1
|
Sato M, Nakamura S, Inada E, Takabayashi S. Recent Advances in the Production of Genome-Edited Rats. Int J Mol Sci 2022; 23:ijms23052548. [PMID: 35269691 PMCID: PMC8910656 DOI: 10.3390/ijms23052548] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
The rat is an important animal model for understanding gene function and developing human disease models. Knocking out a gene function in rats was difficult until recently, when a series of genome editing (GE) technologies, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the type II bacterial clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Cas9 (CRISPR/Cas9) systems were successfully applied for gene modification (as exemplified by gene-specific knockout and knock-in) in the endogenous target genes of various organisms including rats. Owing to its simple application for gene modification and its ease of use, the CRISPR/Cas9 system is now commonly used worldwide. The most important aspect of this process is the selection of the method used to deliver GE components to rat embryos. In earlier stages, the microinjection (MI) of GE components into the cytoplasm and/or nuclei of a zygote was frequently employed. However, this method is associated with the use of an expensive manipulator system, the skills required to operate it, and the egg transfer (ET) of MI-treated embryos to recipient females for further development. In vitro electroporation (EP) of zygotes is next recognized as a simple and rapid method to introduce GE components to produce GE animals. Furthermore, in vitro transduction of rat embryos with adeno-associated viruses is potentially effective for obtaining GE rats. However, these two approaches also require ET. The use of gene-engineered embryonic stem cells or spermatogonial stem cells appears to be of interest to obtain GE rats; however, the procedure itself is difficult and laborious. Genome-editing via oviductal nucleic acids delivery (GONAD) (or improved GONAD (i-GONAD)) is a novel method allowing for the in situ production of GE zygotes existing within the oviductal lumen. This can be performed by the simple intraoviductal injection of GE components and subsequent in vivo EP toward the injected oviducts and does not require ET. In this review, we describe the development of various approaches for producing GE rats together with an assessment of their technical advantages and limitations, and present new GE-related technologies and current achievements using those rats in relation to human diseases.
Collapse
Affiliation(s)
- Masahiro Sato
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo 157-8535, Japan
- Correspondence: (M.S.); (S.T.); Tel.: +81-3-3416-0181 (M.S.); +81-53-435-2001 (S.T.)
| | - Shingo Nakamura
- Division of Biomedical Engineering, National Defense Medical College Research Institute, Saitama 359-8513, Japan;
| | - Emi Inada
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan;
| | - Shuji Takabayashi
- Laboratory Animal Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
- Correspondence: (M.S.); (S.T.); Tel.: +81-3-3416-0181 (M.S.); +81-53-435-2001 (S.T.)
| |
Collapse
|
2
|
Krause F, Mohebian K, Delpero M, Hesse D, Kühn R, Arends D, Brockmann GA. A deletion containing a CTCF-element in intron 8 of the Bbs7 gene is partially responsible for juvenile obesity in the Berlin Fat Mouse. Mamm Genome 2021; 33:465-470. [PMID: 34910225 PMCID: PMC9360062 DOI: 10.1007/s00335-021-09938-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
The Berlin Fat Mouse Inbred (BFMI) line is a model for juvenile obesity. Previous studies on crosses between BFMI and C57Bl/6N (B6N) have identified a recessive defect causing juvenile obesity on chromosome 3 (jObes1). Bbs7 was identified as the most likely candidate gene for the observed effect. Comparative sequence analysis showed a 1578 bp deletion in intron 8 of Bbs7 in BFMI mice. A CTCF-element is located inside this deletion. To investigate the functional effect of this deletion, it was introduced into B6N mice using CRISPR/Cas9. Two mice containing the target deletion were obtained (B6N Bbs7emI8∆1 and Bbs7emI8∆2) and were subsequently mated to BFMI and B6N to generate two families suitable for complementation. Inherited alleles were determined and body composition was measured by quantitative magnetic resonance. Evidence for a partial complementation (13.1-15.1%) of the jObes1 allele by the CRISPR/Cas9 modified B6N Bbs7emI8∆1 and Bbs7emI8∆2 alleles was found. Mice carrying the complementation alleles had a 23-27% higher fat-to-lean ratio compared to animals which have a B6N allele (P(Bbs7emI8∆1) = 4.25 × 10-7; P(Bbs7emI8∆2) = 3.17 × 10-5). Consistent with previous findings, the recessive effect of the BFMI allele was also seen for the B6N Bbs7emI8∆1 and Bbs7emI8∆2 alleles. However, the effect size of the B6N Bbs7emI8∆1 and Bbs7emI8∆2 alleles was smaller than the BFMI allele, and thus showed only a partial complementation. Findings suggest additional variants near Bbs7 in addition to or interacting with the deletion in intron 8.
Collapse
Affiliation(s)
- Florian Krause
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Kourosh Mohebian
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Manuel Delpero
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Deike Hesse
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Danny Arends
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Gudrun A Brockmann
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.
| |
Collapse
|
3
|
Liu Z, Chen Z, Di J, Wang Z, Zhang Y, Li J, An L, Presicce GA, Liu L, Du F. Efficient mutagenesis targeting the IFNAR1 gene in mice using a combination of Cas9 protein and dual gRNAs. Am J Transl Res 2021; 13:12094-12106. [PMID: 34786147 PMCID: PMC8581890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
We injected mouse zygotes with combinations of Cas9 protein, Cas9 mRNA, and two gRNAs targeting a single exon of type I interferon receptor (IFNAR1) to determine the gene targeting efficiencies. Cas9 protein produced on-target mutations more efficiently than Cas9 mRNA when each was used with a single gRNA, regardless of which gRNA was used. When Cas9 mRNA and Cas9 protein were co-injected, the on-target efficiency could reach 97.0% when both gRNAs were used, which was higher than when either gRNA was used alone (61.3% and 75.5%, respectively; P<0.05). Co-injection of Cas9 protein with both gRNAs produced the highest on-target mutation rate of any combination (100.0%). Most on-target mutations were deletions of 2 to 113 nucleotides, and there were few off-target mutations in mutant animals. The expression intensity of IFNAR1 was reduced in heterozygous IFNAR1 +/- mice (IF) and almost or completely absent in homozygous null IFNAR -/- mice compared with that in wild-type mice (IF and Western blot). When both gRNAs targeting IFNAR1 were used simultaneously with two gRNAs targeting FVII, the on-target editing efficiency on each gene was 96.8% and 85.5%, respectively. Co-injection of dual gRNAs and Cas9 protein is an efficient approach for IFNAR1 knockout and multi-gene editing in mice and may be applied in other animal models and breeding livestock.
