indexed: 03/05/2024]
Abstract
Down syndrome (DS) arises from a genetic anomaly characterized by an extra copy of chromosome 21 (exCh21). Despite high incidence of congenital diseases among DS patients, direct impacts of exCh21 remain elusive. Here, we established a robust DS model harnessing human-induced pluripotent stem cells (hiPSCs) from mosaic DS patient. These hiPSC lines encompassed both those with standard karyotype and those carrying an extra copy of exCh21, allowing to generate isogenic cell lines with a consistent genetic background. We unraveled that exCh21 inflicted disruption upon the cellular transcriptome, ushering in alterations in metabolic processes and triggering DNA damage. The impact of exCh21 was also manifested in profound modifications in chromatin accessibility patterns. Moreover, we identified two signature metabolites, 5-oxo-ETE and Calcitriol, whose biosynthesis is affected by exCh21. Notably, supplementation with 5-oxo-ETE promoted DNA damage, in stark contrast to the protective effect elicited by Calcitriol against such damage. We also found that exCh21 disrupted cardiogenesis, and that this impairment could be mitigated through supplementation with Calcitriol. Specifically, the deleterious effects of 5-oxo-ETE unfolded in the form of DNA damage induction and the repression of cardiogenesis. On the other hand, Calcitriol emerged as a potent activator of its nuclear receptor VDR, fostering amplified binding to chromatin and subsequent facilitation of gene transcription. Our findings provide a comprehensive understanding of exCh21's metabolic implications within the context of Down syndrome, offering potential avenues for therapeutic interventions for Down syndrome treatment.
Collapse
Affiliation(s)
- Juli Liu
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
| | - Shaoxian Chen
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Guiping Huang
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Pengju Wen
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Xianwu Zhou
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
- Department of Thoracic and Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
| | - Yueheng Wu
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
| |
Collapse
|
2
|
Forrest MP, Penzes P. Mechanisms of copy number variants in neuropsychiatric disorders: From genes to therapeutics. Curr Opin Neurobiol 2023; 82:102750. [PMID: 37515924 PMCID: PMC10529795 DOI: 10.1016/j.conb.2023.102750] [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: 03/12/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 07/31/2023]
Abstract
Copy number variants (CNVs) are genomic imbalances strongly linked to the aetiology of neuropsychiatric disorders such as schizophrenia and autism. By virtue of their large size, CNVs often contain many genes, providing a multi-genic view of disease processes that can be dissected in model systems. Thus, CNV research provides an important stepping stone towards understanding polygenic disease mechanisms, positioned between monogenic and polygenic risk models. In this review, we will outline hypothetical models for gene interactions occurring within CNVs and discuss different approaches used to study rodent and stem cell disease models. We highlight recent work showing that genetic and pharmacological strategies can be used to rescue important aspects of CNV-mediated pathophysiology, which often converges onto synaptic pathways. We propose that using a rescue approach in complete CNV models provides a new path forward for precise mechanistic understanding of complex disorders and a tangible route towards therapeutic development.
Collapse
Affiliation(s)
- Marc P Forrest
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Peter Penzes
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| |
Collapse
|
3
|
Xie D, Gu B, Liu Y, Ye P, Ma Y, Wen T, Song X, Zhao Z. Efficient targeted recombination with CRISPR/Cas9 in hybrids of Caenorhabditis nematodes with suppressed recombination. BMC Biol 2023; 21:203. [PMID: 37775783 PMCID: PMC10542263 DOI: 10.1186/s12915-023-01704-0] [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: 03/27/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Homology-based recombination (HR) is the cornerstone of genetic mapping. However, a lack of sufficient sequence homology or the presence of a genomic rearrangement prevents HR through crossing, which inhibits genetic mapping in relevant genomic regions. This is particularly true in species hybrids whose genomic sequences are highly divergent along with various genome arrangements, making the mapping of genetic loci, such as hybrid incompatibility (HI) loci, through crossing impractical. We previously mapped tens of HI loci between two nematodes, Caenorhabditis briggsae and C. nigoni, through the repeated backcrossing of GFP-linked C. briggsae fragments into C. nigoni. However, the median introgression size was over 7 Mb, indicating apparent HR suppression and preventing the subsequent cloning of the causative gene underlying a given HI phenotype. Therefore, a robust method that permits recombination independent of sequence homology is desperately desired. RESULTS Here, we report a method of highly efficient targeted recombination (TR) induced by CRISPR/Cas9 with dual guide RNAs (gRNAs), which circumvents the HR suppression in hybrids between the two species. We demonstrated that a single gRNA was able to induce efficient TR between highly homologous sequences only in the F1 hybrids but not in the hybrids that carry a GFP-linked C. briggsae fragment in an otherwise C. nigoni background. We achieved highly efficient TR, regardless of sequence homology or genetic background, when dual gRNAs were used that each specifically targeted one parental chromosome. We further showed that dual gRNAs were able to induce efficient TR within genomic regions that had undergone inversion, in which HR-based recombination was expected to be suppressed, supporting the idea that dual-gRNA-induced TR can be achieved through nonhomology-based end joining between two parental chromosomes. CONCLUSIONS Recombination suppression can be circumvented through CRISPR/Cas9 with dual gRNAs, regardless of sequence homology or the genetic background of the species hybrid. This method is expected to be applicable to other situations in which recombination is suppressed in interspecies or intrapopulation hybrids.
Collapse
Affiliation(s)
- Dongying Xie
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Yiqing Liu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Tongshu Wen
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaoyuan Song
- MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.
| |
Collapse
|
4
|
Zheng R, Zhang L, Parvin R, Su L, Chi J, Shi K, Ye F, Huang X. Progress and Perspective of CRISPR-Cas9 Technology in Translational Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300195. [PMID: 37356052 PMCID: PMC10477906 DOI: 10.1002/advs.202300195] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/29/2023] [Indexed: 06/27/2023]
Abstract
Translational medicine aims to improve human health by exploring potential treatment methods developed during basic scientific research and applying them to the treatment of patients in clinical settings. The advanced perceptions of gene functions have remarkably revolutionized clinical treatment strategies for target agents. However, the progress in gene editing therapy has been hindered due to the severe off-target effects and limited editing sites. Fortunately, the development in the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) system has renewed hope for gene therapy field. The CRISPR-Cas9 system can fulfill various simple or complex purposes, including gene knockout, knock-in, activation, interference, base editing, and sequence detection. Accordingly, the CRISPR-Cas9 system is adaptable to translational medicine, which calls for the alteration of genomic sequences. This review aims to present the latest CRISPR-Cas9 technology achievements and prospect to translational medicine advances. The principle and characterization of the CRISPR-Cas9 system are firstly introduced. The authors then focus on recent pre-clinical and clinical research directions, including the construction of disease models, disease-related gene screening and regulation, and disease treatment and diagnosis for multiple refractory diseases. Finally, some clinical challenges including off-target effects, in vivo vectors, and ethical problems, and future perspective are also discussed.
Collapse
Affiliation(s)
- Ruixuan Zheng
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Division of Pulmonary MedicineThe First Affiliated HospitalWenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Wenzhou Key Laboratory of Interdiscipline and Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
| | - Lexiang Zhang
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Wenzhou Key Laboratory of Interdiscipline and Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Oujiang Laboratory (Zhejiang Lab for Regenerative MedicineVision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325000P. R. China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative MedicineVision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325000P. R. China
| | - Lihuang Su
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Division of Pulmonary MedicineThe First Affiliated HospitalWenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Wenzhou Key Laboratory of Interdiscipline and Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
| | - Junjie Chi
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Wenzhou Key Laboratory of Interdiscipline and Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
| | - Keqing Shi
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Wenzhou Key Laboratory of Interdiscipline and Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
| | - Fangfu Ye
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Oujiang Laboratory (Zhejiang Lab for Regenerative MedicineVision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325000P. R. China
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190P. R. China
| | - Xiaoying Huang
- Joint Centre of Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Division of Pulmonary MedicineThe First Affiliated HospitalWenzhou Medical UniversityWenzhouZhejiang325000P. R. China
- Wenzhou Key Laboratory of Interdiscipline and Translational MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325000P. R. China
| |
Collapse
|
5
|
Wang LB, Li ZK, Wang LY, Xu K, Ji TT, Mao YH, Ma SN, Liu T, Tu CF, Zhao Q, Fan XN, Liu C, Wang LY, Shu YJ, Yang N, Zhou Q, Li W. A sustainable mouse karyotype created by programmed chromosome fusion. Science 2022; 377:967-975. [PMID: 36007034 DOI: 10.1126/science.abm1964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chromosome engineering has been attempted successfully in yeast but remains challenging in higher eukaryotes, including mammals. Here, we report programmed chromosome ligation in mice that resulted in the creation of new karyotypes in the lab. Using haploid embryonic stem cells and gene editing, we fused the two largest mouse chromosomes, chromosomes 1 and 2, and two medium-size chromosomes, chromosomes 4 and 5. Chromatin conformation and stem cell differentiation were minimally affected. However, karyotypes carrying fused chromosomes 1 and 2 resulted in arrested mitosis, polyploidization, and embryonic lethality, whereas a smaller fused chromosome composed of chromosomes 4 and 5 was able to be passed on to homozygous offspring. Our results suggest the feasibility of chromosome-level engineering in mammals.
