1
|
Schreiber T, Prange A, Schäfer P, Iwen T, Grützner R, Marillonnet S, Lepage A, Javelle M, Paul W, Tissier A. Efficient scar-free knock-ins of several kilobases in plants by engineered CRISPR-Cas endonucleases. Mol Plant 2024:S1674-2052(24)00086-8. [PMID: 38520090 DOI: 10.1016/j.molp.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
In plants and mammals, non-homologous end-joining is the dominant pathway to repair DNA double-strand breaks, making it challenging to generate knock-in events. In this study, we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana benthamiana. We achieved precise and scar-free insertion of several kilobases of DNA both in transient and stable transformation systems. In Arabidopsis thaliana, fusion of Cas9 to a herpes virus family exonuclease led to 10-fold higher frequencies of knock-ins in the first generation of transformants. In addition, we demonstrated stable and heritable knock-ins in wheat in 1% of the primary transformants. Taken together, our results open perspectives for the routine production of heritable knock-in and gene replacement events in plants.
Collapse
Affiliation(s)
- Tom Schreiber
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Anja Prange
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Petra Schäfer
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Thomas Iwen
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Ramona Grützner
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Aurélie Lepage
- Limagrain, Centre de Recherche, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Marie Javelle
- Limagrain, Centre de Recherche, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Wyatt Paul
- Limagrain, Centre de Recherche, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
| |
Collapse
|
2
|
Bischof J, Hierl M, Koller U. Emerging Gene Therapeutics for Epidermolysis Bullosa under Development. Int J Mol Sci 2024; 25:2243. [PMID: 38396920 PMCID: PMC10889532 DOI: 10.3390/ijms25042243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
The monogenetic disease epidermolysis bullosa (EB) is characterised by the formation of extended blisters and lesions on the patient's skin upon minimal mechanical stress. Causal for this severe condition are genetic mutations in genes, leading to the functional impairment, reduction, or absence of the encoded protein within the skin's basement membrane zone connecting the epidermis to the underlying dermis. The major burden of affected families justifies the development of long-lasting and curative therapies operating at the genomic level. The landscape of causal therapies for EB is steadily expanding due to recent breakthroughs in the gene therapy field, providing promising outcomes for patients suffering from this severe disease. Currently, two gene therapeutic approaches show promise for EB. The clinically more advanced gene replacement strategy was successfully applied in severe EB forms, leading to a ground-breaking in vivo gene therapy product named beremagene geperpavec (B-VEC) recently approved from the US Food and Drug Administration (FDA). In addition, the continuous innovations in both designer nucleases and gene editing technologies enable the efficient and potentially safe repair of mutations in EB in a potentially permanent manner, inspiring researchers in the field to define and reach new milestones in the therapy of EB.
Collapse
Affiliation(s)
- Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
| | - Markus Hierl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
| |
Collapse
|
3
|
Kim JH, Yu J, Kim JY, Park YJ, Bae S, Kang KK, Jung YJ. Phenotypic characterization of pre-harvest sprouting resistance mutants generated by the CRISPR/Cas9-geminiviral replicon system in rice. BMB Rep 2024; 57:79-85. [PMID: 38303561 PMCID: PMC10910094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 02/03/2024] Open
Abstract
Pre-harvest sprouting is a critical phenomenon involving germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. In this paper, we generated HDR mutant lines with one region SNP (C/T) and an insertion of 6 bp (GGT/GGTGGCGGC) in OsERF1 genes for pre-harvest sprouting (PHS) resistance using CRISPR/Cas9 and a geminiviral replicon system. The incidence of HDR was 2.6% in transformed calli. T1 seeds were harvested from 12 HDR-induced calli and named ERF1-hdr line. Molecular stability, key agronomic properties, physiological properties, and biochemical properties of target genes in the ERF1-hdr line were investigated for three years. The ERF1-hdr line showed significantly enhanced seed dormancy and pre-harvest sprouting resistance. qRT-PCR analysis suggested that enhanced ABA signaling resulted in a stronger phenotype of PHS resistance. These results indicate that efficient HDR can be achieved through SNP/InDel replacement using a single and modular configuration applicable to different rice targets and other crops. This work demonstrates the potential to replace all genes with elite alleles within one generation and greatly expands our ability to improve agriculturally important traits. [BMB Reports 2024; 57(2): 79-85].
Collapse
Affiliation(s)
- Jong Hee Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Korea
| | - Jihyeon Yu
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jin Young Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea
| | - Yong Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea
| | - Sangsu Bae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Kwon Kyoo Kang
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Korea
| | - Yu Jin Jung
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Korea
| |
Collapse
|
4
|
Li Y, Huang C, Liu Y, Zeng J, Yu H, Tong Z, Yuan X, Sui X, Fang D, Xiao B, Zhao S, Yuan C. CRISPR/Cas9-mediated seamless gene replacement in protoplasts expands the resistance spectrum to TMV-U1 strain in regenerated Nicotiana tabacum. Plant Biotechnol J 2023; 21:2641-2653. [PMID: 37610064 PMCID: PMC10651143 DOI: 10.1111/pbi.14159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/17/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023]
Abstract
CRISPR/Cas-based genome editing is now extensively used in plant breeding and continues to evolve. Most CRISPR/Cas current applications in plants focus on gene knock-outs; however, there is a pressing need for new methods to achieve more efficient delivery of CRISPR components and gene knock-ins to improve agronomic traits of crop cultivars. We report here a genome editing system that combines the advantages of protoplast technologies with recent CRISPR/Cas advances to achieve seamless large fragment insertions in the model Solanaceae plant Nicotiana tabacum. With this system, two resistance-related regions of the N' gene were replaced with homologous fragments from the N'alata gene to confer TMV-U1 resistance in the T0 generation of GMO-free plants. Our study establishes a reliable genome-editing tool for efficient gene modifications and provides a detailed description of the optimization process to assist other researchers adapt this system for their needs.