Collapse
Affiliation(s)
- Zhihui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, China
| | - Zongxiang Chen
- Chengdu Institute of Biological Products Co. LtdChengdu 610023, Sichuan, China
| | - Jingya Di
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, China
| | - Zhisong Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, China
| | - Yongxia Zhang
- Chengdu Institute of Biological Products Co. LtdChengdu 610023, Sichuan, China
| | - Jinshan Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, China
| | - Liyou An
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, China
| | | | - Lanjun Liu
- Chengdu Institute of Biological Products Co. LtdChengdu 610023, Sichuan, China
| | - Fuliang Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, China
- Lannuo Biotechnologies Wuxi Inc.Wuxi 214000, Jiangsu, China
| |
Collapse
|
4
|
Akazawa S, Mackin L, Jhala G, Fynch S, Catterall T, Selck C, Graham KL, Krishnamurthy B, Pappas EG, Kwong CTJ, Sutherland APR, Kay TWH, Brodnicki TC, Thomas HE. Deficiency of the innate immune adaptor STING promotes autoreactive T cell expansion in NOD mice. Diabetologia 2021; 64:878-889. [PMID: 33483762 DOI: 10.1007/s00125-020-05378-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/17/2020] [Indexed: 01/07/2023]
Abstract
AIMS/HYPOTHESIS Stimulator of IFN genes (STING) is a central hub for cytosolic nucleic acid sensing and its activation results in upregulation of type I IFN production in innate immune cells. A type I IFN gene signature seen before the onset of type 1 diabetes has been suggested as a driver of disease initiation both in humans and in the NOD mouse model. A possible source of type I IFN is through activation of the STING pathway. Recent studies suggest that STING also has antiproliferative and proapoptotic functions in T cells that are independent of IFN. To investigate whether STING is involved in autoimmune diabetes, we examined the impact of genetic deletion of STING in NOD mice. METHODS CRISPR/Cas9 gene editing was used to generate STING-deficient NOD mice. Quantitative real-time PCR was used to assess the level of type I IFN-regulated genes in islets from wild-type and STING-deficient NOD mice. The number of islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP)206-214-specific CD8+ T cells was determined by magnetic bead-based MHC tetramer enrichment and flow cytometry. The incidence of spontaneous diabetes and diabetes after adoptive transfer of T cells was determined. RESULTS STING deficiency partially attenuated the type I IFN gene signature in islets but did not suppress insulitis. STING-deficient NOD mice accumulated an increased number of IGRP206-214-specific CD8+ T cells (2878 ± 642 cells in NOD.STING-/- mice and 728.8 ± 196 cells in wild-type NOD mice) in peripheral lymphoid tissue, associated with a higher incidence of spontaneous diabetes (95.5% in NOD.STING-/- mice and 86.2% in wild-type NOD mice). Splenocytes from STING-deficient mice rapidly induced diabetes after adoptive transfer into irradiated NOD recipients (median survival 75 days for NOD recipients of NOD.STING-/- mouse splenocytes and 121 days for NOD recipients of NOD mouse splenocytes). CONCLUSIONS/INTERPRETATION Data suggest that sensing of endogenous nucleic acids through the STING pathway may be partially responsible for the type I IFN gene signature but not autoimmunity in NOD mice. Our results show that the STING pathway may play an unexpected intrinsic role in suppressing the number of diabetogenic T cells.
Collapse
Affiliation(s)
- Satoru Akazawa
- St Vincent's Institute, Fitzroy, VIC, Australia
- Department of Endocrinology and Metabolism, Unit of Translational Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | | | | | | | | | - Kate L Graham
- St Vincent's Institute, Fitzroy, VIC, Australia
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia
| | - Balasubramanian Krishnamurthy
- St Vincent's Institute, Fitzroy, VIC, Australia
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia
| | | | - Chun-Ting J Kwong
- St Vincent's Institute, Fitzroy, VIC, Australia
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia
| | - Andrew P R Sutherland
- St Vincent's Institute, Fitzroy, VIC, Australia
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia
| | - Thomas W H Kay
- St Vincent's Institute, Fitzroy, VIC, Australia
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia
| | - Thomas C Brodnicki
- St Vincent's Institute, Fitzroy, VIC, Australia
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia
| | - Helen E Thomas
- St Vincent's Institute, Fitzroy, VIC, Australia.
- The University of Melbourne, Department of Medicine, St Vincent's Hospital, Fitzroy, VIC, Australia.
| |
Collapse
|
5
|
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
|
6
|
Hansen J, von Melchner H, Wurst W. Mutant non-coding RNA resource in mouse embryonic stem cells. Dis Model Mech 2021; 14:14/2/dmm047803. [PMID: 33729986 PMCID: PMC7875499 DOI: 10.1242/dmm.047803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/14/2020] [Indexed: 01/23/2023] Open
Abstract
Gene trapping is a high-throughput approach that has been used to introduce insertional mutations into the genome of mouse embryonic stem (ES) cells. It is performed with generic gene trap vectors that simultaneously mutate and report the expression of the endogenous gene at the site of insertion and provide a DNA sequence tag for the rapid identification of the disrupted gene. Large-scale international efforts assembled a gene trap library of 566,554 ES cell lines with single gene trap integrations distributed throughout the genome. Here, we re-investigated this unique library and identified mutations in 2202 non-coding RNA (ncRNA) genes, in addition to mutations in 12,078 distinct protein-coding genes. Moreover, we found certain types of gene trap vectors preferentially integrating into genes expressing specific long non-coding RNA (lncRNA) biotypes. Together with all other gene-trapped ES cell lines, lncRNA gene-trapped ES cell lines are readily available for functional in vitro and in vivo studies.
Collapse
Affiliation(s)
- Jens Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Harald von Melchner
- Department of Molecular Hematology, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany .,Technische Universität München-Weihenstephan, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Site Munich, Feodor-Lynen-Str. 17, D-81377 Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, D-81377 München, Germany
| |
Collapse
|
7
|
Danner E, Lebedin M, de la Rosa K, Kühn R. A homology independent sequence replacement strategy in human cells using a CRISPR nuclease. Open Biol 2021; 11:200283. [PMID: 33499763 PMCID: PMC7881171 DOI: 10.1098/rsob.200283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Precision genomic alterations largely rely on homology directed repair (HDR), but targeting without homology using the non-homologous end-joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double-strand break in both dividing and non-dividing cells. Here, we demonstrate the use of NHEJ repair to replace genomic segments with donor sequences; we name this method 'Replace' editing (Rational end-joining protocol delivering a targeted sequence exchange). Using CRISPR/Cas9, we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci in cell lines and show successful exchange of exons in 16-54% of human cells. Using linear amplification methods and deep sequencing, we quantify the diversity of outcomes following Replace editing and profile the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.