Collapse
Affiliation(s)
- Li-Bin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zhi-Kun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Le-Yun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Kai Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Tian-Tian Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Huan Mao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Si-Nan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Cheng-Fang Tu
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Qian Zhao
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Xu-Ning Fan
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Li-Ying Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - You-Jia Shu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Yang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| |
Collapse
|
6
|
Ansai S, Kitano J. Speciation and adaptation research meets genome editing. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200516. [PMID: 35634923 PMCID: PMC9149800 DOI: 10.1098/rstb.2020.0516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/07/2022] [Indexed: 07/20/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations. We describe examples of their application to demonstrate functional analysis of naturally occurring genetic variations and discuss how these technologies can be applied to speciation and adaptation research. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
Collapse
Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
7
|
Lansing F, Mukhametzyanova L, Rojo-Romanos T, Iwasawa K, Kimura M, Paszkowski-Rogacz M, Karpinski J, Grass T, Sonntag J, Schneider PM, Günes C, Hoersten J, Schmitt LT, Rodriguez-Muela N, Knöfler R, Takebe T, Buchholz F. Correction of a Factor VIII genomic inversion with designer-recombinases. Nat Commun 2022; 13:422. [PMID: 35058465 PMCID: PMC8776779 DOI: 10.1038/s41467-022-28080-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023] Open
Abstract
Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct the 140 kb inversion of the F8 gene frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we develop a coupled heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient-derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, results in 12% correction of the inversion and restores Factor VIII mRNA expression. In this work, we present designer-recombinases as an efficient and specific means towards treatment of monogenic diseases caused by large gene inversions. Correction of disease-causing large genomic inversions remains challenging. Here, the authors developed a dual designer-recombinase system (RecF8) that efficiently corrects a 140 kb inversion frequently found in patients with severe Hemophilia A.
Collapse
|
8
|
Abstract
The identification of large chromosomal rearrangements in cancers has multiplied exponentially over the last decade. These complex and often rare genomic events have traditionally been challenging to study, in part owing to lack of tools that efficiently engineer disease-associated inversions, deletions and translocations in model systems. The emergence and refinement of genome editing technologies, such as CRISPR, have significantly expanded our ability to generate and interrogate chromosomal aberrations to better understand the networks that govern cancer growth. Here we review how existing technologies are employed to faithfully model cancer-associated chromosome rearrangements in the laboratory, with the ultimate goal of developing more accurate pre-clinical models of and therapeutic strategies for cancers driven by these genomic events. Summary: Chromosome rearrangements can be potent cancer drivers and effective therapeutic targets. Here, we review how genome-editing technologies can be exploited to engineer and study complex structural variants, and identify new treatment options.
Collapse
Affiliation(s)
- Salvador Alonso
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
9
|
Stecker IR, Freeman MS, Sitaraman S, Hall CS, Niedbalski PJ, Hendricks AJ, Martin EP, Weaver TE, Cleveland ZI. Preclinical MRI to Quantify Pulmonary Disease Severity and Trajectories in Poorly Characterized Mouse Models: A Pedagogical Example Using Data from Novel Transgenic Models of Lung Fibrosis. JOURNAL OF MAGNETIC RESONANCE OPEN 2021; 6-7. [PMID: 34414381 PMCID: PMC8372031 DOI: 10.1016/j.jmro.2021.100013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Structural remodeling in lung disease is progressive and heterogeneous, making temporally and spatially explicit information necessary to understand disease initiation and progression. While mouse models are essential to elucidate mechanistic pathways underlying disease, the experimental tools commonly available to quantify lung disease burden are typically invasive (e.g., histology). This necessitates large cross-sectional studies with terminal endpoints, which increases experimental complexity and expense. Alternatively, magnetic resonance imaging (MRI) provides information noninvasively, thus permitting robust, repeated-measures statistics. Although lung MRI is challenging due to low tissue density and rapid apparent transverse relaxation (T2* <1 ms), various imaging methods have been proposed to quantify disease burden. However, there are no widely accepted strategies for preclinical lung MRI. As such, it can be difficult for researchers who lack lung imaging expertise to design experimental protocols-particularly for novel mouse models. Here, we build upon prior work from several research groups to describe a widely applicable acquisition and analysis pipeline that can be implemented without prior preclinical pulmonary MRI experience. Our approach utilizes 3D radial ultrashort echo time (UTE) MRI with retrospective gating and lung segmentation is facilitated with a deep-learning algorithm. This pipeline was deployed to assess disease dynamics over 255 days in novel, transgenic mouse models of lung fibrosis based on disease-associated, loss-of-function mutations in Surfactant Protein-C. Previously identified imaging biomarkers (tidal volume, signal coefficient of variation, etc.) were calculated semi-automatically from these data, with an objectively-defined high signal volume identified as the most robust metric. Beyond quantifying disease dynamics, we discuss common pitfalls encountered in preclinical lung MRI and present systematic approaches to identify and mitigate these challenges. While the experimental results and specific pedagogical examples are confined to lung fibrosis, the tools and approaches presented should be broadly useful to quantify structural lung disease in a wide range of mouse models.
Collapse
Affiliation(s)
- Ian R Stecker
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221
- Center for Pulmonary Imaging Research, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Matthew S Freeman
- Center for Pulmonary Imaging Research, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Sneha Sitaraman
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Chase S Hall
- Division of Pulmonary and Critical Care, University of Kansas Medical Center, Kansas City, KS 66160
| | - Peter J Niedbalski
- Center for Pulmonary Imaging Research, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Division of Pulmonary and Critical Care, University of Kansas Medical Center, Kansas City, KS 66160
| | - Alexandra J Hendricks
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221
- Center for Pulmonary Imaging Research, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Emily P Martin
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Timothy E Weaver
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Zackary I Cleveland
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221
- Center for Pulmonary Imaging Research, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221
| |
Collapse
|
10
|
Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
Collapse
Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
11
|
Mapping of Sensory Nerve Subsets within the Vagal Ganglia and the Brainstem Using Reporter Mice for Pirt, TRPV1, 5-HT3, and Tac1 Expression. eNeuro 2020; 7:ENEURO.0494-19.2020. [PMID: 32060036 PMCID: PMC7294455 DOI: 10.1523/eneuro.0494-19.2020] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 11/21/2022] Open
Abstract
Vagal afferent sensory nerves, originating in jugular and nodose ganglia, are composed of functionally distinct subsets whose activation evokes distinct thoracic and abdominal reflex responses. We used Cre-expressing mouse strains to identify specific vagal afferent populations and map their central projections within the brainstem. We show that Pirt is expressed in virtually all vagal afferents; whereas, 5-HT3 is expressed only in nodose neurons, with little expression in jugular neurons. Transient receptor potential vanilloid 1 (TRPV1), the capsaicin receptor, is expressed in a subset of small nodose and jugular neurons. Tac1, the gene for tachykinins, is expressed predominantly in jugular neurons, some of which also express TRPV1. Vagal fibers project centrally to the nucleus tractus solitarius (nTS), paratrigeminal complex, area postrema, and to a limited extent the dorsal motor nucleus of the vagus. nTS subnuclei preferentially receive projections by specific afferent subsets, with TRPV1+ fibers terminating in medial and dorsal regions predominantly caudal of obex, whereas TRPV1− fibers terminate in ventral and lateral regions throughout the rostral–caudal aspect of the medulla. Many vagal Tac1+ afferents (mostly derived from the jugular ganglion) terminate in the nTS. The paratrigeminal complex was the target of multiple vagal afferent subsets. Importantly, lung-specific TRPV1+ and Tac1+ afferent terminations were restricted to the caudal medial nTS, with no innervation of other medulla regions. In summary, this study identifies the specific medulla regions innervated by vagal afferent subsets. The distinct terminations provide a neuroanatomic substrate for the diverse range of reflexes initiated by vagal afferent activation.
Collapse
|
12
|
García-García MJ. A History of Mouse Genetics: From Fancy Mice to Mutations in Every Gene. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:1-38. [PMID: 32304067 DOI: 10.1007/978-981-15-2389-2_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The laboratory mouse has become the model organism of choice in numerous areas of biological and biomedical research, including the study of congenital birth defects. The appeal of mice for these experimental studies stems from the similarities between the physiology, anatomy, and reproduction of these small mammals with our own, but it is also based on a number of practical reasons: mice are easy to maintain in a laboratory environment, are incredibly prolific, and have a relatively short reproductive cycle. Another compelling reason for choosing mice as research subjects is the number of tools and resources that have been developed after more than a century of working with these small rodents in laboratory environments. As will become obvious from the reading of the different chapters in this book, research in mice has already helped uncover many of the genes and processes responsible for congenital birth malformations and human diseases. In this chapter, we will provide an overview of the methods, scientific advances, and serendipitous circumstances that have made these discoveries possible, with a special emphasis on how the use of genetics has propelled scientific progress in mouse research and paved the way for future discoveries.