Collapse
Affiliation(s)
- Yanli Li
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Changjun Huang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yong Liu
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Jianmin Zeng
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Haiqin Yu
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Zhijun Tong
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xinjie Yuan
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Xueyi Sui
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Dunhuang Fang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Bingguang Xiao
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | | | - Cheng Yuan
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| |
Collapse
|
5
|
Prokopchuk G, Butenko A, Dacks JB, Speijer D, Field MC, Lukeš J. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc 2023; 98:1910-1927. [PMID: 37336550 PMCID: PMC10952624 DOI: 10.1111/brv.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
Collapse
Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
- Life Science Research Centre, Faculty of ScienceUniversity of OstravaChittussiho 983/10Ostrava71000Czech Republic
| | - Joel B. Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Division of Infectious Diseases, Department of MedicineUniversity of Alberta1‐124 Clinical Sciences Building, 11350‐83 AvenueEdmontonT6G 2R3AlbertaCanada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and the EnvironmentUniversity College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMCUniversity of AmsterdamMeibergdreef 15Amsterdam1105 AZThe Netherlands
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| |
Collapse
|
6
|
Smith JB, Cancedda L, Jozwiak S, Mercer AC. Editorial: Viral vector-based gene therapy in neurological disease: The future is now. Front Neurol 2023; 14:1153681. [PMID: 36864918 PMCID: PMC9972099 DOI: 10.3389/fneur.2023.1153681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Affiliation(s)
- Jared B. Smith
- Research and Early Development, REGENXBIO Inc., Rockville, MD, United States,*Correspondence: Jared B. Smith ✉
| | - Laura Cancedda
- Brain Development and Disorders Lab, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Sergiusz Jozwiak
- Research Department, The Children's Memorial Health Institute (IPCZD), Warsaw, Poland
| | - Andrew C. Mercer
- Research and Early Development, REGENXBIO Inc., Rockville, MD, United States
| |
Collapse
|
7
|
Badura J, van Wyk N, Zimmer K, Pretorius IS, von Wallbrunn C, Wendland J. PCR-based gene targeting in Hanseniaspora uvarum. FEMS Yeast Res 2023; 23:foad034. [PMID: 37500280 DOI: 10.1093/femsyr/foad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Lack of gene-function analyses tools limits studying the biology of Hanseniaspora uvarum, one of the most abundant yeasts on grapes and in must. We investigated a rapid PCR-based gene targeting approach for one-step gene replacement in this diploid yeast. To this end, we generated and validated two synthetic antibiotic resistance genes, pFA-hygXL and pFA-clnXL, providing resistance against hygromycin and nourseothricin, respectively, for use with H. uvarum. Addition of short flanking-homology regions of 56-80 bp to these selection markers via PCR was sufficient to promote gene targeting. We report here the deletion of the H. uvarum LEU2 and LYS2 genes with these marker genes via two rounds of consecutive transformations, each resulting in the generation of auxotrophic strains (leu2/leu2; lys2/lys2). The hereby constructed leucine auxotrophic leu2/leu2 strain was subsequently complemented in a targeted manner, thereby further validating this approach. PCR-based gene targeting in H. uvarum was less efficient than in Saccharomyces cerevisiae. However, this approach, combined with the availability of two marker genes, provides essential tools for directed gene manipulations in H. uvarum.
Collapse
Affiliation(s)
- Jennifer Badura
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Niël van Wyk
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Kerstin Zimmer
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Christian von Wallbrunn
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| |
Collapse
|
8
|
Zhang H, Zhang S, Zhang J, Qi H, Wang H, Zhang L, Huang J, Wang J. Acyltransferase Domain Swapping for the Production of Tenvermectin B Metabolites in Genetically Engineered Strain Streptomyces avermitilis HU02. J Agric Food Chem 2022; 70:11994-12003. [PMID: 36121904 DOI: 10.1021/acs.jafc.2c04482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tenvermectins A and B (TVMs A and B) are hybrid natural compounds of avermectins and milbemycins with enhanced insecticidal activity. Aiming at obtaining a strain for the production of the higher activity metabolite-TVM-B as a major constituent, a recombinant strain Streptomyces avermitilis HU02 was constructed by a domain swapping strategy in which milA1-AT0 gene in S. avermitilis MHJ1011 was replaced by eryA1-AT0 gene from Saccharopolyspora erythraea ATCC 40137. Chemical investigation on the culture of S. avermitilis HU02 led to the isolation of a large amount of TVM-B and trace amounts of five new TVM-B analogues. The structures of new metabolites were elucidated by extensive spectroscopic analysis including 1D and 2D nuclear magnetic resonance and high-resolution electrospray ionization mass spectrometry data. The bioassay test indicated that five new TVM-B analogues exhibited potent insecticidal activity against Tetranychus cinnabarinus and Bursaphelenchus xylophilus. This study provided a feasible route to the low-cost production of TVM-B and enriched the structural diversity of TVM-B metabolites.
Collapse
Affiliation(s)
- Hui Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
- Institute of Natural Active Substances Research and Utilization, School of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou 318020, China
- Life Science and Biotechnology Research Center, School of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shaoyong Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Ji Zhang
- Life Science and Biotechnology Research Center, School of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Huan Qi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Han Wang
- Life Science and Biotechnology Research Center, School of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Jun Huang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
- Zhejiang Makohs Biotech Co., Ltd, Taizhou 318000, P.R. China
| | - Jidong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| |
Collapse
|
9
|
Sait H, Srivastava S, Saxena D. Integrated Management Strategies for Epidermolysis Bullosa: Current Insights. Int J Gen Med 2022; 15:5133-5144. [PMID: 35637703 PMCID: PMC9148209 DOI: 10.2147/ijgm.s342740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022] Open
Abstract
Epidermolysis bullosa (EB) is a group of rare genodermatoses that is characterized by skin fragility resulting from minor trauma. There are four major subtypes, namely, EB simplex, junctional EB, dystrophic EB and Kindler EB, depending upon the localization of defective protein and resulting plane of blister formation. The phenotype is heterogeneous in terms of severity and majority of them present at birth or neonatal period. Currently, the treatment is mainly supportive and requires multidisciplinary care. The complex molecular pathology creates difficulty in discovering a unified curative treatment approach. But with arduous efforts, significant progress has been made in the development of treatment strategies in the last decade. The management strategies range from targeting the underlying causative factor to symptom-relieving approaches, and include gene, mRNA, protein, cell and combination therapies. In this review, we enumerate the promising approaches that are currently under various stages of investigation to provide effective treatment for patients with EB.