Collapse
Affiliation(s)
- Eric Danner
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
| | | | | | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
| |
Collapse
|
8
|
GPRIN3 Controls Neuronal Excitability, Morphology, and Striatal-Dependent Behaviors in the Indirect Pathway of the Striatum. J Neurosci 2019; 39:7513-7528. [PMID: 31363062 DOI: 10.1523/jneurosci.2454-18.2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 12/15/2022] Open
Abstract
The regulation of the striatum by the GPCR signaling through neuromodulators is essential for its physiology and physiopathology, so it is necessary to know all the compounds of these pathways. In this study, we identified a new important partner of the dopaminergic pathway: GPRIN3 (a member of the GPRIN family). GPRIN3 is highly expressed in the striatum but with undefined function. Cell sorting of medium spiny neurons (MSNs) in indirect MSNs and direct MSNs indicated the presence of the GPRIN3 gene in both populations with a preferential expression in indirect MSNs. This led us to generate GPRIN3 KO mice by CRISPR/Cas9 and test male animals to access possible alterations in morphological, electrophysiological, and behavioral parameters following its absence. 3D reconstruction analysis of MSNs revealed increased neuronal arborization in GPRIN3 KO and modified passive and active electrophysiological properties. These cellular alterations were coupled with increased motivation and cocaine-induced hyperlocomotion. Additionally, using a specific indirect MSN knockdown, we showed a preferential role for GPRIN3 in indirect MSNs related to the D2R signaling. Together, these results show that GPRIN3 is a mediator of D2R function in the striatum playing a major role in striatal physiology.SIGNIFICANCE STATEMENT The striatum is the main input of the basal ganglia processing information from different brain regions through the combined actions of direct pathway neurons and indirect pathway neurons. Both neuronal populations are defined by the expression of dopamine D1R or D2R GPCRs, respectively. How these neurons signal to the respective G-protein is still debatable. Here we identified GPRIN3 as a putative selective controller of D2R function in the striatum playing a critical role in striatal-associated behaviors and cellular functions. This study represents the identification of a new target to tackle striatal dysfunction associated with the D2R, such as schizophrenia, Parkinson's disease, and drug addiction.
Collapse
|
9
|
Hansmeier NR, Widdershooven PJM, Khani S, Kornfeld JW. Rapid Generation of Long Noncoding RNA Knockout Mice Using CRISPR/Cas9 Technology. Noncoding RNA 2019; 5:ncrna5010012. [PMID: 30678101 PMCID: PMC6468733 DOI: 10.3390/ncrna5010012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, long noncoding RNAs (lncRNAs) have emerged as multifaceted regulators of gene expression, controlling key developmental and disease pathogenesis processes. However, due to the paucity of lncRNA loss-of-function mouse models, key questions regarding the involvement of lncRNAs in organism homeostasis and (patho)-physiology remain difficult to address experimentally in vivo. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 platform provides a powerful genome-editing tool and has been successfully applied across model organisms to facilitate targeted genetic mutations, including Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Mus musculus. However, just a few lncRNA-deficient mouse lines have been created using CRISPR/Cas9-mediated genome engineering, presumably due to the need for lncRNA-specific gene targeting strategies considering the absence of open-reading frames in these loci. Here, we describe a step-wise procedure for the generation and validation of lncRNA loss-of-function mouse models using CRISPR/Cas9-mediated genome engineering. In a proof-of-principle approach, we generated mice deficient for the liver-enriched lncRNA Gm15441, which we found downregulated during development of metabolic disease and induced during the feeding/fasting transition. Further, we discuss guidelines for the selection of lncRNA targets and provide protocols for in vitro single guide RNA (sgRNA) validation, assessment of in vivo gene-targeting efficiency and knockout confirmation. The procedure from target selection to validation of lncRNA knockout mouse lines can be completed in 18–20 weeks, of which <10 days hands-on working time is required.
Collapse
Affiliation(s)
- Nils R Hansmeier
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
- Cologne Cluster of Excellence: Cellular Stress Responses in Ageing-associated Diseases, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
| | - Pia J M Widdershooven
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
- Cologne Cluster of Excellence: Cellular Stress Responses in Ageing-associated Diseases, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
- Institute for Prophylaxis and Epidemiology of Cardiovascular Diseases (IPEK), Ludwig Maximilian University of Munich, 80336 Munich, Germany.
| | - Jan-Wilhelm Kornfeld
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
- Cologne Cluster of Excellence: Cellular Stress Responses in Ageing-associated Diseases, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
- Department for Biochemistry and Molecular Biology, Functional Genomics and Metabolism Unit, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
10
|
Abstract
Pronuclear microinjection remains the most widely used method for the germline modification of mice and other species. The method is conceptually quite simple and at least in rodents can produce transgenic offspring with relatively high efficiency. Here, we describe the various components of the production of transgenic mice including a detailed list of materials and equipment. We outline in detail the preparation of animals, the retrieval, culture and transfer of embryos, the preparation of DNA, and the microinjection process. We have added a substantial collection of notes with helpful suggestions that reflect the many years of experience we have using this technology and our continuing efforts to improve animal welfare and the efficiency of producing transgenics.
Collapse
Affiliation(s)
- Xin-An Pu
- Comprehensive Cancer Center (CCC), Genetically Engineered Mouse Model Core (GEMMC), The Ohio State University, Columbus, OH, USA.
| | - Anthony P Young
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | | |
Collapse
|
11
|
Lainšček D, Kadunc L, Keber MM, Bratkovič IH, Romih R, Jerala R. Delivery of an Artificial Transcription Regulator dCas9-VPR by Extracellular Vesicles for Therapeutic Gene Activation. ACS Synth Biol 2018; 7:2715-2725. [PMID: 30513193 DOI: 10.1021/acssynbio.8b00192] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The CRISPR/Cas system has been developed as a potent tool for genome engineering and transcription regulation. However, the efficiency of the delivery of the system into cells, particularly for therapeutic in vivo applications, remains a major bottleneck. Extracellular vesicles (EVs), released by eukaryotic cells, can mediate the transfer of various molecules, including nucleic acids and proteins. We show the packaging and delivery of the CRISPR/Cas system via EVs to the target cells, combining the advantages of both technological platforms. A genome editing with designed extracellular vesicles (GEDEX) system generated by the producer cells can transfer the designed transcriptional regulator dCas9-VPR complexed with appropriate targeting gRNAs enabling activation of gene transcription. We show functional delivery in mammalian cells as well in the animals. The therapeutic efficiency of in vivo delivery of dCas9-VPR/sgRNA GEDEX is demonstrated in a mouse model of liver damage counteracted by upregulation of the endogenous hepatocyte growth factor, demonstrating the potential for therapeutic applications.