Collapse
|
13
|
Li J, Li HY, Gu SY, Zi HX, Jiang L, Du JL. One-step generation of zebrafish carrying a conditional knockout-knockin visible switch via CRISPR/Cas9-mediated intron targeting. SCIENCE CHINA. LIFE SCIENCES 2020; 63:59-67. [PMID: 31872378 DOI: 10.1007/s11427-019-1607-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/16/2019] [Indexed: 01/05/2023]
Abstract
The zebrafish has become a popular vertebrate animal model in biomedical research. However, it is still challenging to make conditional gene knockout (CKO) models in zebrafish due to the low efficiency of homologous recombination (HR). Here we report an efficient non-HR-based method for generating zebrafish carrying a CKO and knockin (KI) switch (zCKOIS) coupled with dual-color fluorescent reporters. Using this strategy, we generated hey2zKOIS which served as a hey2 KI reporter with EGFP expression. Upon Cre induction in targeted cells, the hey2zCKOIS was switched to a non-functional CKO allele hey2zCKOIS-invassociated with TagRFP expression, enabling visualization of the CKO alleles. Thus, simplification of the design, and the visibility and combination of both CKO and KI alleles make our zCKOIS strategy an applicable CKO approach for zebrafish.
Collapse
Affiliation(s)
- Jia Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Hong-Yu Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan-Ye Gu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Hua-Xing Zi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China.
| |
Collapse
|
14
|
Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
Collapse
|
15
|
Iwata S, Nakadai H, Fukushi D, Jose M, Nagahara M, Iwamoto T. Simple and large-scale chromosomal engineering of mouse zygotes via in vitro and in vivo electroporation. Sci Rep 2019; 9:14713. [PMID: 31604975 PMCID: PMC6789149 DOI: 10.1038/s41598-019-50900-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/19/2019] [Indexed: 01/25/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has facilitated dramatic progress in the field of genome engineering. Whilst microinjection of the Cas9 protein and a single guide RNA (sgRNA) into mouse zygotes is a widespread method for producing genetically engineered mice, in vitro and in vivo electroporation (which are much more convenient strategies) have recently been developed. However, it remains unknown whether these electroporation methods are able to manipulate genomes at the chromosome level. In the present study, we used these techniques to introduce chromosomal inversions of several megabases (Mb) in length in mouse zygotes. Using in vitro electroporation, we successfully introduced a 7.67 Mb inversion, which is longer than any previously reported inversion produced using microinjection-based methods. Additionally, using in vivo electroporation, we also introduced a long chromosomal inversion by targeting an allele in F1 hybrid mice. To our knowledge, the present study is the first report of target-specific chromosomal inversions in mammalian zygotes using electroporation.
Collapse
Affiliation(s)
- Satoru Iwata
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Japan.
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Japan.
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan.
| | - Hitomi Nakadai
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Japan
| | - Daisuke Fukushi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Mami Jose
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Japan
| | - Miki Nagahara
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Japan
| | - Takashi Iwamoto
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Japan
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Japan
| |
Collapse
|
16
|
Abstract
Large-scale sequencing of human tumours has uncovered a vast array of genomic alterations. Genetically engineered mouse models recapitulate many features of human cancer and have been instrumental in assigning biological meaning to specific cancer-associated alterations. However, their time, cost and labour-intensive nature limits their broad utility; thus, the functional importance of the majority of genomic aberrations in cancer remains unknown. Recent advances have accelerated the functional interrogation of cancer-associated alterations within in vivo models. Specifically, the past few years have seen the emergence of CRISPR-Cas9-based strategies to rapidly generate increasingly complex somatic alterations and the development of multiplexed and quantitative approaches to ascertain gene function in vivo.
Collapse
|
17
|
Rehmani T, Salih M, Tuana BS. Cardiac-Specific Cre Induces Age-Dependent Dilated Cardiomyopathy (DCM) in Mice. Molecules 2019; 24:molecules24061189. [PMID: 30917606 PMCID: PMC6471127 DOI: 10.3390/molecules24061189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 11/16/2022] Open
Abstract
The genetic modification of the mouse genome using the cre-lox system has been an invaluable tool in deciphering gene and protein function in a temporal and/or spatial manner. However, it has its pitfalls, as researchers have shown that the unregulated expression of cre recombinase can cause DNA damage, the consequences of which can be very detrimental to mouse health. Previously published literature on the most utilized cardiac-specific cre, αMHC-cre, mouse model exhibited a nonlethal hypertrophic cardiomyopathy (HCM) with aging. However, using the same αMHC-cre mice, we observed a cardiac pathology, resulting in complete lethality by 11 months of age. Echocardiography and histology revealed that the αMHC-cre mice were displaying symptoms of dilated cardiomyopathy (DCM) by seven months of age, which ultimately led to their demise in the absence of any HCM at any age. Molecular analysis showed that this phenotype was associated with the DNA damage response through the downregulation of activated p38 and increased expression of JNK, p53, and Bax, known inducers of myocyte death resulting in fibrosis. Our data urges strong caution when interpreting the phenotypic impact of gene responses using αMHC-cre mice, since a lethal DCM was induced by the cre driver in an age-dependent manner in this commonly utilized model system.
Collapse
Affiliation(s)
- Taha Rehmani
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Maysoon Salih
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Balwant S Tuana
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| |
Collapse
|
18
|
Shou J, Li J, Liu Y, Wu Q. Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion. Mol Cell 2018; 71:498-509.e4. [PMID: 30033371 DOI: 10.1016/j.molcel.2018.06.021] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/22/2018] [Accepted: 06/13/2018] [Indexed: 01/21/2023]
Abstract
Chromosomal rearrangements including large DNA-fragment inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate genome structural variations and developmental gene regulation, but little is known about the underlying mechanisms. Here, we report that disrupting CtIP or FANCD2, which have roles in alternative non-homologous end joining, enhances precise DNA-fragment deletion. By analyzing the inserted nucleotides at the junctions of DNA-fragment editing of deletions, inversions, and duplications and characterizing the cleaved products, we find that Cas9 endonucleolytically cleaves the noncomplementary strand with a flexible scissile profile upstream of the -3 position of the PAM site in vivo and in vitro, generating double-strand break ends with 5' overhangs of 1-3 nucleotides. Moreover, we find that engineered Cas9 nucleases have distinct cleavage profiles. Finally, Cas9-mediated nucleotide insertions are nonrandom and are equal to the combined sequences upstream of both PAM sites with predicted frequencies. Thus, precise and predictable DNA-fragment editing could be achieved by perturbing DNA repair genes and using appropriate PAM configurations.
Collapse
Affiliation(s)
- Jia Shou
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Jinhuan Li
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Yingbin Liu
- Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Qiang Wu
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China.
| |
Collapse
|
19
|
Chen X, Liao S, Huang X, Xu T, Feng X, Guang S. Targeted Chromosomal Rearrangements via Combinatorial Use of CRISPR/Cas9 and Cre/ LoxP Technologies in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2018; 8:2697-2707. [PMID: 29950430 PMCID: PMC6071600 DOI: 10.1534/g3.118.200473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/18/2018] [Indexed: 11/18/2022]
Abstract
Rearranged chromosomes have been applied to construct genetic balancers to manipulate essential genes in C. elegans Although much effort has been put into constructing balancer chromosomes, approximately 6% (map units) of the C. elegans genome has not been covered, and this area lies mostly in pairing centers (PCs). Here, we developed a method for conditional chromosomal engineering through combinatorial use of the CRISPR/Cas9 and Cre/LoxP technologies. Functional DNA fragments containing LoxP sequences were inserted into designated genomic loci using a modified counterselection (cs)-CRISPR method. Then, heat-shock-induced Cre recombinase induced an inversion of the chromosomal region between the two LoxP sites. The chromosomal inversions were subsequently detected by the appearance of pharyngeal GFP. Through this method, we have successfully generated several chromosomal inversion lines, providing valuable resources for studying essential genes in pairing centers.
Collapse
Affiliation(s)
- Xiangyang Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shimiao Liao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xinya Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Ting Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, P.R. China
| |
Collapse
|
20
|
Herault Y, Delabar JM, Fisher EMC, Tybulewicz VLJ, Yu E, Brault V. Rodent models in Down syndrome research: impact and future opportunities. Dis Model Mech 2018; 10:1165-1186. [PMID: 28993310 PMCID: PMC5665454 DOI: 10.1242/dmm.029728] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Down syndrome is caused by trisomy of chromosome 21. To date, a multiplicity of mouse models with Down-syndrome-related features has been developed to understand this complex human chromosomal disorder. These mouse models have been important for determining genotype-phenotype relationships and identification of dosage-sensitive genes involved in the pathophysiology of the condition, and in exploring the impact of the additional chromosome on the whole genome. Mouse models of Down syndrome have also been used to test therapeutic strategies. Here, we provide an overview of research in the last 15 years dedicated to the development and application of rodent models for Down syndrome. We also speculate on possible and probable future directions of research in this fast-moving field. As our understanding of the syndrome improves and genome engineering technologies evolve, it is necessary to coordinate efforts to make all Down syndrome models available to the community, to test therapeutics in models that replicate the whole trisomy and design new animal models to promote further discovery of potential therapeutic targets. Summary: Mouse models have boosted therapeutic options for Down syndrome, and improved models are being developed to better understand the pathophysiology of this genetic condition.