Collapse
Affiliation(s)
- Haseena Sait
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Somya Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| |
Collapse
|
10
|
Happi Mbakam C, Lamothe G, Tremblay JP. Therapeutic Strategies for Dystrophin Replacement in Duchenne Muscular Dystrophy. Front Med (Lausanne) 2022; 9:859930. [PMID: 35419381 PMCID: PMC8995704 DOI: 10.3389/fmed.2022.859930] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 12/12/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked hereditary disease characterized by progressive muscle wasting due to modifications in the DMD gene (exon deletions, nonsense mutations, intra-exonic insertions or deletions, exon duplications, splice site defects, and deep intronic mutations) that result in a lack of functional dystrophin expression. Many therapeutic approaches have so far been attempted to induce dystrophin expression and improve the patient phenotype. In this manuscript, we describe the relevant updates for some therapeutic strategies for DMD aiming to restore dystrophin expression. We also present and analyze in vitro and in vivo ongoing experimental approaches to treat the disease.
Collapse
Affiliation(s)
- Cedric Happi Mbakam
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada.,Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Gabriel Lamothe
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada.,Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Jacques P Tremblay
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada.,Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| |
Collapse
|
11
|
Tu JL, Bai XY, Xu YL, Li N, Xu JW. Targeted Gene Insertion and Replacement in the Basidiomycete Ganoderma lucidum by Inactivation of Nonhomologous End Joining Using CRISPR/Cas9. Appl Environ Microbiol 2021; 87:e0151021. [PMID: 34524900 DOI: 10.1128/AEM.01510-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Targeted gene insertion or replacement is a promising genome-editing tool for molecular breeding and gene engineering. Although CRISPR/Cas9 works well for gene disruption and deletion in Ganoderma lucidum, targeted gene insertion and replacement remain a serious challenge due to the low efficiency of homologous recombination (HR) in this species. In this work, we demonstrate that the DNA double-strand breaks induced by Cas9 were mainly repaired via the nonhomologous end joining (NHEJ) pathway, at a frequency of 96.7%. To establish an efficient target gene insertion and replacement tool in Ganoderma, we first inactivated the NHEJ pathway via disruption of the Ku70 gene (ku70) using a dual single guide RNA (sgRNA)-directed gene deletion method. Disruption of the ku70 gene significantly decreased NHEJ activity in G. lucidum. Moreover, ku70 disruption strains exhibited 96.3% and 93.1% frequencies of targeted gene insertion and replacement, respectively, when target DNA with the orotidine 5'-monophosphate decarboxylase (ura3) gene and 1.5-kb homologous 5'- and 3'-flanking sequences was used as a donor template, compared to 3.3% and 0%, respectively, at these targeted sites for a control strain (Cas9 strain). Our results indicated that ku70 disruption strains were efficient recipients for targeted gene insertion and replacement. This tool will advance our understanding of functional genomics in G. lucidum. IMPORTANCE Functional genomic studies in Ganoderma have been hindered by the absence of adequate genome-engineering tools. Although CRISPR/Cas9 works well for gene disruption and deletion in G. lucidum, targeted gene insertion and replacement have remained a serious challenge due to the low efficiency of HR in these species, although such precise genome modifications, including site mutations, site-specific integrations, and allele or promoter replacements, would be incredibly valuable. In this work, we inactivated the NHEJ repair mechanism in G. lucidum by disrupting the ku70 gene using the CRISPR/Cas9 system. Moreover, we established a target gene insertion and replacement method in ku70-disrupted G. lucidum that possessed high-efficiency gene targeting. This technology will advance our understanding of the functional genomics of G. lucidum.
Collapse
|
12
|
Weuring W, Geerligs J, Koeleman BPC. Gene Therapies for Monogenic Autism Spectrum Disorders. Genes (Basel) 2021; 12:genes12111667. [PMID: 34828273 PMCID: PMC8617899 DOI: 10.3390/genes12111667] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
Novel genome editing and transient gene therapies have been developed the past ten years, resulting in the first in-human clinical trials for monogenic disorders. Syndromic autism spectrum disorders can be caused by mutations in a single gene. Given the monogenic aspect and severity of syndromic ASD, it is an ideal candidate for gene therapies. Here, we selected 11 monogenic ASD syndromes, validated by animal models, and reviewed current gene therapies for each syndrome. Given the wide variety and novelty of some forms of gene therapy, the best possible option must be decided based on the gene and mutation.