Collapse
Affiliation(s)
- Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Lucija Kadunc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000, Slovenia
| | - Iva Hafner Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Rok Romih
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000, Slovenia
| |
Collapse
|
12
|
Zhou G, Wu W, Yu L, Yu T, Yang W, Wang P, Zhang X, Cong Y, Liu Z. Tripartite motif-containing (TRIM) 21 negatively regulates intestinal mucosal inflammation through inhibiting TH1/TH17 cell differentiation in patients with inflammatory bowel diseases. J Allergy Clin Immunol 2018; 142:1218-1228.e12. [DOI: 10.1016/j.jaci.2017.09.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 08/26/2017] [Accepted: 09/12/2017] [Indexed: 01/18/2023]
|
13
|
Xiang X, Piers TM, Wefers B, Zhu K, Mallach A, Brunner B, Kleinberger G, Song W, Colonna M, Herms J, Wurst W, Pocock JM, Haass C. The Trem2 R47H Alzheimer's risk variant impairs splicing and reduces Trem2 mRNA and protein in mice but not in humans. Mol Neurodegener 2018; 13:49. [PMID: 30185230 PMCID: PMC6126019 DOI: 10.1186/s13024-018-0280-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The R47H variant of the Triggering Receptor Expressed on Myeloid cells 2 (TREM2) significantly increases the risk for late onset Alzheimer's disease. Mouse models accurately reproducing phenotypes observed in Alzheimer' disease patients carrying the R47H coding variant are required to understand the TREM2 related dysfunctions responsible for the enhanced risk for late onset Alzheimer's disease. METHODS A CRISPR/Cas9-assisted gene targeting strategy was used to generate Trem2 R47H knock-in mice. Trem2 mRNA and protein levels as well as Trem2 splicing patterns were assessed in these mice, in iPSC-derived human microglia-like cells, and in human brains from Alzheimer's patients carrying the TREM2 R47H risk factor. RESULTS Two independent Trem2 R47H knock-in mouse models show reduced Trem2 mRNA and protein production. In both mouse models Trem2 haploinsufficiency was due to atypical splicing of mouse Trem2 R47H, which introduced a premature stop codon. Cellular splicing assays using minigene constructs demonstrate that the R47H variant induced abnormal splicing only occurs in mice but not in humans. TREM2 mRNA levels and splicing patterns were both normal in iPSC-derived human microglia-like cells and patient brains with the TREM2 R47H variant. CONCLUSIONS The Trem2 R47H variant activates a cryptic splice site that generates miss-spliced transcripts leading to Trem2 haploinsufficiency only in mice but not in humans. Since Trem2 R47H related phenotypes are mouse specific and do not occur in humans, humanized TREM2 R47H knock-in mice should be generated to study the cellular consequences caused by the human TREM2 R47H coding variant. Currently described phenotypes of Trem2 R47H knock-in mice can therefore not be translated to humans.
Collapse
Affiliation(s)
- Xianyuan Xiang
- Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,Graduate School of Systemic Neuroscience, Ludwig- Maximilians- University Munich, Munich, Germany
| | - Thomas M Piers
- Department of Neuroinflammation, Cell Signalling Lab, University College London Institute of Neurology, WC1N 1PJ, London, UK
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kaichuan Zhu
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Anna Mallach
- Department of Neuroinflammation, Cell Signalling Lab, University College London Institute of Neurology, WC1N 1PJ, London, UK
| | - Bettina Brunner
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Gernot Kleinberger
- Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Wilbur Song
- Department of Immunology and Pathology, Washington University in St. Louis, St. Louis, MO, USA
| | - Marco Colonna
- Department of Immunology and Pathology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jochen Herms
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Technische Universität München-Weihenstephan, 85764, Neuherberg/Munich, Germany
| | - Jennifer M Pocock
- Department of Neuroinflammation, Cell Signalling Lab, University College London Institute of Neurology, WC1N 1PJ, London, UK
| | - Christian Haass
- Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany. .,German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| |
Collapse
|
14
|
Islam W. CRISPR-Cas9; an efficient tool for precise plant genome editing. Mol Cell Probes 2018; 39:47-52. [PMID: 29621557 DOI: 10.1016/j.mcp.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 01/09/2023]
Abstract
Efficient plant genome editing is dependent upon induction of double stranded DNA breaks (DSBs) through site specified nucleases. These DSBs initiate the process of DNA repair which can either base upon homologous recombination (HR) or non-homologous end jointing (NHEJ). Recently, CRISPR-Cas9 mechanism got highlighted as revolutionizing genetic tool due to its simpler frame work along with the broad range of adaptability and applications. So, in this review, I have tried to sum up the application of this biotechnological tool in plant genome editing. Furthermore, I have tried to explain successful adaptation of CRISPR in various plant species where it is used for the successful generation of stable mutations in a steadily growing number of species through NHEJ. The review also sheds light upon other biotechnological approaches relying upon single DNA lesion induction such as genomic deletion or pair wise nickases for evasion of offsite effects.
Collapse
Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Govt.of Punjab, Agriculture Department, Lahore, Pakistan.
| |
Collapse
|
15
|
Yang L, Liu Y, Zhang N, Ding X, Zhang W, Shen K, Huang L, Zhou J, Cui S, Zhu Z, Hu Z, Xiao M. Novel impact of the DNMT3A R882H mutation on GSH metabolism in a K562 cell model established by TALENs. Oncotarget 2018; 8:30395-30409. [PMID: 28418922 PMCID: PMC5444751 DOI: 10.18632/oncotarget.16449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 02/20/2017] [Indexed: 01/22/2023] Open
Abstract
DNA methyltransferase 3A (DNMT3A) mutations occurred in 18%~23% of acute myeloid leukemia (AML) patients, and were considered to be an adverse prognostic factor for adult de novo AML cases. However, the relevant molecular mechanism of the mutation in AML pathogenesis remains obscure. In this study, we established K562 and SKM1 cell model carrying the DNMT3A R882H mutation via transcription activator-like effector nuclease (TALEN) and Clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology, and discovered that mutated DNMT3A could promote the proliferative capability of malignant cell clones. Further RNA microarray analysis revealed that some genes crucial for glutathione (GSH) synthesis, including CTH, PSPH, PSAT1 and especially SLC7A11 (the cysteine/glutamate transporter) were significantly up-regulated, which resulted in significant elevation of intracellular GSH levels. A subsequent experiment demonstrated that the mutant clones are resistant to chemotherapy as well as SLC7A11-inhibitorsBy shRNA induced SLC7A11 silencing, we discovered profoundly decreased cellular GSH and cell proliferative ability of DNMT3A mutated clones. Our results provided novel insight into the role of the DNMT3A R882H mutation in AML pathogenesis and suggested that targeting the cellular GSH synthetic pathway could enhance the current therapy for AML patients with the DNMT3A R882H mutation.