Collapse
Affiliation(s)
- Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris
| | - Jean M Delabar
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, 75205 Paris, France.,INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et la Moelle épinière, ICM, 75013 Paris, France.,Brain and Spine Institute (ICM) CNRS UMR7225, INSERM UMRS 975, 75013 Paris, France
| | - Elizabeth M C Fisher
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, WC1N 3BG, UK.,LonDownS Consortium, London, W1T 7NF UK
| | - Victor L J Tybulewicz
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,LonDownS Consortium, London, W1T 7NF UK.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Eugene Yu
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.,Department of Cellular and Molecular Biology, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
| | - Veronique Brault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| |
Collapse
|
21
|
Buchman AB, Ivy T, Marshall JM, Akbari OS, Hay BA. Engineered Reciprocal Chromosome Translocations Drive High Threshold, Reversible Population Replacement in Drosophila. ACS Synth Biol 2018. [PMID: 29608276 DOI: 10.1101/088393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions using gene drive provides a self-perpetuating method of disease prevention. Mechanisms that require the gene drive element and linked cargo to exceed a high threshold frequency in order for spread to occur are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminated by reintroducing wildtypes into the population so as to drive the frequency of transgenes below the threshold frequency required for drive. Reciprocal chromosome translocations were proposed as a tool for bringing about high threshold population replacement in 1940 and 1968. However, translocations able to achieve this goal have only been reported once, in the spider mite Tetranychus urticae, a haplo-diploid species in which there is strong selection in haploid males for fit homozygotes. We report the creation of engineered translocation-bearing strains of Drosophila melanogaster, generated through targeted chromosomal breakage and homologous recombination. These strains drive high threshold population replacement in laboratory populations. While it remains to be shown that engineered translocations can bring about population replacement in wild populations, these observations suggest that further exploration of engineered translocations as a tool for controlled population replacement is warranted.
Collapse
Affiliation(s)
- Anna B Buchman
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Tobin Ivy
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - John M Marshall
- School of Public Health , University of California , Berkeley , California 94720 , United States
| | - Omar S Akbari
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Bruce A Hay
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| |
Collapse
|
22
|
Buchman AB, Ivy T, Marshall JM, Akbari OS, Hay BA. Engineered Reciprocal Chromosome Translocations Drive High Threshold, Reversible Population Replacement in Drosophila. ACS Synth Biol 2018; 7:1359-1370. [PMID: 29608276 DOI: 10.1021/acssynbio.7b00451] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions using gene drive provides a self-perpetuating method of disease prevention. Mechanisms that require the gene drive element and linked cargo to exceed a high threshold frequency in order for spread to occur are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminated by reintroducing wildtypes into the population so as to drive the frequency of transgenes below the threshold frequency required for drive. Reciprocal chromosome translocations were proposed as a tool for bringing about high threshold population replacement in 1940 and 1968. However, translocations able to achieve this goal have only been reported once, in the spider mite Tetranychus urticae, a haplo-diploid species in which there is strong selection in haploid males for fit homozygotes. We report the creation of engineered translocation-bearing strains of Drosophila melanogaster, generated through targeted chromosomal breakage and homologous recombination. These strains drive high threshold population replacement in laboratory populations. While it remains to be shown that engineered translocations can bring about population replacement in wild populations, these observations suggest that further exploration of engineered translocations as a tool for controlled population replacement is warranted.
Collapse
Affiliation(s)
- Anna B Buchman
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Tobin Ivy
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - John M Marshall
- School of Public Health , University of California , Berkeley , California 94720 , United States
| | - Omar S Akbari
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Bruce A Hay
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| |
Collapse
|
23
|
Li L, Zhang QY, Ding X. A CYP2B6-humanized mouse model and its potential applications. Drug Metab Pharmacokinet 2018; 33:2-8. [PMID: 29402634 DOI: 10.1016/j.dmpk.2018.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/21/2017] [Accepted: 12/12/2017] [Indexed: 01/03/2023]
Abstract
CYP2B6 is a human microsomal cytochrome P450 enzyme with broad substrate selectivity. CYP2B6 is the only functional member of the human CYP2B gene subfamily, which differs from the situation in rodents, such as mouse, where multiple functional Cyp2b genes are expressed. Recent studies with Cyp2b knockout or knockdown mouse models have yielded insights into the in vivo roles of mouse CYP2B enzymes in drug disposition and xenobiotic toxicity. A CYP2B6-humanized mouse model (CYP2A13/2B6/2F1-transgenic/Cyp2abfgs-null), which expresses human CYP2B6 in the liver, and human CYP2A13 and CYP2F1 in the respiratory tract, but not any of the mouse Cyp2b genes, has also been established. In the CYP2B6-humanized mouse, the CYP2B6 transgene is expressed primarily in the liver, where it was found to be active toward prototype CYP2B6 substrate drugs. The regulatory elements of the CYP2B6 transgene appear to be compatible with mouse nuclear receptors that mediate CYP2B induction. Therefore, the CYP2B6-humanized mouse is a valuable animal model for studying the impact of CYP2B6 expression or induction on drug metabolism, drug efficacy, drug-drug interaction, and drug/xenobiotic toxicity. In this mini-review, we provide a brief background on CYP2B6 and the Cyp2b-knockout and CYP2B6-humanized mice, and discuss the potential applications and limitations of the current models.
Collapse
Affiliation(s)
- Lei Li
- Wadsworth Center, New York State Department of Health, School of Public Health, State University of New York at Albany, NY, 12201, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Xinxin Ding
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
| |
Collapse
|
24
|
Connolly LR, Erlendson AA, Fargo CM, Jackson KK, Pelker MMG, Mazzola JW, Geisler MS, Freitag M. Application of the Cre/lox System to Construct Auxotrophic Markers for Quantitative Genetic Analyses in Fusarium graminearum. Methods Mol Biol 2018; 1848:235-263. [PMID: 30182239 DOI: 10.1007/978-1-4939-8724-5_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The bacteriophage P1 Cre/lox system has been utilized in diverse fungi for marker recycling and exchange, generation of targeted chromosome translocations, and targeted deletion of interstitial chromosome segments. Here we show the application of this tool in the wheat and maize pathogen, Fusarium graminearum. We explored three different ways to introduce Cre into strains with floxed genes, namely transformation with an episomal or integrative plasmid (pLC28), fusion of protoplasts of strains carrying floxed genes with strains expressing Cre by forcing heterokaryons, and crosses between strains with floxed genes and strains expressing Cre to isolate progeny in which the target genes had been deleted during the cross. We used this system for the construction of strains bearing auxotrophic markers that were generated by gene replacement with positively selectable markers followed by Cre-mediated marker excision. In addition, updated protocols for transformation and crosses for F. graminearum are provided. In combination, strains and tools developed here add to the arsenal of methods that can be used to carry out molecular genetics with F. graminearum.
Collapse
Affiliation(s)
- Lanelle R Connolly
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Corinne M Fargo
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Kendra K Jackson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Morgan M G Pelker
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Jacob W Mazzola
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Mark S Geisler
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
| |
Collapse
|
25
|
Site-specific chromosomal gene insertion: Flp recombinase versus Cas9 nuclease. Sci Rep 2017; 7:17771. [PMID: 29259215 PMCID: PMC5736728 DOI: 10.1038/s41598-017-17651-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/24/2017] [Indexed: 12/16/2022] Open
Abstract
Site-specific recombination systems like those based on the Flp recombinase proved themselves as efficient tools for cell line engineering. The recent emergence of designer nucleases, especially RNA guided endonucleases like Cas9, has considerably broadened the available toolbox for applications like targeted transgene insertions. Here we established a recombinase-mediated cassette exchange (RMCE) protocol for the fast and effective, drug-free isolation of recombinant cells. Distinct fluorescent protein patterns identified the recombination status of individual cells. In derivatives of a CHO master cell line the expression of the introduced transgene of interest could be dramatically increased almost 20-fold by subsequent deletion of the fluorescent protein gene that provided the initial isolation principle. The same master cell line was employed in a comparative analysis using CRISPR/Cas9 for transgene integration in identical loci. Even though the overall targeting efficacy was comparable, multi-loci targeting was considerably more effective for Cas9-mediated transgene insertion when compared to RMCE. While Cas9 is inherently more flexible, our results also alert to the risk of aberrant recombination events around the cut site. Together, this study points at the individual strengths in performance of both systems and provides guidance for their appropriate use.
Collapse
|
26
|
Revealing hidden complexities of genomic rearrangements generated with Cas9. Sci Rep 2017; 7:12867. [PMID: 28993641 PMCID: PMC5634419 DOI: 10.1038/s41598-017-12740-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/18/2017] [Indexed: 12/26/2022] Open
Abstract
Modelling human diseases caused by large genomic rearrangements has become more accessible since the utilization of CRISPR/Cas9 in mammalian systems. In a previous study, we showed that genomic rearrangements of up to one million base pairs can be generated by direct injection of CRISPR/Cas9 reagents into mouse zygotes. Although these rearrangements are ascertained by junction PCR, we describe here a variety of unanticipated structural changes often involving reintegration of the region demarcated by the gRNAs in the vicinity of the edited locus. We illustrate here some of this diversity detected by high-resolution fibre-FISH and conclude that extensive molecular analysis is required to fully understand the structure of engineered chromosomes generated by Cas9.