Collapse
|
13
|
Wang Z, Wan L, Xin Q, Zhang X, Song Y, Wang P, Hong D, Fan Z, Yang G. Optimizing glyphosate tolerance in rapeseed by CRISPR/Cas9-based geminiviral donor DNA replicon system with Csy4-based single-guide RNA processing. J Exp Bot 2021; 72:4796-4808. [PMID: 33872346 DOI: 10.1093/jxb/erab167] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oil crop worldwide, and effective weed control can protect its yield and quality. Farmers can benefit from cultivars tolerant to herbicides such as glyphosate. Amino acid substitutions in enolpyruvylshikimate-3-phosphate synthase (EPSPS) render the plant less sensitive to glyphosate. Therefore, we aimed to optimize the glyphosate tolerance trait in rapeseed via endogenous EPSPS modification. To achieve effective gene replacement in B. napus L., we employed a CRISPR/Cas9 system expressing single-guide RNAs (sgRNAs) cleaved by the CRISPR-associated RNA endoribonuclease Csy4 from Pseudomonas aeruginosa, for targeted induction of double-strand breaks. Both the donor template and a geminiviral replicon harbouring an sgRNA expression cassette were introduced into plant cells. Using sgRNAs targeting adjacent donor DNA template containing synonymous mutations in sgRNA sites, we achieved precise gene replacements in the endogenous B. napus EPSPS gene, BnaC04EPSPS, resulting in amino acid substitutions at frequencies up to 20%. Rapeseed seedlings harbouring these substitutions were glyphosate-tolerant. Furthermore, modifications in BnaC04EPSPS were precisely transmitted to the next generation. Our genome editing strategy enables highly efficient gene targeting and the induction of glyphosate tolerance in oilseed rape.
Collapse
Affiliation(s)
- Zhuanrong Wang
- Institute of Crop Science, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lili Wan
- Institute of Crop Science, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhixiong Fan
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
14
|
Lee BH, Waldrop MA, Connolly AM, Ciafaloni E. Time is muscle: A recommendation for early treatment for preterm infants with spinal muscular atrophy. Muscle Nerve 2021; 64:153-155. [PMID: 33959970 DOI: 10.1002/mus.27261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/10/2022]
Abstract
Implementation of newborn screening for spinal muscular atrophy (SMA) in 33 US states and increased genetic carrier screening have led to an increase in early, presymptomatic diagnosis of SMA. Early treatment is critically important and is recommended for presymptomatic infants with two to four copies of survival motor neuron 2. Currently, no specific treatment recommendations exist for preterm infants with SMA. The US Food and Drug Administration does not recommend using onasemnogene abeparvovec-xioi in preterm infants. Some insurance companies interpret "preterm" to be less than 40 weeks gestational age (GA) instead of the commonly accepted 37 weeks GA, which can be a barrier to treatment access. Given the risk of rapid decline in some infants, we recommend treatment of preterm infants when they reach 37 weeks GA, based on the definitions of term GA from the World Health Organization and Centers for Disease Control and Prevention, assuming all other treatment criteria are met.
Collapse
Affiliation(s)
- Bo Hoon Lee
- Child Neurology Division, Department of Neurology, University of Rochester, Rochester, New York, USA.,Neuromuscular Division, Department of Neurology, University of Rochester, Rochester, New York, USA
| | - Megan A Waldrop
- Center for Gene Therapy, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Center for Gene Therapy, Department of Neurology, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Anne M Connolly
- Center for Gene Therapy, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Center for Gene Therapy, Department of Neurology, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Emma Ciafaloni
- Neuromuscular Division, Department of Neurology, University of Rochester, Rochester, New York, USA
| |
Collapse
|
15
|
Abstract
Epidermolysis bullosa (EB) is a genodermatosis, characterized by the formation of extended blisters and lesions on the skin and mucous membranes upon minimal mechanical trauma. The disease is caused by mutations in genes encoding proteins that are essential for skin stability. Functional impairment, reduction, or absence of one of these proteins results in skin fragility due to reduced connectivity between dermis and epidermis. Currently, gene therapy represents the only treatment option with the potential to cure this severe blistering skin disease. Two promising forms of gene therapy are potentially feasible for EB: gene replacement and genome editing. While genome editing for genodermatoses remains at the preclinical stage, gene replacement approaches are clinically advanced and have been applied already to a small number of patients with junctional and dystrophic forms of EB. Here, the viral transduction of the “wild-type” transgene into skin stem cells, followed by autologous grafting of corrected epidermal sheets, led to the regeneration of stable skin. Recent developments regarding designer nuclease-based gene editing strategies enable the establishment of alternative options to restore the gene function in genodermatoses. This is particularly true in cases wherein genetic constellation hinders gene therapy-based gene replacement.
Collapse
Affiliation(s)
- Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Johann W Bauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| |
Collapse
|
16
|
Oborník M. Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs. Biology (Basel) 2021; 10:biology10050386. [PMID: 33946769 PMCID: PMC8145841 DOI: 10.3390/biology10050386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.
Collapse
Affiliation(s)
- Miroslav Oborník
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| |
Collapse
|
17
|
Gu B, Shao G, Gao W, Miao J, Wang Q, Liu X, Tyler BM. Transcriptional Variability Associated With CRISPR-Mediated Gene Replacements at the Phytophthora sojae Avr1b-1 Locus. Front Microbiol 2021; 12:645331. [PMID: 33815332 PMCID: PMC8012851 DOI: 10.3389/fmicb.2021.645331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
Transcriptional plasticity enables oomycetes to rapidly adapt to environmental challenges including emerging host resistance. For example, the soybean pathogen Phytophthora sojae can overcome resistance conferred by the host resistance gene Rps1b through natural silencing of its corresponding effector gene, Avr1b-1. With the Phytophthora CRISPR/Cas9 genome editing system, it is possible to generate site-specific knock-out (KO) and knock-in (KI) mutants and to investigate the biological functions of target genes. In this study, the Avr1b-1 gene was deleted from the P. sojae genome using a homology-directed recombination strategy that replaced Avr1b-1 with a gene encoding the fluorescent protein mCherry. As expected, all selected KO transformants gained virulence on Rps1b plants, while infection of plants lacking Rps1b was not compromised. When a sgRNA-resistant version of Avr1b-1 was reintroduced into the Avr1b-1 locus of an Avr1b KO transformant, KI transformants with a well-transcribed Avr1b-1 gene were unable to infect Rps1b-containing soybeans. However, loss of expression of the incoming Avr1b-1 gene was frequently observed in KI transformants, which resulted in these transformants readily infecting Rps1b soybeans. A similar variability in the expression levels of the incoming gene was observed with AVI- or mCherry-tagged Avr1b-1 constructs. Our results suggest that Avr1b-1 may be unusually susceptible to transcriptional variation.