Collapse
Affiliation(s)
- Li Yang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Ya'Nan Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, P.R. China
| | - Na Zhang
- Department of Hematology, Xijing Hospital Affiliated by The Fourth Military Medical University (FMMU), Xi'an, Shanxi Province, P.R.China
| | - Xiao'Yi Ding
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Wei Zhang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Ke'Feng Shen
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Liang Huang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Jian'Feng Zhou
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China.,Qinghai University, XiNing, Qinghai Province, P.R.China
| | - Sen Cui
- Department of Hematology, Qinghai University Affiliated Hospital, Qinghai University, XiNing, Qinghai Province, P.R.China
| | - Zun'Min Zhu
- Department of Hematology, Henan Provincial People's Hospital, ZhengZhou, Henan Province, P.R.China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen 14 University, Guangzhou, Guangdong, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| |
Collapse
|
16
|
Ahmad G, Amiji M. Use of CRISPR/Cas9 gene-editing tools for developing models in drug discovery. Drug Discov Today 2018; 23:519-533. [DOI: 10.1016/j.drudis.2018.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/09/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022]
|
17
|
Peddle CF, MacLaren RE. The Application of CRISPR/Cas9 for the Treatment of Retinal Diseases. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:533-541. [PMID: 29259519 PMCID: PMC5733850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The CRISPR/Cas9 system of genome editing has revolutionized molecular biology, offering a simple, and relatively inexpensive method of creating precise DNA edits. It has potential application in gene therapy treatment of retinal diseases providing targeted disruption, alteration, or transcriptional regulation of pathogenic genes. In vivo studies have demonstrated therapeutic benefit for a variety of diseases. Despite this, there are many challenges to clinical use of CRISPR/Cas9, including editing efficiency, off-target effects, and disease heterogeneity. This review details the mechanisms of the CRISPR/Cas9 system and the treatment strategies that can be applied to retinal diseases. It gives an overview of in vivo studies published to date and discusses the challenges and potential solutions to the wide-scale clinical use of CRISPR/Cas9 as a therapeutic intervention.
Collapse
Affiliation(s)
- Caroline F. Peddle
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, UK,To whom all correspondence should be addressed: Caroline F. Peddle, NDCN, Level 6, West Wing, John Radcliffe Hospital, Oxford, United Kingdom, OX3 9DU, .
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, UK,Oxford Eye Hospital, Oxford, UK
| |
Collapse
|
18
|
GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency. Proc Natl Acad Sci U S A 2017; 114:E9579-E9588. [PMID: 29078328 PMCID: PMC5692555 DOI: 10.1073/pnas.1708341114] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
To elucidate the molecular basis of BMP4-induced differentiation of human pluripotent stem cells (PSCs) toward progeny with trophectoderm characteristics, we produced transcriptome, epigenome H3K4me3, H3K27me3, and CpG methylation maps of trophoblast progenitors, purified using the surface marker APA. We combined them with the temporally resolved transcriptome of the preprogenitor phase and of single APA+ cells. This revealed a circuit of bivalent TFAP2A, TFAP2C, GATA2, and GATA3 transcription factors, coined collectively the "trophectoderm four" (TEtra), which are also present in human trophectoderm in vivo. At the onset of differentiation, the TEtra factors occupy multiple sites in epigenetically inactive placental genes and in OCT4 Functional manipulation of GATA3 and TFAP2A indicated that they directly couple trophoblast-specific gene induction with suppression of pluripotency. In accordance, knocking down GATA3 in primate embryos resulted in a failure to form trophectoderm. The discovery of the TEtra circuit indicates how trophectoderm commitment is regulated in human embryogenesis.
Collapse
|
19
|
Piwecka M, Glažar P, Hernandez-Miranda LR, Memczak S, Wolf SA, Rybak-Wolf A, Filipchyk A, Klironomos F, Cerda Jara CA, Fenske P, Trimbuch T, Zywitza V, Plass M, Schreyer L, Ayoub S, Kocks C, Kühn R, Rosenmund C, Birchmeier C, Rajewsky N. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 2017; 357:science.aam8526. [DOI: 10.1126/science.aam8526] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/26/2017] [Indexed: 12/29/2022]
|
20
|
Kleinberger G, Brendel M, Mracsko E, Wefers B, Groeneweg L, Xiang X, Focke C, Deußing M, Suárez-Calvet M, Mazaheri F, Parhizkar S, Pettkus N, Wurst W, Feederle R, Bartenstein P, Mueggler T, Arzberger T, Knuesel I, Rominger A, Haass C. The FTD-like syndrome causing TREM2 T66M mutation impairs microglia function, brain perfusion, and glucose metabolism. EMBO J 2017; 36:1837-1853. [PMID: 28559417 DOI: 10.15252/embj.201796516] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/21/2017] [Accepted: 04/27/2017] [Indexed: 12/31/2022] Open
Abstract
Genetic variants in the triggering receptor expressed on myeloid cells 2 (TREM2) increase the risk for several neurodegenerative diseases including Alzheimer's disease and frontotemporal dementia (FTD). Homozygous TREM2 missense mutations, such as p.T66M, lead to the FTD-like syndrome, but how they cause pathology is unknown. Using CRISPR/Cas9 genome editing, we generated a knock-in mouse model for the disease-associated Trem2 p.T66M mutation. Consistent with a loss-of-function mutation, we observe an intracellular accumulation of immature mutant Trem2 and reduced generation of soluble Trem2 similar to patients with the homozygous p.T66M mutation. Trem2 p.T66M knock-in mice show delayed resolution of inflammation upon in vivo lipopolysaccharide stimulation and cultured macrophages display significantly reduced phagocytic activity. Immunohistochemistry together with in vivo TSPO small animal positron emission tomography (μPET) demonstrates an age-dependent reduction in microglial activity. Surprisingly, perfusion magnetic resonance imaging and FDG-μPET imaging reveal a significant reduction in cerebral blood flow and brain glucose metabolism. Thus, we demonstrate that a TREM2 loss-of-function mutation causes brain-wide metabolic alterations pointing toward a possible function of microglia in regulating brain glucose metabolism.
Collapse
Affiliation(s)
- Gernot Kleinberger
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Matthias Brendel
- Department of Nuclear Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eva Mracsko
- NORD Discovery & Translational Area, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Linda Groeneweg
- NORD Discovery & Translational Area, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Xianyuan Xiang
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carola Focke
- Department of Nuclear Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian Deußing
- Department of Nuclear Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marc Suárez-Calvet
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Fargol Mazaheri
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Samira Parhizkar
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nadine Pettkus
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Technische Universität München, Freising-Weihenstephan, Germany
| | - Regina Feederle
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Helmholtz Center Munich, German Research Center for Environmental Health, Institute for Diabetes and Obesity, Core Facility Monoclonal Antibody Development, Munich, Germany
| | - Peter Bartenstein
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Department of Nuclear Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Mueggler
- NORD Discovery & Translational Area, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Thomas Arzberger
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Irene Knuesel
- NORD Discovery & Translational Area, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Axel Rominger
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Department of Nuclear Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Haass
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| |
Collapse
|
21
|
Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017; 121-122:118-129. [PMID: 28288828 PMCID: PMC5483188 DOI: 10.1016/j.ymeth.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA.