Collapse
|
27
|
Chen WV, Nwakeze CL, Denny CA, O'Keeffe S, Rieger MA, Mountoufaris G, Kirner A, Dougherty JD, Hen R, Wu Q, Maniatis T. Pcdhαc2 is required for axonal tiling and assembly of serotonergic circuitries in mice. Science 2017; 356:406-411. [PMID: 28450636 PMCID: PMC5529183 DOI: 10.1126/science.aal3231] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/21/2017] [Indexed: 12/19/2022]
Abstract
Serotonergic neurons project their axons pervasively throughout the brain and innervate various target fields in a space-filling manner, leading to tiled arrangements of their axon terminals to allow optimal allocation of serotonin among target neurons. Here we show that conditional deletion of the mouse protocadherin α (Pcdhα) gene cluster in serotonergic neurons disrupts local axonal tiling and global assembly of serotonergic circuitries and results in depression-like behaviors. Genetic dissection and expression profiling revealed that this role is specifically mediated by Pcdhαc2, which is the only Pcdhα isoform expressed in serotonergic neurons. We conclude that, in contrast to neurite self-avoidance, which requires single-cell identity mediated by Pcdh diversity, a single cell-type identity mediated by the common C-type Pcdh isoform is required for axonal tiling and assembly of serotonergic circuitries.
Collapse
Affiliation(s)
- Weisheng V Chen
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Chiamaka L Nwakeze
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Christine A Denny
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Integrative Neuroscience, Research Foundation for Mental Hygiene, New York, NY 10032, USA
| | - Sean O'Keeffe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Michael A Rieger
- Departments of Genetics and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - George Mountoufaris
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Amy Kirner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Joseph D Dougherty
- Departments of Genetics and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - René Hen
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Integrative Neuroscience, Research Foundation for Mental Hygiene, New York, NY 10032, USA
- Departments of Neuroscience and Pharmacology, Columbia University, New York, NY 10032, USA
| | - Qiang Wu
- Center for Comparative Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| |
Collapse
|
28
|
Jung CJ, Zhang J, Trenchard E, Lloyd KC, West DB, Rosen B, de Jong PJ. Efficient gene targeting in mouse zygotes mediated by CRISPR/Cas9-protein. Transgenic Res 2017; 26:263-277. [PMID: 27905063 PMCID: PMC5350237 DOI: 10.1007/s11248-016-9998-5] [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: 06/17/2016] [Accepted: 11/10/2016] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has rapidly advanced targeted genome editing technologies. However, its efficiency in targeting with constructs in mouse zygotes via homology directed repair (HDR) remains low. Here, we systematically explored optimal parameters for targeting constructs in mouse zygotes via HDR using mouse embryonic stem cells as a model system. We characterized several parameters, including single guide RNA cleavage activity and the length and symmetry of homology arms in the construct, and we compared the targeting efficiency between Cas9, Cas9nickase, and dCas9-FokI. We then applied the optimized conditions to zygotes, delivering Cas9 as either mRNA or protein. We found that Cas9 nucleo-protein complex promotes highly efficient, multiplexed targeting of circular constructs containing reporter genes and floxed exons. This approach allows for a one-step zygote injection procedure targeting multiple genes to generate conditional alleles via homologous recombination, and simultaneous knockout of corresponding genes in non-targeted alleles via non-homologous end joining.
Collapse
Affiliation(s)
- Chris J Jung
- University of California, San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
| | - Junli Zhang
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | | | - Kent C Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - David B West
- University of California, San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
| | - Barry Rosen
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Pieter J de Jong
- University of California, San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| |
Collapse
|
29
|
Su D, Wang M, Ye C, Fang J, Duan Y, Zhang Z, Hua Q, Shi C, Zhang L, Zhang R, Xie X. One-step generation of mice carrying a conditional allele together with an HA-tag insertion for the delta opioid receptor. Sci Rep 2017; 7:44476. [PMID: 28300205 PMCID: PMC5353682 DOI: 10.1038/srep44476] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/09/2017] [Indexed: 12/11/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are important modulators of many physiological functions and excellent drug targets for many diseases. However, to study the functions of endogenous GPCRs is still a challenging task, partially due to the low expression level of GPCRs and the lack of highly potent and selective GPCR antibodies. Overexpression or knock-in of tagged GPCRs, or knockout of specific GPCRs in mice, are common strategies used to study the in vivo functions of these receptors. However, generating separate mice carrying tagged GPCRs or conditional alleles for GPCRs is labor intensive, and requires additional breeding costs. Here we report the generation of mice carrying an HA-tagged DOR (delta opioid receptor) flanked by LoxP sequences at the endogenous DOR locus using a single recombination step, aided by the TALEN system. These animals can be used directly to study the expression, localization, protein-protein interaction and signal transduction of endogenous DOR using anti-HA antibodies. By crossing with mice expressing tissue-specific Cre, these mice can also generate offspring with DOR knockout within specific tissues. These mice are powerful tools to study the in vivo functions of DOR. Furthermore, the gene modification strategy could also be used to study the functions of many other GPCRs.
Collapse
Affiliation(s)
- Dongru Su
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Min Wang
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenli Ye
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiahui Fang
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhui Duan
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhenghong Zhang
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qiuhong Hua
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Changjie Shi
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lihong Zhang
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ru Zhang
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xin Xie
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
30
|
Klar AJS. Split hand/foot malformation genetics supports the chromosome 7 copy segregation mechanism for human limb development. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150415. [PMID: 27821526 PMCID: PMC5104513 DOI: 10.1098/rstb.2015.0415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/17/2022] Open
Abstract
Genetic aberrations of several unlinked loci cause human congenital split hand/foot malformation (SHFM) development. Mutations of the DLX5 (distal-less) transcription factor-encoding gene in chromosome 7 cause SHFM through haploinsufficiency, but the vast majority of cases result from heterozygous chromosomal aberrations of the region without mutating the DLX5 gene. To resolve this paradox, we invoke a chromosomal epigenetic mechanism for limb development. It is composed of a monochromatid gene expression phenomenon that we discovered in two fission yeasts with the selective chromosome copy segregation phenomenon that we discovered in mouse cells. Accordingly, one daughter cell inherits both expressed DLX5 copies while the other daughter inherits both epigenetically silenced ones from a single deterministic cell of the developing limb. Thus, differentiated daughter cells after further proliferation will correspondingly produce proximal/distal-limb tissues. Published results of a Chr. 7 translocation with a centromere-proximal breakpoint situated over 41 million bases away from the DLX locus, centromeric and DLX5-region inversions have satisfied key genetic and developmental biology predictions of the mechanism. Further genetic tests of the mechanism are proposed. We propose that the DNA double helical structure itself causes the development of sister cells' gene regulation asymmetry. We also argue against the conventionally invoked morphogen model of development.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.
Collapse
Affiliation(s)
- Amar J S Klar
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Building 539, Room 154, Frederick, MD 21702-1201, USA
| |
Collapse
|
31
|
Chen X, Feng X, Guang S. Targeted genome engineering in Caenorhabditis elegans. Cell Biosci 2016; 6:60. [PMID: 27980716 PMCID: PMC5146831 DOI: 10.1186/s13578-016-0125-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
The generation of mutants and transgenes are indispensible for biomedical research. In the nematode Caenorhabditis elegans, a series of methods have been developed to introduce genome modifications, including random mutagenesis by chemical reagents, ionizing radiation and transposon insertion. In addition, foreign DNA can be integrated into the genome through microparticle bombardment approach or by irradiation of animals carrying microinjected extrachromosomal arrays. Recent research has revolutionized the genome engineering technologies by using customized DNA nucleases to manipulate particular genes and genomic sequences. Many streamlined editing strategies are developed to simplify the experimental procedure and minimize the cost. In this review, we will summarize the recent progress of the site-specific genome editing methods in C. elegans, including the Cre/LoxP, FLP/FRT, MosTIC system, zinc-finger nucleases (ZFNs), transcriptional activator-like nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease. Particularly, the recent studies of CRISPR/Cas9-mediated genome editing method in C. elegans will be emphatically discussed.
Collapse
Affiliation(s)
- Xiangyang Chen
- School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China
| | - Xuezhu Feng
- School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China
| | - Shouhong Guang
- School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China
| |
Collapse
|
32
|
Xing Z, Li Y, Pao A, Bennett AS, Tycko B, Mobley WC, Yu YE. Mouse-based genetic modeling and analysis of Down syndrome. Br Med Bull 2016; 120:111-122. [PMID: 27789459 PMCID: PMC5146682 DOI: 10.1093/bmb/ldw040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/07/2016] [Accepted: 10/03/2016] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Down syndrome (DS), caused by human trisomy 21 (Ts21), can be considered as a prototypical model for understanding the effects of chromosomal aneuploidies in other diseases. Human chromosome 21 (Hsa21) is syntenically conserved with three regions in the mouse genome. SOURCES OF DATA A review of recent advances in genetic modeling and analysis of DS. Using Cre/loxP-mediated chromosome engineering, a substantial number of new mouse models of DS have recently been generated, which facilitates better understanding of disease mechanisms in DS. AREAS OF AGREEMENT Based on evolutionary conservation, Ts21 can be modeled by engineered triplication of Hsa21 syntenic regions in mice. The validity of the models is supported by the exhibition of DS-related phenotypes. AREAS OF CONTROVERSY Although substantial progress has been made, it remains a challenge to unravel the relative importance of specific candidate genes and molecular mechanisms underlying the various clinical phenotypes. GROWING POINTS Further understanding of mechanisms based on data from mouse models, in parallel with human studies, may lead to novel therapies for clinical manifestations of Ts21 and insights to the roles of aneuploidies in other developmental disorders and cancers.