Collapse
Affiliation(s)
- Biao Gu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Guangda Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wenxin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Brett M Tyler
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
18
|
Hoecker N, Hennecke Y, Schrott S, Marino G, Schmidt SB, Leister D, Schneider A. Gene Replacement in Arabidopsis Reveals Manganese Transport as an Ancient Feature of Human, Plant and Cyanobacterial UPF0016 Proteins. Front Plant Sci 2021; 12:697848. [PMID: 34194462 PMCID: PMC8236900 DOI: 10.3389/fpls.2021.697848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/20/2021] [Indexed: 05/08/2023]
Abstract
The protein family 0016 (UPF0016) is conserved through evolution, and the few members characterized share a function in Mn2+ transport. So far, little is known about the history of these proteins in Eukaryotes. In Arabidopsis thaliana five such proteins, comprising four different subcellular localizations including chloroplasts, have been described, whereas non-photosynthetic Eukaryotes have only one. We used a phylogenetic approach to classify the eukaryotic proteins into two subgroups and performed gene-replacement studies to investigate UPF0016 genes of various origins. Replaceability can be scored readily in the Arabidopsis UPF0016 transporter mutant pam71, which exhibits a functional deficiency in photosystem II. The N-terminal region of the Arabidopsis PAM71 was used to direct selected proteins to chloroplast membranes. Transgenic pam71 lines overexpressing the closest plant homolog (CMT1), human TMEM165 or cyanobacterial MNX successfully restored photosystem II efficiency, manganese binding to photosystem II complexes and consequently plant growth rate and biomass production. Thus AtCMT1, HsTMEM165, and SynMNX can operate in the thylakoid membrane and substitute for PAM71 in a non-native environment, indicating that the manganese transport function of UPF0016 proteins is an ancient feature of the family. We propose that the two chloroplast-localized UPF0016 proteins, CMT1 and PAM71, in plants originated from the cyanobacterial endosymbiont that gave rise to the organelle.
Collapse
Affiliation(s)
- Natalie Hoecker
- Molekularbiologie der Pflanzen (Botanik), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Yvonne Hennecke
- Molekularbiologie der Pflanzen (Botanik), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Simon Schrott
- Molekularbiologie der Pflanzen (Botanik), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Giada Marino
- Molekularbiologie der Pflanzen (Botanik), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Massenspektrometrie von Biomolekülen an der LMU (MSBioLMU), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Sidsel Birkelund Schmidt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Dario Leister
- Molekularbiologie der Pflanzen (Botanik), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Anja Schneider
- Molekularbiologie der Pflanzen (Botanik), Fakultät für Biologie, Ludwig-Maximilians-Universität München, Martinsried, Germany
- *Correspondence: Anja Schneider,
| |
Collapse
|
19
|
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
Collapse
Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| |
Collapse
|
20
|
Feng Y, Yu Z, Zhang S, Xue Z, Huang J, Zhang H, Wan X, Chen A, Wang J. Isolation and Characterization of New 16-Membered Macrolides from the aveA3 Gene Replacement Mutant Strain Streptomyces avermitilis TM24 with Acaricidal and Nematicidal Activities. J Agric Food Chem 2019; 67:4782-4792. [PMID: 30973721 DOI: 10.1021/acs.jafc.9b00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polyketides represent an important class of biologically active and structurally diverse compounds found in nature. They are biosynthesized from acyl CoA precursors by polyketide synthases (PKSs). The use of combinatorial biosynthesis to form hybrid PKSs is considered to be an excellent approach for the development of novel polyketides. Here, 10 new 16-membered macrolide compounds were isolated from the broth of the genetically engineered strain Streptomyces avermitilis TM24, in which the PKS gene aveA3 was seamlessly replaced by the milbemycin PKS gene milA3. Their structures were elucidated on the basis of NMR and MS spectroscopic analyses. The acaricidal and nematicidal activities of them against Tetranychus cinnabarinus and Bursaphelenchus xylophilus were tested. The results indicated that compound 1 had potent acaricidal activity against adult mites with an LC50 value of 0.0022 mg L-1, while compounds 5 and 7 possessed potent nematicidal activity with LC50 values of 4.56 and 4.30 mg L-1, respectively.
Collapse
Affiliation(s)
- Youling Feng
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Zhen Yu
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Shaoyong Zhang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Zhenglian Xue
- College of Biochemical Engineering , Anhui Polytechnic University , Wuhu 241000 , People's Republic of China
| | - Jun Huang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
- Zhejiang Makohs Biotech Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Xu Wan
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Anliang Chen
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
- College of Biochemical Engineering , Anhui Polytechnic University , Wuhu 241000 , People's Republic of China
| |
Collapse
|
21
|
Al-Zaidy S, Pickard AS, Kotha K, Alfano LN, Lowes L, Paul G, Church K, Lehman K, Sproule DM, Dabbous O, Maru B, Berry K, Arnold WD, Kissel JT, Mendell JR, Shell R. Health outcomes in spinal muscular atrophy type 1 following AVXS-101 gene replacement therapy. Pediatr Pulmonol 2019; 54:179-185. [PMID: 30548438 PMCID: PMC6590370 DOI: 10.1002/ppul.24203] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/04/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Spinal Muscular Atrophy type 1 (SMA1) is a rare genetic neuromuscular disease where 75% of SMA1 patients die/require permanent-ventilation by 13.6 months. This study assessed the health outcomes of SMA1 infants treated with AVXS-101 gene replacement therapy. METHODS Twelve genetically confirmed SMA1 infants with homozygous deletions of the SMN1 gene and two SMN2 gene copies received a one-time intravenous proposed therapeutic dose of AVXS-101 in an open label study conducted between December 2014 and 2017. Patients were followed for 2-years post-treatment for outcomes including (1) pulmonary interventions; (2) nutritional interventions; (3) swallow function; (4) hospitalization rates; and (5) motor function. RESULTS All 12 patients completed the study. Seven infants did not require noninvasive ventilation (NIV) by study completion. Eleven patients had stable or improved swallow function, demonstrated by the ability to feed orally; 11 patients were able to speak. The mean proportion of time hospitalized was 4.4%; the mean unadjusted annualized hospitalization rate was 2.1 (range = 0, 7.6), with a mean length of stay/hospitalization of 6.7 (range = 3, 12.1) days. Eleven patients achieved full head control and sitting unassisted and two patients were walking independently. CONCLUSIONS AVXS-101 treatment in SMA1 was associated with reduced pulmonary and nutritional support requirements, improved motor function, and decreased hospitalization rate over the follow-up period. This contrasts with the natural history of progressive respiratory failure and reduced survival. The reduced healthcare utilization could potentially alleviate patient and caregiver burden, suggesting an overall improved quality of life following gene replacement therapy. TRIAL REGISTRATION ClinicalTrials.gov number, NCT02122952.