Collapse
Affiliation(s)
| | - Daniel E Bauer
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
| |
Collapse
|
22
|
Creation of targeted inversion mutations in plants using an RNA-guided endonuclease. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2016.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
23
|
Ruan GX, Barry E, Yu D, Lukason M, Cheng SH, Scaria A. CRISPR/Cas9-Mediated Genome Editing as a Therapeutic Approach for Leber Congenital Amaurosis 10. Mol Ther 2017; 25:331-341. [PMID: 28109959 PMCID: PMC5368591 DOI: 10.1016/j.ymthe.2016.12.006] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/06/2016] [Accepted: 12/06/2016] [Indexed: 12/18/2022] Open
Abstract
As the most common subtype of Leber congenital amaurosis (LCA), LCA10 is a severe retinal dystrophy caused by mutations in the CEP290 gene. The most frequent mutation found in patients with LCA10 is a deep intronic mutation in CEP290 that generates a cryptic splice donor site. The large size of the CEP290 gene prevents its use in adeno-associated virus (AAV)-mediated gene augmentation therapy. Here, we show that targeted genomic deletion using the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system represents a promising therapeutic approach for the treatment of patients with LCA10 bearing the CEP290 splice mutation. We generated a cellular model of LCA10 by introducing the CEP290 splice mutation into 293FT cells and we showed that guide RNA pairs coupled with SpCas9 were highly efficient at removing the intronic splice mutation and restoring the expression of wild-type CEP290. In addition, we demonstrated that a dual AAV system could effectively delete an intronic fragment of the Cep290 gene in the mouse retina. To minimize the immune response to prolonged expression of SpCas9, we developed a self-limiting CRISPR/Cas9 system that minimizes the duration of SpCas9 expression. These results support further studies to determine the therapeutic potential of CRISPR/Cas9-based strategies for the treatment of patients with LCA10.
Collapse
Affiliation(s)
- Guo-Xiang Ruan
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA.
| | | | - Dan Yu
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA
| | | | - Seng H Cheng
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA
| | - Abraham Scaria
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA
| |
Collapse
|
24
|
Roointan A, Morowvat MH. Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production. Biotechnol Genet Eng Rev 2017; 32:74-91. [PMID: 28052722 DOI: 10.1080/02648725.2016.1270095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The rising potential for CRISPR-Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR-Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR-Cas technology for metabolic engineering of a recombinant host for heterologous protein production. We describe the mechanisms involved in this metabolic engineering approach and present the diverse features of its application in biotechnology and protein production.
Collapse
Affiliation(s)
- Amir Roointan
- a Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies , Shiraz , Iran.,c Department of Medical Biotechnology, School of Medicine , Fasa University of Medical Sciences , Fasa , Iran
| | - Mohammad Hossein Morowvat
- a Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies , Shiraz , Iran.,b Pharmaceutical Sciences Research Center, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran
| |
Collapse
|
25
|
Kopischke S, Schüßler E, Althoff F, Zachgo S. TALEN-mediated genome-editing approaches in the liverwort Marchantia polymorpha yield high efficiencies for targeted mutagenesis. PLANT METHODS 2017; 13:20. [PMID: 28360929 PMCID: PMC5370431 DOI: 10.1186/s13007-017-0167-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/16/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND The liverwort Marchantia polymorpha occupies a crucial position in land plant evolution and provides the opportunity to investigate adaptations to a terrestrial plant life style. Marchantia reverse genetic analyses have thus far been conducted by employing a homologous recombination approach, which yields an efficiency of around 3%. Availability of the characterized and suitable endogenous MpEF1α promoter prompted us to establish the TALEN gene targeting technique for Marchantia. RESULTS Here, two different TALEN techniques, using custom and self-assembled TALEN constructs, were applied and compared. The MpNOP1 gene was selected as a candidate gene, as the respective knockout mutant has been shown to lack air chamber formation, representing an easily traceable phenotype. We demonstrate that both TALEN approaches are successful in Marchantia yielding high gene targeting efficiencies of over 20%. Investigation of selected G1 up to G4 generations proved the stability of the knockout mutants. In 392 analyzed T1 plants, no additional phenotypes were observed and only one chimeric knockout plant was detected after an extended cultivation period. Interestingly, two out of the 24 sequenced mutants harbored indels causing in-frame mutations and revealed novel Mpnop1-related phenotypes. This demonstrates the potential to detect crucial amino acids and motives of targeted proteins, which is of special interest for essential genes where full knockouts are lethal. The FastTALE™ TALEN assembly kit enables the rapid assembly and ligation of the TALEN arms within half a day. For transformations, custom and assembled constructs were subcloned into Marchantia binary vectors possessing the MpEF1α promoter. CONCLUSION Considering time, costs and practicability, the assembly TALEN approach represents a rapid and highly efficient gene targeting system to generate Marchantia knockout mutants, which can be further adapted for future advanced genome-editing applications.
Collapse
Affiliation(s)
- Sarah Kopischke
- Botany Department, School of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
| | - Esther Schüßler
- Botany Department, School of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
| | - Felix Althoff
- Botany Department, School of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
| |
Collapse
|
26
|
Chen KY, Knoepfler PS. To CRISPR and beyond: the evolution of genome editing in stem cells. Regen Med 2016; 11:801-816. [PMID: 27905217 PMCID: PMC5221123 DOI: 10.2217/rme-2016-0107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022] Open
Abstract
The goal of editing the genomes of stem cells to generate model organisms and cell lines for genetic and biological studies has been pursued for decades. There is also exciting potential for future clinical impact in humans. While recent, rapid advances in targeted nuclease technologies have led to unprecedented accessibility and ease of gene editing, biology has benefited from past directed gene modification via homologous recombination, gene traps and other transgenic methodologies. Here we review the history of genome editing in stem cells (including via zinc finger nucleases, transcription activator-like effector nucleases and CRISPR-Cas9), discuss recent developments leading to the implementation of stem cell gene therapies in clinical trials and consider the prospects for future advances in this rapidly evolving field.
Collapse
Affiliation(s)
- Kuang-Yui Chen
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA, USA
- Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA
- Genome Center, University of California Davis, Davis, CA, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA, USA
- Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA
- Genome Center, University of California Davis, Davis, CA, USA
| |
Collapse
|
27
|
Takasu Y, Kobayashi I, Tamura T, Uchino K, Sezutsu H, Zurovec M. Precise genome editing in the silkworm Bombyx mori using TALENs and ds- and ssDNA donors - A practical approach. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 78:29-38. [PMID: 27569417 DOI: 10.1016/j.ibmb.2016.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
Engineered nucleases are able to introduce double stranded breaks at desired genomic locations. The breaks can be repaired by an error-prone non-homologous end joining (NHEJ) mechanism, or the repair process can be exploited to introduce precise DNA modifications by homology-directed repair (HDR) when provided with a suitable donor template. We designed a series of DNA donors including long dsDNA plasmids as well as short ssDNA oligonucleotides and compared the effectiveness of their utilization during gene targeting with highly efficient transcription activator-like effector nucleases (TALENs). While the use of long dsDNA donors for the incorporation of larger DNA fragments in Bombyx is still a problem, short single-stranded oligodeoxynucleotides (ssODNs) are incorporated quite efficiently. We show that appropriately designed ssODNs were integrated into germ cells in up to 79% of microinjected individuals and describe in more detail the conditions for the precise genome editing of Bombyx genes. We specify the donor sequence requirements that affected knock-in efficiency, and demonstrate the successful applications of this method of sequence deletion, insertion and replacement in the Bombyx genome.