Collapse
Affiliation(s)
- Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yichen Li
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Abigail S Bennett
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - William C Mobley
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA .,Cellular and Molecular Biology Program, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
| |
Collapse
|
33
|
Rutkowski TP, Schroeder JP, Gafford GM, Warren ST, Weinshenker D, Caspary T, Mulle JG. Unraveling the genetic architecture of copy number variants associated with schizophrenia and other neuropsychiatric disorders. J Neurosci Res 2016; 95:1144-1160. [PMID: 27859486 DOI: 10.1002/jnr.23970] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
Recent studies show that the complex genetic architecture of schizophrenia (SZ) is driven in part by polygenic components, or the cumulative effect of variants of small effect in many genes, as well as rare single-locus variants with large effect sizes. Here we discuss genetic aberrations known as copy number variants (CNVs), which fall in the latter category and are associated with a high risk for SZ and other neuropsychiatric disorders. We briefly review recurrent CNVs associated with SZ, and then highlight one CNV in particular, a recurrent 1.6-Mb deletion on chromosome 3q29, which is estimated to confer a 40-fold increased risk for SZ. Additionally, we describe the use of genetic mouse models, behavioral tools, and patient-derived induced pluripotent stem cells as a means to study CNVs in the hope of gaining mechanistic insight into their respective disorders. Taken together, the genomic data connecting CNVs with a multitude of human neuropsychiatric disease, our current technical ability to model such chromosomal anomalies in mouse, and the existence of precise behavioral measures of endophenotypes argue that the time is ripe for systematic dissection of the genetic mechanisms underlying such disease. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Timothy P Rutkowski
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jason P Schroeder
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Georgette M Gafford
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| |
Collapse
|
34
|
Maddalo D, Ventura A. Somatic Engineering of Oncogenic Chromosomal Rearrangements: A Perspective. Cancer Res 2016; 76:4918-23. [PMID: 27520450 DOI: 10.1158/0008-5472.can-16-0726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/05/2016] [Indexed: 11/16/2022]
Abstract
The ability to engineer specific mutations in mice has proven essential to advancing our understanding of the molecular basis of cancer. Chromosomal rearrangements, a common and clinically relevant class of cancer-causing mutations, have however remained difficult to faithfully recapitulate in vivo The development of genetic tools for in vivo somatic genome editing has recently overcome this limitation and led to the generation of more sophisticated and accurate preclinical models of human cancers. Here, we review the potential applications of these new technologies to the study of tumor biology and discuss their advantages over more conventional strategies, their limitations, and the remaining challenges. Cancer Res; 76(17); 4918-23. ©2016 AACR.
Collapse
Affiliation(s)
- Danilo Maddalo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
35
|
Intron-based genomic editing: a highly efficient method for generating knockin zebrafish. Oncotarget 2016; 6:17891-4. [PMID: 26143640 PMCID: PMC4627223 DOI: 10.18632/oncotarget.4547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 06/06/2015] [Indexed: 01/17/2023] Open
Abstract
The TALEN and CRISPR/Cas9 nuclease systems have been extensively utilized in genomic engineering of model organisms. In zebrafish, the nuclease systems have been successfully applied in generating loss-of–function knockout lines. However, genome-specific knockin techniques in zebrafish are still at the beginning. In this perspective, we briefly summarize the recent progresses on knockin approaches in zebrafish with a special focus on the newly developed intron-based knockin method.
Collapse
|
36
|
Meek S, Thomson AJ, Sutherland L, Sharp MGF, Thomson J, Bishop V, Meddle SL, Gloaguen Y, Weidt S, Singh-Dolt K, Buehr M, Brown HK, Gill AC, Burdon T. Reduced levels of dopamine and altered metabolism in brains of HPRT knock-out rats: a new rodent model of Lesch-Nyhan Disease. Sci Rep 2016; 6:25592. [PMID: 27185277 PMCID: PMC4869022 DOI: 10.1038/srep25592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/19/2016] [Indexed: 02/07/2023] Open
Abstract
Lesch-Nyhan disease (LND) is a severe neurological disorder caused by loss-of-function mutations in the gene encoding hypoxanthine phosphoribosyltransferase (HPRT), an enzyme required for efficient recycling of purine nucleotides. Although this biochemical defect reconfigures purine metabolism and leads to elevated levels of the breakdown product urea, it remains unclear exactly how loss of HPRT activity disrupts brain function. As the rat is the preferred rodent experimental model for studying neurobiology and diseases of the brain, we used genetically-modified embryonic stem cells to generate an HPRT knock-out rat. Male HPRT-deficient rats were viable, fertile and displayed normal caged behaviour. However, metabolomic analysis revealed changes in brain biochemistry consistent with disruption of purine recycling and nucleotide metabolism. Broader changes in brain biochemistry were also indicated by increased levels of the core metabolite citrate and reduced levels of lipids and fatty acids. Targeted MS/MS analysis identified reduced levels of dopamine in the brains of HPRT-deficient animals, consistent with deficits noted previously in human LND patients and HPRT knock-out mice. The HPRT-deficient rat therefore provides a new experimental platform for future investigation of how HPRT activity and disruption of purine metabolism affects neural function and behaviour.
Collapse
Affiliation(s)
- Stephen Meek
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Alison J. Thomson
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Linda Sutherland
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Matthew G. F. Sharp
- Central Bioresearch Services, University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland
| | - Julie Thomson
- Central Bioresearch Services, University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland
| | - Valerie Bishop
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Simone L. Meddle
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Yoann Gloaguen
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Campus, Bearsden, G61 1QH, Scotland
| | - Stefan Weidt
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Campus, Bearsden, G61 1QH, Scotland
| | - Karamjit Singh-Dolt
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Mia Buehr
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Helen K. Brown
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Andrew C. Gill
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland,
| | - Tom Burdon
- The Roslin Institute and R(D)VS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland,
| |
Collapse
|
37
|
Mariscal AM, González-González L, Querol E, Piñol J. All-in-one construct for genome engineering using Cre-lox technology. DNA Res 2016; 23:263-70. [PMID: 27084897 PMCID: PMC4909314 DOI: 10.1093/dnares/dsw015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/02/2016] [Indexed: 12/25/2022] Open
Abstract
Mycoplasma genitalium is an appealing model of a minimal cell and synthetic biology study, and it was one of the first organisms whose genome was fully sequenced and chemically synthesized. Despite its usefulness as a model organism, many genetic tools well established for other microorganisms are not currently available in mycoplasmas. We have developed several vectors to adapt the Cre-lox technology for genome engineering in M. genitalium, providing an all-in-one construct that could be also useful to obtain unmarked genetic modifications in many other slow growing microorganisms. This construct contains a modified promoter sequence based in TetR system that exhibits an enhanced control on Cre recombinase expression, virtually abolishing the presence of this recombinase in the absence of inducer. This allows to introduce the Cre recombinase gene and the desired genetic modification in a single transformation step. In addition, this inducible promoter may be a very promising tool for a wide range of molecular applications.
Collapse
Affiliation(s)
- Ana M Mariscal
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 0819, Spain
| | - Luis González-González
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 0819, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 0819, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 0819, Spain
| |
Collapse
|
38
|
Lana-Elola E, Watson-Scales S, Slender A, Gibbins D, Martineau A, Douglas C, Mohun T, Fisher EM, Tybulewicz VL. Genetic dissection of Down syndrome-associated congenital heart defects using a new mouse mapping panel. eLife 2016; 5:11614. [PMID: 26765563 PMCID: PMC4764572 DOI: 10.7554/elife.11614] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/04/2016] [Indexed: 01/24/2023] Open
Abstract
Down syndrome (DS), caused by trisomy of human chromosome 21 (Hsa21), is the most common cause of congenital heart defects (CHD), yet the genetic and mechanistic causes of these defects remain unknown. To identify dosage-sensitive genes that cause DS phenotypes, including CHD, we used chromosome engineering to generate a mapping panel of 7 mouse strains with partial trisomies of regions of mouse chromosome 16 orthologous to Hsa21. Using high-resolution episcopic microscopy and three-dimensional modeling we show that these strains accurately model DS CHD. Systematic analysis of the 7 strains identified a minimal critical region sufficient to cause CHD when present in 3 copies, and showed that it contained at least two dosage-sensitive loci. Furthermore, two of these new strains model a specific subtype of atrio-ventricular septal defects with exclusive ventricular shunting and demonstrate that, contrary to current hypotheses, these CHD are not due to failure in formation of the dorsal mesenchymal protrusion. Down syndrome is a condition caused by having an extra copy of one of the 46 chromosomes found inside human cells. Specifically, instead of two copies, people with Down syndrome are born with three copies of chromosome 21. This results in many different effects, including learning and memory problems, heart defects and Alzheimer’s disease. Each of these different effects is caused by having a third copy of one or more of the approximately 230 genes found on chromosome 21. However, it is not known which of these genes cause any of these effects, and how an extra copy of the genes results in such changes. Now, Lana-Elola et al. have investigated which genes on chromosome 21 cause the heart defects seen in Down syndrome, and how those heart defects come about. This involved engineering a new strain of mouse that has an extra copy of 148 mouse genes that are very similar to 148 genes found on chromosome 21 in humans. Like people with Down syndrome, this mouse strain developed heart defects when it was an embryo. Using a series of six further mouse strains, Lana-Elola et al. then narrowed down the potential genes that, when in three copies, are needed to cause the heart defects, to a list of just 39 genes. Further experiments then showed that at least two genes within these 39 genes were required in three copies to cause the heart defects. The next step will be to identify the specific genes that actually cause the heart defects, and then work out how a third copy of these genes causes the developmental problems.