Collapse
Affiliation(s)
- Samiah Al-Zaidy
- Department of Pediatrics, Ohio State University, Columbus, Ohio.,Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - A Simon Pickard
- Department of Pharmacy Systems, Outcomes, and Policy, University of Illinois, Chicago, Illinois
| | - Kavitha Kotha
- Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - Lindsay N Alfano
- Department of Pediatrics, Ohio State University, Columbus, Ohio.,Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - Linda Lowes
- Department of Pediatrics, Ohio State University, Columbus, Ohio.,Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - Grace Paul
- Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - Kathleen Church
- Department of Pediatrics, Ohio State University, Columbus, Ohio.,Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - Kelly Lehman
- Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | | | | | | | - Katherine Berry
- Department of Pediatrics, Ohio State University, Columbus, Ohio.,Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio
| | - W David Arnold
- Department of Neurology, Ohio State University, Columbus, Ohio
| | - John T Kissel
- Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Jerry R Mendell
- Department of Pediatrics, Ohio State University, Columbus, Ohio.,Center for Gene Therapy Nationwide Children's Hospital, Columbus, Ohio.,Department of Neurology, Ohio State University, Columbus, Ohio
| | - Richard Shell
- Department of Pediatrics, Ohio State University, Columbus, Ohio
| |
Collapse
|
22
|
Murphy KC, Nelson SJ, Nambi S, Papavinasasundaram K, Baer CE, Sassetti CM. ORBIT: a New Paradigm for Genetic Engineering of Mycobacterial Chromosomes. mBio 2018; 9:e01467-18. [PMID: 30538179 PMCID: PMC6299477 DOI: 10.1128/mbio.01467-18] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022] Open
Abstract
Two efficient recombination systems were combined to produce a versatile method for chromosomal engineering that obviates the need to prepare double-stranded DNA (dsDNA) recombination substrates. A synthetic "targeting oligonucleotide" is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annealase. This oligonucleotide contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a "payload plasmid" that contains a cognate recombination site and a selectable marker. The targeting oligonucleotide and payload plasmid are cotransformed into a RecT- and Int-expressing strain, and drug-resistant homologous recombinants are selected in a single step. A library of reusable target-independent payload plasmids is available to generate gene knockouts, promoter replacements, or C-terminal tags. This new system is called ORBIT (for "oligonucleotide-mediated recombineering followed by Bxb1 integrase targeting") and is ideally suited for the creation of libraries consisting of large numbers of deletions, insertions, or fusions in a bacterial chromosome. We demonstrate the utility of this "drag and drop" strategy by the construction of insertions or deletions in over 100 genes in Mycobacteriumtuberculosis and M. smegmatisIMPORTANCE We sought to develop a system that could increase the usefulness of oligonucleotide-mediated recombineering of bacterial chromosomes by expanding the types of modifications generated by an oligonucleotide (i.e., insertions and deletions) and by making recombinant formation a selectable event. This paper describes such a system for use in M. smegmatis and M. tuberculosis By incorporating a single-stranded DNA (ssDNA) version of the phage Bxb1 attP site into the oligonucleotide and coelectroporating it with a nonreplicative plasmid that carries an attB site and a drug selection marker, we show both formation of a chromosomal attP site and integration of the plasmid in a single transformation. No target-specific dsDNA substrates are required. This system will allow investigators studying mycobacterial diseases, including tuberculosis, to easily generate multiple mutants for analysis of virulence factors, identification of new drug targets, and development of new vaccines.
Collapse
Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Samantha J Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christina E Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
23
|
Li S, Li J, Zhang J, Du W, Fu J, Sutar S, Zhao Y, Xia L. Synthesis-dependent repair of Cpf1-induced double strand DNA breaks enables targeted gene replacement in rice. J Exp Bot 2018; 69:4715-4721. [PMID: 29955893 PMCID: PMC6137971 DOI: 10.1093/jxb/ery245] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/25/2018] [Indexed: 05/17/2023]
Abstract
The recently developed CRISPR (clustered regularly interspaced short palindromic repeats)/Cpf1 system expands the range of genome editing and is emerging as an alternative powerful tool for both plant functional genomics and crop improvement. Cpf1-CRISPR RNA (crRNA) produces double strand DNA breaks (DSBs) with long 5'-protruding ends, which may facilitate the pairing and insertion of repair templates through homology-directed repair (HDR) for targeted gene replacement and introduction of the desired DNA elements at specific gene loci for crop improvement. However, the potential mechanism underlying HDR of DSBs generated by Cpf1-crRNA remains to be investigated, and the inherent low efficiency of HDR and poor availability of exogenous donor DNA as repair templates strongly impede the use of HDR for precise genome editing in crop plants. Here, we provide evidence of synthesis-dependent repair of Cpf1-induced DSBs, which enables us precisely to replace the wild-type ALS gene with the intended mutant version that carries two discrete point mutations conferring herbicide resistance to rice plants. Our observation that the donor repair template (DRT) with only the left homologous arm is sufficient for precise targeted allele replacement offers a better understanding of the mechanism underlying HDR in plants, and greatly simplifies the design of DRTs for precision genome editing in crop improvement.