Collapse
Affiliation(s)
- Yoko Takasu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Isao Kobayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Toshiki Tamura
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Keiro Uchino
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hideki Sezutsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Michal Zurovec
- Biology Centre of the ASCR, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
| |
Collapse
|
28
|
Abstract
Gene engineering for generating targeted mouse mutants is a key technology for biomedical research. Using TALENs as sequence-specific nucleases to induce targeted double-strand breaks, the mouse genome can be directly modified in zygotes in a single step without the need for embryonic stem cells. By embryo microinjection of TALEN mRNAs and targeting vectors, knockout and knock-in alleles can be generated fast and efficiently. In this chapter we provide protocols for the application of TALENs in mouse zygotes.
Collapse
Affiliation(s)
- 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), 81377, Munich, Germany.
| | - 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.
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), 81377, Munich, Germany.
- Technische Universität München, 85350, Freising-Weihenstephan, Germany.
- Max Planck Institute of Psychiatry, 80804, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 81377, 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-Center for Molecular Medicine, 13125, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
| |
Collapse
|
29
|
Zhou Y, Liu Y, Hussmann D, Brøgger P, Al-Saaidi RA, Tan S, Lin L, Petersen TS, Zhou GQ, Bross P, Aagaard L, Klein T, Rønn SG, Pedersen HD, Bolund L, Nielsen AL, Sørensen CB, Luo Y. Enhanced genome editing in mammalian cells with a modified dual-fluorescent surrogate system. Cell Mol Life Sci 2016; 73:2543-63. [PMID: 26755436 PMCID: PMC11108510 DOI: 10.1007/s00018-015-2128-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/09/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
Programmable DNA nucleases such as TALENs and CRISPR/Cas9 are emerging as powerful tools for genome editing. Dual-fluorescent surrogate systems have been demonstrated by several studies to recapitulate DNA nuclease activity and enrich for genetically edited cells. In this study, we created a single-strand annealing-directed, dual-fluorescent surrogate reporter system, referred to as C-Check. We opted for the Golden Gate Cloning strategy to simplify C-Check construction. To demonstrate the utility of the C-Check system, we used the C-Check in combination with TALENs or CRISPR/Cas9 in different scenarios of gene editing experiments. First, we disrupted the endogenous pIAPP gene (3.0 % efficiency) by C-Check-validated TALENs in primary porcine fibroblasts (PPFs). Next, we achieved gene-editing efficiencies of 9.0-20.3 and 4.9 % when performing single- and double-gene targeting (MAPT and SORL1), respectively, in PPFs using C-Check-validated CRISPR/Cas9 vectors. Third, fluorescent tagging of endogenous genes (MYH6 and COL2A1, up to 10.0 % frequency) was achieved in human fibroblasts with C-Check-validated CRISPR/Cas9 vectors. We further demonstrated that the C-Check system could be applied to enrich for IGF1R null HEK293T cells and CBX5 null MCF-7 cells with frequencies of nearly 100.0 and 86.9 %, respectively. Most importantly, we further showed that the C-Check system is compatible with multiplexing and for studying CRISPR/Cas9 sgRNA specificity. The C-Check system may serve as an alternative dual-fluorescent surrogate tool for measuring DNA nuclease activity and enrichment of gene-edited cells, and may thereby aid in streamlining programmable DNA nuclease-mediated genome editing and biological research.
Collapse
Affiliation(s)
- Yan Zhou
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Yong Liu
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Dianna Hussmann
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Peter Brøgger
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Rasha Abdelkadhem Al-Saaidi
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and University Hospital, 8200, Aarhus N, Denmark
| | - Shuang Tan
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
- Shenzhen Key Laboratory for Anti-aging and Regenerative Medicine, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Trine Skov Petersen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Guang Qian Zhou
- Shenzhen Key Laboratory for Anti-aging and Regenerative Medicine, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Peter Bross
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and University Hospital, 8200, Aarhus N, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Tino Klein
- Department of Histology, Gubra A/S, 2970, Hørsholm, Denmark
| | - Sif Groth Rønn
- Department of Incretin and Obesity Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | | | - Lars Bolund
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
- BGI-Shenzhen, Shenzhen, 518083, China
- The Danish Regenerative Engineering Alliance for Medicine (DREAM), Aarhus University, Aarhus, Denmark
| | - Anders Lade Nielsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Charlotte Brandt Sørensen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and University Hospital, 8200, Aarhus N, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark.
- Department of Incretin and Obesity Research, Novo Nordisk A/S, 2760, Måløv, Denmark.
- The Danish Regenerative Engineering Alliance for Medicine (DREAM), Aarhus University, Aarhus, Denmark.
| |
Collapse
|
30
|
Zhao Y, Zhang C, Liu W, Gao W, Liu C, Song G, Li WX, Mao L, Chen B, Xu Y, Li X, Xie C. An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci Rep 2016; 6:23890. [PMID: 27033976 PMCID: PMC4817149 DOI: 10.1038/srep23890] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Precision DNA/gene replacement is a promising genome-editing tool that is highly desirable for molecular engineering and breeding by design. Although the CRISPR/Cas9 system works well as a tool for gene knockout in plants, gene replacement has rarely been reported. Towards this end, we first designed a combinatory dual-sgRNA/Cas9 vector (construct #1) that successfully deleted miRNA gene regions (MIR169a and MIR827a). The deletions were confirmed by PCR and subsequent sequencing, yielding deletion efficiencies of 20% and 24% on MIR169a and MIR827a loci, respectively. We designed a second structure (construct #2) that contains sites homologous to Arabidopsis TERMINAL FLOWER 1 (TFL1) for homology-directed repair (HDR) with regions corresponding to the two sgRNAs on the modified construct #1. The two constructs were co-transformed into Arabidopsis plants to provide both targeted deletion and donor repair for targeted gene replacement by HDR. Four of 500 stably transformed T0 transgenic plants (0.8%) contained replaced fragments. The presence of the expected recombination sites was further confirmed by sequencing. Therefore, we successfully established a gene deletion/replacement system in stably transformed plants that can potentially be utilized to introduce genes of interest for targeted crop improvement.