Collapse
Affiliation(s)
| | | | - Amy Slender
- The Francis Crick Institute, London, United Kingdom
| | | | | | | | | | - Elizabeth Mc Fisher
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - Victor Lj Tybulewicz
- The Francis Crick Institute, London, United Kingdom.,Imperial College London, London, United Kingdom
| |
Collapse
|
39
|
Jiang X, Liu C, Yu T, Zhang L, Meng K, Xing Z, Belichenko PV, Kleschevnikov AM, Pao A, Peresie J, Wie S, Mobley WC, Yu YE. Genetic dissection of the Down syndrome critical region. Hum Mol Genet 2015; 24:6540-51. [PMID: 26374847 DOI: 10.1093/hmg/ddv364] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/02/2015] [Indexed: 01/11/2023] Open
Abstract
Down syndrome (DS), caused by trisomy 21, is the most common chromosomal disorder associated with developmental cognitive deficits. Despite intensive efforts, the genetic mechanisms underlying developmental cognitive deficits remain poorly understood, and no treatment has been proven effective. The previous mouse-based experiments suggest that the so-called Down syndrome critical region of human chromosome 21 is an important region for this phenotype, which is demarcated by Setd4/Cbr1 and Fam3b/Mx2. We first confirmed the importance of the Cbr1-Fam3b region using compound mutant mice, which carry a duplication spanning the entire human chromosome 21 orthologous region on mouse chromosome 16 [Dp(16)1Yey] and Ms1Rhr. By dividing the Setd4-Mx2 region into complementary Setd4-Kcnj6 and Kcnj15-Mx2 intervals, we started an unbiased dissection through generating and analyzing Dp(16)1Yey/Df(16Setd4-Kcnj6)Yey and Dp(16)1Yey/Df(16Kcnj15-Mx2)Yey mice. Surprisingly, the Dp(16)1Yey-associated cognitive phenotypes were not rescued by either deletion in the compound mutants, suggesting the possible presence of at least one causative gene in each of the two regions. The partial rescue by a Dyrk1a mutation in a compound mutant carrying Dp(16)1Yey and the Dyrk1a mutation confirmed the causative role of Dyrk1a, whereas the absence of a similar rescue by Df(16Dyrk1a-Kcnj6)Yey in Dp(16)1Yey/Df(16Dyrk1a-Kcnj6)Yey mice demonstrated the importance of Kcnj6. Our results revealed the high levels of complexities of gene actions and interactions associated with the Setd4/Cbr1-Fam3b/Mx2 region as well as their relationship with developmental cognitive deficits in DS.
Collapse
Affiliation(s)
- Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Chunhong Liu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Tao Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Department of Medical Genetics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Zhang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Department of Physiology and Pathophysiology, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Kai Meng
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Department of Physiology and Pathophysiology, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Pavel V Belichenko
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA and
| | - Alexander M Kleschevnikov
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA and
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Jennifer Peresie
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Sarah Wie
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - William C Mobley
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA and
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Genetics, Genomics and Bioinformatics Program, Department of Cellular and Molecular Biology, Roswell Park Division of Graduate School,State University of New York at Buffalo, Buffalo, NY 14263, USA
| |
Collapse
|
40
|
Nakai N, Otsuka S, Myung J, Takumi T. Autism spectrum disorder model mice: Focus on copy number variation and epigenetics. SCIENCE CHINA-LIFE SCIENCES 2015; 58:976-84. [DOI: 10.1007/s11427-015-4891-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
41
|
Li J, Shou J, Guo Y, Tang Y, Wu Y, Jia Z, Zhai Y, Chen Z, Xu Q, Wu Q. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J Mol Cell Biol 2015; 7:284-98. [PMID: 25757625 PMCID: PMC4524425 DOI: 10.1093/jmcb/mjv016] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/02/2015] [Indexed: 12/26/2022] Open
Abstract
The human genome contains millions of DNA regulatory elements and a large number of gene clusters, most of which have not been tested experimentally. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) programed with a synthetic single-guide RNA (sgRNA) emerges as a method for genome editing in virtually any organisms. Here we report that targeted DNA fragment inversions and duplications could easily be achieved in human and mouse genomes by CRISPR with two sgRNAs. Specifically, we found that, in cultured human cells and mice, efficient precise inversions of DNA fragments ranging in size from a few tens of bp to hundreds of kb could be generated. In addition, DNA fragment duplications and deletions could also be generated by CRISPR through trans-allelic recombination between the Cas9-induced double-strand breaks (DSBs) on two homologous chromosomes (chromatids). Moreover, junctions of combinatorial inversions and duplications of the protocadherin (Pcdh) gene clusters induced by Cas9 with four sgRNAs could be detected. In mice, we obtained founders with alleles of precise inversions, duplications, and deletions of DNA fragments of variable sizes by CRISPR. Interestingly, we found that very efficient inversions were mediated by microhomology-mediated end joining (MMEJ) through short inverted repeats. We showed for the first time that DNA fragment inversions could be transmitted through germlines in mice. Finally, we applied this CRISPR method to a regulatory element of the Pcdhα cluster and found a new role in the regulation of members of the Pcdhγ cluster. This simple and efficient method should be useful in manipulating mammalian genomes to study millions of regulatory DNA elements as well as vast numbers of gene clusters.
Collapse
Affiliation(s)
- Jinhuan Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Jia Shou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Ya Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yuanxiao Tang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yonghu Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Zhilian Jia
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yanan Zhai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Zhifeng Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Quan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Qiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| |
Collapse
|
42
|
He Z, Proudfoot C, Mileham AJ, McLaren DG, Whitelaw CBA, Lillico SG. Highly efficient targeted chromosome deletions using CRISPR/Cas9. Biotechnol Bioeng 2015; 112:1060-4. [PMID: 25362885 DOI: 10.1002/bit.25490] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/21/2014] [Indexed: 01/13/2023]
Abstract
The CRISPR/Cas9 system has emerged as an intriguing new technology for genome engineering. It utilizes the bacterial endonuclease Cas9 which, when delivered to eukaryotic cells in conjunction with a user-specified small guide RNA (gRNA), cleaves the chromosomal DNA at the target site. Here we show that concurrent delivery of gRNAs designed to target two different sites in a human chromosome introduce DNA double-strand breaks in the chromosome and give rise to targeted deletions of the intervening genomic segment. Predetermined genomic DNA segments ranging from several-hundred base pairs to 1 Mbp can be precisely deleted at frequencies of 1-10%, with no apparent correlation between the size of the deleted fragment and the deletion frequency. The high efficiency of this technique holds promise for large genomic deletions that could be useful in generation of cell and animal models with engineered chromosomes.
Collapse
Affiliation(s)
- Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | | | | | | | | | | |
Collapse
|
43
|
Grigoryan T, Birchmeier W. Molecular signaling mechanisms of axon-glia communication in the peripheral nervous system. Bioessays 2015; 37:502-13. [PMID: 25707700 DOI: 10.1002/bies.201400172] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this article we discuss the molecular signaling mechanisms that coordinate interactions between Schwann cells and the neurons of the peripheral nervous system. Such interactions take place perpetually during development and in adulthood, and are critical for the homeostasis of the peripheral nervous system (PNS). Neurons provide essential signals to control Schwann cell functions, whereas Schwann cells promote neuronal survival and allow efficient transduction of action potentials. Deregulation of neuron-Schwann cell interactions often results in developmental abnormalities and diseases. Recent investigations have shown that during development, neuronally provided signals, such as Neuregulin, Jagged, and Wnt interact to fine-tune the Schwann cell lineage progression. In adult, the signal exchange between neurons and Schwann cells ensures proper nerve function and regeneration. Identification of the mechanisms of neuron-Schwann cell interactions is therefore essential for our understanding of the development, function and pathology of the peripheral nervous system as a whole.
Collapse
Affiliation(s)
- Tamara Grigoryan
- Max-Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | | |
Collapse
|
44
|
Huang W, Olsen BR. Skeletal defects in Osterix-Cre transgenic mice. Transgenic Res 2015; 24:167-72. [PMID: 25139670 PMCID: PMC4276445 DOI: 10.1007/s11248-014-9828-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 08/06/2014] [Indexed: 01/05/2023]
Abstract
Cre/loxP recombination is a powerful strategy widely used for in vivo conditional gene targeting. This technique has made possible many important discoveries of gene function in normal and disease biology. However, due to the transgenic nature of most Cre mouse strains undesired phenotypes occasionally occur in Cre mice. Here we report skeletal defects in Osterix-Cre (Osx-Cre) transgenic mice including delayed calvarial ossification and fracture calluses at multiple skeletal sites. These data suggest that Osx-Cre containing controls should be used for both in vivo and in vitro skeletal analyses of conditional knockout mice generated with this Osx-Cre mouse strain.