Collapse
Affiliation(s)
- Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jiahui Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Wenming Du
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jindong Fu
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Suhas Sutar
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Correspondence: or
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Correspondence: or
| |
Collapse
|
24
|
Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, Starker CG, Bart R, Voytas DF, Taylor NJ. Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol J 2018; 16:1275-1282. [PMID: 29223136 PMCID: PMC5999311 DOI: 10.1111/pbi.12868] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/22/2017] [Accepted: 12/03/2017] [Indexed: 05/20/2023]
Abstract
Effective weed control can protect yields of cassava (Manihot esculenta) storage roots. Farmers could benefit from using herbicide with a tolerant cultivar. We applied traditional transgenesis and gene editing to generate robust glyphosate tolerance in cassava. By comparing promoters regulating expression of transformed 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) genes with various paired amino acid substitutions, we found that strong constitutive expression is required to achieve glyphosate tolerance during in vitro selection and in whole cassava plants. Using strategies that exploit homologous recombination (HR) and nonhomologous end-joining (NHEJ) DNA repair pathways, we precisely introduced the best-performing allele into the cassava genome, simultaneously creating a promoter swap and dual amino acid substitutions at the endogenous EPSPS locus. Primary EPSPS-edited plants were phenotypically normal, tolerant to high doses of glyphosate, with some free of detectable T-DNA integrations. Our methods demonstrate an editing strategy for creating glyphosate tolerance in crop plants and demonstrate the potential of gene editing for further improvement of cassava.
Collapse
Affiliation(s)
- Aaron W. Hummel
- Department of Genetics, Cell Biology, & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Present address:
KWS Gateway Research CenterSt. LouisMOUSA
| | | | - Tomas Cermak
- Department of Genetics, Cell Biology, & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Present address:
Inari Agriculture Inc200 Sidney StSuite 340, CambridgeMA 02139USA
| | - Andrew M. Mutka
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
Elemental EnzymesSt. LouisMOUSA
| | - Anupama Vijayaraghavan
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
MonsantoSt. LouisMOUSA
| | - Adam Boyher
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Colby G. Starker
- Department of Genetics, Cell Biology, & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Rebecca Bart
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology, & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | | |
Collapse
|
25
|
Dahan-Meir T, Filler-Hayut S, Melamed-Bessudo C, Bocobza S, Czosnek H, Aharoni A, Levy AA. Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system. Plant J 2018; 95:5-16. [PMID: 29668111 DOI: 10.1111/tpj.13932] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 05/21/2023]
Abstract
Current breeding relies mostly on random mutagenesis and recombination to generate novel genetic variation. However, targeted genome editing is becoming an increasingly important tool for precise plant breeding. Using the CRISPR-Cas system combined with the bean yellow dwarf virus rolling circle replicon, we optimized a method for targeted mutagenesis and gene replacement in tomato. The carotenoid isomerase (CRTISO) and phytoene synthase 1 (PSY1) genes from the carotenoid biosynthesis pathway were chosen as targets due to their easily detectable change of phenotype. We took advantage of the geminiviral replicon amplification as a means to provide a large amount of donor template for the repair of a CRISPR-Cas-induced DNA double-strand break (DSB) in the target gene, via homologous recombination (HR). Mutagenesis experiments, performed in the Micro-Tom variety, achieved precise modification of the CRTISO and PSY1 loci at an efficiency of up to 90%. In the gene targeting (GT) experiments, our target was a fast-neutron-induced crtiso allele that contained a 281-bp deletion. This deletion was repaired with the wild-type sequence through HR between the CRISPR-Cas-induced DSB in the crtiso target and the amplified donor in 25% of the plants transformed. This shows that efficient GT can be achieved in the absence of selection markers or reporters using a single and modular construct that is adaptable to other tomato targets and other crops.
Collapse
Affiliation(s)
- Tal Dahan-Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shdema Filler-Hayut
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Cathy Melamed-Bessudo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Bocobza
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Henryk Czosnek
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem Rehovot, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
26
|
Nonaka M, Kishi T. Marker-free insertion of a series of C-terminal epitopes based on the 50:50 method in Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2018; 64:99-102. [PMID: 29491249 DOI: 10.2323/jgam.2017.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
27
|
Castro-Bravo N, Hidalgo-Cantabrana C, Rodriguez-Carvajal MA, Ruas-Madiedo P, Margolles A. Gene Replacement and Fluorescent Labeling to Study the Functional Role of Exopolysaccharides in Bifidobacterium animalis subsp. lactis. Front Microbiol 2017; 8:1405. [PMID: 28790996 PMCID: PMC5524739 DOI: 10.3389/fmicb.2017.01405] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 01/01/2023] Open
Abstract
An extracellular layer of exopolysaccharides (EPS) covers the surface of some Bifidobacterium animalis subsp. lactis strains, which could be of relevance for its probiotic performance. In order to understand the functional characteristics of B. animalis subsp. lactis, two isogenic strains that differ in their EPS-producing phenotype, due to a single mutation in the gene Balat_1410, were studied. By means of a double crossover recombination strategy, successfully used for the first time in bifidobacteria, Balat_1410 in the type strain B. animalis subsp. lactis DSM10140 was replaced by a mutated gene containing a non-synonymous mutation previously associated with the appearance of a mucoid-ropy phenotype. Nuclear magnetic resonance and SEC-MALS analyses showed that the novel strain harboring the mutation acquired a ropy phenotype, due to the production of a high molecular weight (HMW)-EPS that is not produced in the wild-type strain. Fluorescence labeling of both strains with two fluorescent proteins, m-Cherry and Green Fluorescent Protein, was achieved by expressing the corresponding genes under the control of a native selected promoter (the elongation factor Tu promoter). Remarkably, qualitative and quantitative fluorescence analyses demonstrated that the ropy strain displays a lower capability to adhere to human intestinal epithelial cells. In addition, the presence of the HMW-EPS reduced the capability of the producing strain to form biofilms upon three different abiotic surfaces. This work also highlights the fact that different EPS confer variable functional characteristics to the bifidobacterial surface, which may be relevant for the performance of B. animalis subsp. lactis as a probiotic. The construction of molecular tools allowing the functional characterization of surface structures in next generation probiotics is still a challenging issue that deserves further attention, given the relevant role that such molecules must play in the interaction with the host.