Collapse
Affiliation(s)
- Yongping Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Congsheng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China.,Anhui Agricultural University, Hefei, Anhui Province, 230036 China
| | - Wenwen Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Wei Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Changlin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Gaoyuan Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Wen-Xue Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Long Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Beijiu Chen
- Anhui Agricultural University, Hefei, Anhui Province, 230036 China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 China
| |
Collapse
|
31
|
Chu VT, Weber T, Graf R, Sommermann T, Petsch K, Sack U, Volchkov P, Rajewsky K, Kühn R. Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol 2016; 16:4. [PMID: 26772810 PMCID: PMC4715285 DOI: 10.1186/s12896-016-0234-4] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/07/2016] [Indexed: 01/03/2023] Open
Abstract
Background The CRISPR/Cas9 system is increasingly used for gene inactivation in mouse zygotes, but homology-directed mutagenesis and use of inbred embryos are less established. In particular, Rosa26 knock-in alleles for the insertion of transgenes in a genomic ‘safe harbor’ site, have not been produced. Here we applied CRISPR/Cas9 for the knock-in of 8–11 kb inserts into Rosa26 of C57BL/6 zygotes. Results We found that 10–20 % of live pups derived from microinjected zygotes were founder mutants, without apparent off-target effects, and up to 50 % knock-in embryos were recovered upon coinjection of Cas9 mRNA and protein. Using this approach, we established a new mouse line for the Cre/loxP-dependent expression of Cas9. Conclusions Altogether, our protocols and resources support the fast and direct generation of new Rosa26 knock-in alleles and of Cas9-mediated in vivo gene editing in the widely used C57BL/6 inbred strain. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0234-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Van Trung Chu
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Timm Weber
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Robin Graf
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | | | - Kerstin Petsch
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Ulrike Sack
- Present Address: Bayer Pharma AG Building S107, 13353, Berlin, Germany.
| | | | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany. .,Berlin Institute of Health, Kapelle-Ufer 2, 10117, Berlin, Germany.
| |
Collapse
|
32
|
Abstract
The rapid advances in the field of genome editing using targeted endonucleases have called considerable attention to the potential of this technology for human gene therapy. Targeted correction of disease-causing mutations could ensure lifelong, tissue-specific expression of the relevant gene, thereby alleviating or resolving a specific disease phenotype. In this review, we aim to explore the potential of this technology for the therapy of β-thalassemia. This blood disorder is caused by mutations in the gene encoding the β-globin chain of hemoglobin, leading to severe anemia in affected patients. Curative allogeneic bone marrow transplantation is available only to a small subset of patients, leaving the majority of patients dependent on regular blood transfusions and iron chelation therapy. The transfer of gene-corrected autologous hematopoietic stem cells could provide a therapeutic alternative, as recent results from gene therapy trials using a lentiviral gene addition approach have demonstrated. Genome editing has the potential to further advance this approach as it eliminates the need for semi-randomly integrating viral vectors and their associated risk of insertional mutagenesis. In the following pages we will highlight the advantages and risks of genome editing compared to standard therapy for β-thalassemia and elaborate on lessons learned from recent gene therapy trials.
Collapse
Affiliation(s)
- Astrid Glaser
- 1Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Bradley McColl
- 1Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Jim Vadolas
- 1Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| |
Collapse
|
33
|
CRISPR/Cas9 system as an innovative genetic engineering tool: Enhancements in sequence specificity and delivery methods. Biochim Biophys Acta Rev Cancer 2015; 1856:234-43. [DOI: 10.1016/j.bbcan.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/26/2015] [Accepted: 09/29/2015] [Indexed: 01/30/2023]
|
34
|
Wang L, Shao Y, Guan Y, Li L, Wu L, Chen F, Liu M, Chen H, Ma Y, Ma X, Liu M, Li D. Large genomic fragment deletion and functional gene cassette knock-in via Cas9 protein mediated genome editing in one-cell rodent embryos. Sci Rep 2015; 5:17517. [PMID: 26620761 PMCID: PMC4664917 DOI: 10.1038/srep17517] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/30/2015] [Indexed: 11/14/2022] Open
Abstract
The CRISPR-Cas RNA-guided system has versatile uses in many organisms and allows modification of multiple target sites simultaneously. Generating novel genetically modified mouse and rat models is one valuable application of this system. Through the injection of Cas9 protein instead of mRNA into embryos, we observed fewer off-target effects of Cas9 and increased point mutation knock-in efficiency. Large genomic DNA fragment (up to 95 kb) deletion mice were generated for in vivo study of lncRNAs and gene clusters. Site-specific insertion of a 2.7 kb CreERT2 cassette into the mouse Nfatc1 locus allowed labeling and tracing of hair follicle stem cells. In addition, we combined the Cre-Loxp system with a gene-trap strategy to insert a GFP reporter in the reverse orientation into the rat Lgr5 locus, which was later inverted by Cre-mediated recombination, yielding a conditional knockout/reporter strategy suitable for mosaic mutation analysis.
Collapse
Affiliation(s)
- Liren Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,The Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Yanjiao Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yuting Guan
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Liang Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lijuan Wu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fangrui Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Meizhen Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Huaqing Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, Hainan Reproductive Medical Center, the Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Xueyun Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,The Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| |
Collapse
|
35
|
Truong DJJ, Kühner K, Kühn R, Werfel S, Engelhardt S, Wurst W, Ortiz O. Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic Acids Res 2015; 43:6450-8. [PMID: 26082496 PMCID: PMC4513872 DOI: 10.1093/nar/gkv601] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 05/26/2015] [Indexed: 11/14/2022] Open
Abstract
Using CRISPR/Cas9, it is possible to target virtually any gene in any organism. A major limitation to its application in gene therapy is the size of Cas9 (>4 kb), impeding its efficient delivery via recombinant adeno-associated virus (rAAV). Therefore, we developed a split–Cas9 system, bypassing the packaging limit using split-inteins. Each Cas9 half was fused to the corresponding split-intein moiety and, only upon co-expression, the intein-mediated trans-splicing occurs and the full Cas9 protein is reconstituted. We demonstrated that the nuclease activity of our split-intein system is comparable to wild-type Cas9, shown by a genome-integrated surrogate reporter and by targeting three different endogenous genes. An analogously designed split-Cas9D10A nickase version showed similar activity as Cas9D10A. Moreover, we showed that the double nick strategy increased the homologous directed recombination (HDR). In addition, we explored the possibility of delivering the repair template accommodated on the same dual-plasmid system, by transient transfection, showing an efficient HDR. Most importantly, we revealed for the first time that intein-mediated split–Cas9 can be packaged, delivered and its nuclease activity reconstituted efficiently, in cells via rAAV.
Collapse
Affiliation(s)
- Dong-Jiunn Jeffery Truong
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany Institute of Developmental Genetics,Technische Universität München, Freising-Weihenstephan 85354, Germany
| | - Karin Kühner
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany Max Delbrück Center for Molecular Medicine (MDC), Berlin 13125, Germany
| | - Stanislas Werfel
- Institute of Pharmacology and Toxicology. Technische Universität München, Munich 80802, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology. Technische Universität München, Munich 80802, Germany German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich 80802, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany Institute of Developmental Genetics,Technische Universität München, Freising-Weihenstephan 85354, Germany Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Munich 80336, Germany Munich Cluster for Systems Neurology (SyNergy) Adolf-Butenandt-Institut Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Oskar Ortiz
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany
| |
Collapse
|