Collapse
Affiliation(s)
- Wei Huang
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA,
| | | |
Collapse
|
45
|
Brandl C, Ortiz O, Röttig B, Wefers B, Wurst W, Kühn R. Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one-cell mouse embryos. FEBS Open Bio 2014; 5:26-35. [PMID: 25685662 PMCID: PMC4309836 DOI: 10.1016/j.fob.2014.11.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 12/26/2022] Open
Abstract
Targeted genomic deletions can be generated directly in one-cell mouse embryos using sequence-specific nucleases. Deletions occur by end ligation repair and are not supported by homologous recombination. TALEN as well as CRISPR/Cas nucleases can be used. Homozygous mutants exhibiting phenotypes can be obtained in a single step.
The use of TALEN and CRISPR/CAS nucleases is becoming increasingly popular as a means to edit single target sites in one-cell mouse embryos. Nevertheless, an area that has received less attention concerns the engineering of structural genome variants and the necessary religation of two distant double-strand breaks. Herein, we applied pairs of TALEN or sgRNAs and Cas9 to create deletions in the Rab38 gene. We found that the deletion of 3.2 or 9.3 kb, but not of 30 kb, occurs at a frequency of 6–37%. This is sufficient for the direct production of mutants by embryo microinjection. Therefore, deletions up to ∼10 kb can be readily achieved for modeling human disease alleles. This work represents an important step towards the establishment of new protocols that support the ligation of remote DSB ends to achieve even larger rearrangements.
Collapse
Affiliation(s)
- Christina Brandl
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Oskar Ortiz
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Bernhard Röttig
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Benedikt Wefers
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany ; Max-Planck-Institute of Psychiatry, 80804 Munich, Germany ; Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
| |
Collapse
|
46
|
Khaled WT, Liu P. Cancer mouse models: past, present and future. Semin Cell Dev Biol 2014; 27:54-60. [PMID: 24718321 DOI: 10.1016/j.semcdb.2014.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/29/2014] [Accepted: 04/01/2014] [Indexed: 12/26/2022]
Abstract
The development and advances in gene targeting technology over the past three decades has facilitated the generation of cancer mouse models that recapitulate features of human malignancies. These models have been and still remain instrumental in revealing the complexities of human cancer biology. However, they will need to evolve in the post-genomic era of cancer research. In this review we will highlight some of the key developments over the past decades and will discuss the new possibilities of cancer mouse models in the light of emerging powerful gene manipulating tools.
Collapse
Affiliation(s)
- Walid T Khaled
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.
| |
Collapse
|
47
|
Ishii T. Genetic manipulation to analyze pheromone responses: knockouts of multiple receptor genes. Methods Mol Biol 2014; 1068:133-54. [PMID: 24014359 DOI: 10.1007/978-1-62703-619-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Gene targeting in the mouse is an essential technique to study gene function in vivo. Multigene families encoding vomeronasal receptor (VR) type 1 and type 2 consist of ~300 intact genes, which are clustered at multiple loci in the mouse genome. To understand the function of VRs and neurons expressing a particular VR in vivo, individual endogenous receptor genes can be manipulated by conventional gene targeting to create loss-of-function mutations or to visualize neurons and their axons expressing the VR. Multiple receptor genes in a cluster can also be deleted simultaneously by chromosome engineering, allowing analysis of function of a particular VR subfamily. Here, we describe protocols for conventional gene targeting and chromosome engineering for deleting a large genomic region in mouse embryonic stem (ES) cells.
Collapse
Affiliation(s)
- Tomohiro Ishii
- Department of Cell Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
48
|
Engineered chromosome-based genetic mapping establishes a 3.7 Mb critical genomic region for Down syndrome-associated heart defects in mice. Hum Genet 2013; 133:743-53. [PMID: 24362460 DOI: 10.1007/s00439-013-1407-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/06/2013] [Indexed: 02/01/2023]
Abstract
Trisomy 21 (Down syndrome, DS) is the most common human genetic anomaly associated with heart defects. Based on evolutionary conservation, DS-associated heart defects have been modeled in mice. By generating and analyzing mouse mutants carrying different genomic rearrangements in human chromosome 21 (Hsa21) syntenic regions, we found the triplication of the Tiam1-Kcnj6 region on mouse chromosome 16 (Mmu16) resulted in DS-related cardiovascular abnormalities. In this study, we developed two tandem duplications spanning the Tiam1-Kcnj6 genomic region on Mmu16 using recombinase-mediated genome engineering, Dp(16)3Yey and Dp(16)4Yey, spanning the 2.1 Mb Tiam1-Il10rb and 3.7 Mb Ifnar1-Kcnj6 regions, respectively. We found that Dp(16)4Yey/+, but not Dp(16)3Yey/+, led to heart defects, suggesting the triplication of the Ifnar1-Kcnj6 region is sufficient to cause DS-associated heart defects. Our transcriptional analysis of Dp(16)4Yey/+ embryos showed that the Hsa21 gene orthologs located within the duplicated interval were expressed at the elevated levels, reflecting the consequences of the gene dosage alterations. Therefore, we have identified a 3.7 Mb genomic region, the smallest critical genomic region, for DS-associated heart defects, and our results should set the stage for the final step to establish the identities of the causal gene(s), whose elevated expression(s) directly underlie this major DS phenotype.
Collapse
|
49
|
Zhang G, Vemulapalli TH, Yang JY. Phylooncogenomics: Examining the cancer genome in the context of vertebrate evolution. Appl Transl Genom 2013; 2:48-54. [PMID: 27896055 PMCID: PMC5121254 DOI: 10.1016/j.atg.2013.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 06/20/2013] [Accepted: 06/22/2013] [Indexed: 06/06/2023]
Abstract
Currently, human cancer genomics is making great progress, and many mutations of new cancer driver genes have been detected at an unprecedented rate in a variety of human cancers. Many details of the genetic alterations in cancer cell genomes have been revealed by the massively parallel sequencing. Long-lasting aneuploidy caused large-scale somatic copy number alterations remains a difficulty as there are too many genes located on such big chromosomal fragments, and this cannot simply be solved by increasing sequencing depth and tumor sample numbers. Comparative oncogenomics may provide us with a solution to this problem. Here, we review some of the common animal cancer models and propose to analyze cancer cell genomics in vertebrate phylogenetic backgrounds. Thus phylooncogenomics may provide us with a unique perspective on he nature of cancer biology unattainable by single species studies.
Collapse
Affiliation(s)
- GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, College of Veterinary Medicine, United States
- Purdue University Center for Cancer Research, United States
| | - Tracy H. Vemulapalli
- Department of Comparative Pathobiology, Purdue University, College of Veterinary Medicine, United States
| | - Jer-Yen Yang
- Purdue University Center for Cancer Research, United States
- Department of Basic Medical Sciences, Purdue University, College of Veterinary Medicine, United States
| |
Collapse
|
50
|
Olme CH, Finnon R, Brown N, Kabacik S, Bouffler S, Badie C. Live cell detection of chromosome 2 deletion and Sfpi1/PU1 loss in radiation-induced mouse acute myeloid leukaemia. Leuk Res 2013; 37:1374-82. [PMID: 23806234 PMCID: PMC3775122 DOI: 10.1016/j.leukres.2013.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/24/2013] [Accepted: 05/26/2013] [Indexed: 12/20/2022]
Abstract
The CBA/H mouse model of radiation-induced acute myeloid leukaemia (rAML) has been studied for decades to bring to light the molecular mechanisms associated with multistage carcinogenesis. A specific interstitial deletion of chromosome 2 found in a high proportion of rAML is recognised as the initiating event. The deletion leads to the loss of Sfpi, a gene essential for haematopoietic development. Its product, the transcription factor PU.1 acts as a tumour suppressor in this model. Although the deletion can be detected early following ionising radiation exposure by cytogenetic techniques, precise characterisation of the haematopoietic cells carrying the deletion and the study of their fate in vivo cannot be achieved. Here, using a genetically engineered C57BL/6 mouse model expressing the GFP fluorescent molecule under the control of the Sfpi1 promoter, which we have bred onto the rAML-susceptible CBA/H strain, we demonstrate that GFP expression did not interfere with X-ray induced leukaemia incidence and that GFP fluorescence in live leukaemic cells is a surrogate marker of radiation-induced chromosome 2 deletions with or without point mutations on the remaining allele of the Sfpi1 gene. This study presents the first experimental evidence for the detection of this leukaemia initiating event in live leukemic cells.
Collapse
MESH Headings
- Animals
- Bone Marrow Cells/metabolism
- Bone Marrow Cells/pathology
- Chromosome Deletion
- Disease Models, Animal
- Exons
- Female
- Flow Cytometry
- Gene Deletion
- Gene Expression
- Genes, Reporter
- Genetic Predisposition to Disease
- Immunophenotyping
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Radiation-Induced/genetics
- Leukemia, Radiation-Induced/metabolism
- Mice
- Mutation
- Proto-Oncogene Proteins/genetics
- Trans-Activators/genetics
- Transcription, Genetic
Collapse
Affiliation(s)
| | | | | | | | | | - C. Badie
- Biological Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, UK
| |
Collapse
|