Collapse
Affiliation(s)
- Nuria Castro-Bravo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | | | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| |
Collapse
|
28
|
|
29
|
Prondzynski M, Krämer E, Laufer SD, Shibamiya A, Pless O, Flenner F, Müller OJ, Münch J, Redwood C, Hansen A, Patten M, Eschenhagen T, Mearini G, Carrier L. Evaluation of MYBPC3 trans-Splicing and Gene Replacement as Therapeutic Options in Human iPSC-Derived Cardiomyocytes. Mol Ther Nucleic Acids 2017. [PMID: 28624223 PMCID: PMC5458066 DOI: 10.1016/j.omtn.2017.05.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gene therapy is a promising option for severe forms of genetic diseases. We previously provided evidence for the feasibility of trans-splicing, exon skipping, and gene replacement in a mouse model of hypertrophic cardiomyopathy (HCM) carrying a mutation in MYBPC3, encoding cardiac myosin-binding protein C (cMyBP-C). Here we used human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from an HCM patient carrying a heterozygous c.1358-1359insC MYBPC3 mutation and from a healthy donor. HCM hiPSC-CMs exhibited ∼50% lower MYBPC3 mRNA and cMyBP-C protein levels than control, no truncated cMyBP-C, larger cell size, and altered gene expression, thus reproducing human HCM features. We evaluated RNA trans-splicing and gene replacement after transducing hiPSC-CMs with adeno-associated virus. trans-splicing with 5' or 3' pre-trans-splicing molecules represented ∼1% of total MYBPC3 transcripts in healthy hiPSC-CMs. In contrast, gene replacement with the full-length MYBPC3 cDNA resulted in ∼2.5-fold higher MYBPC3 mRNA levels in HCM and control hiPSC-CMs. This restored the cMyBP-C level to 81% of the control level, suppressed hypertrophy, and partially restored gene expression to control level in HCM cells. This study provides evidence for (1) the feasibility of trans-splicing, although with low efficiency, and (2) efficient gene replacement in hiPSC-CMs with a MYBPC3 mutation.
Collapse
Affiliation(s)
- Maksymilian Prondzynski
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Elisabeth Krämer
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Sandra D Laufer
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany; Hamburg Zentrum für Experimentelle Therapieforschung (HEXT) Stem Cell Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Aya Shibamiya
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany; Hamburg Zentrum für Experimentelle Therapieforschung (HEXT) Stem Cell Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Ole Pless
- Fraunhofer IME Screening-Port, 22525 Hamburg, Germany
| | - Frederik Flenner
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Oliver J Müller
- Department of Cardiology, Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Julia Münch
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany; University Heart Center Hamburg, 20246 Hamburg, Germany
| | - Charles Redwood
- Radcliffe Department of Medicine, University of Oxford, Oxford OX1 3PA, UK
| | - Arne Hansen
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Monica Patten
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany; University Heart Center Hamburg, 20246 Hamburg, Germany
| | - Thomas Eschenhagen
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Giulia Mearini
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany.
| | - Lucie Carrier
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany.
| |
Collapse
|
30
|
Fang Y, Cui L, Gu B, Arredondo F, Tyler BM. Efficient Genome Editing in the Oomycete Phytophthora sojae Using CRISPR/Cas9. ACTA ACUST UNITED AC 2017; 44:21A.1.1-21A.1.26. [PMID: 28166383 DOI: 10.1002/cpmc.25] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Phytophthora is a filamentous fungus-like microorganism, but belongs to the oomycetes, in the kingdom Stramenopila. Phytophthora species are notorious as plant destroyers, causing multibillion-dollar damage to agriculture and natural ecosystems worldwide annually. For a long time, genome editing has been unattainable in oomycetes, because of their extremely low rate of homologous recombination. The recent implementation of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system in the soybean pathogen Phytophthora sojae, an experimental model for oomycetes, has opened up a powerful new research capability for the oomycete community. Here, we describe a detailed protocol for CRISPR/Cas9-mediated genome editing in P. sojae, including single guide RNA (sgRNA) design and construction, efficient gene replacement, and mutant-screening strategies. This protocol should be generally applicable for most culturable oomycetes. We also describe an optimized transformation method that is useful for other Phytophthora spp. including P. capsici and P. parasitica. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Yufeng Fang
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, Virginia.,Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Linkai Cui
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Biao Gu
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Felipe Arredondo
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Brett M Tyler
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, Virginia.,Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| |
Collapse
|
31
|
Horvath M, Steinbiss HH, Reiss B. Gene Targeting Without DSB Induction Is Inefficient in Barley. Front Plant Sci 2017; 7:1973. [PMID: 28105032 PMCID: PMC5214849 DOI: 10.3389/fpls.2016.01973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
Double strand-break (DSB) induction allowed efficient gene targeting in barley (Hordeum vulgare), but little is known about efficiencies in its absence. To obtain such data, an assay system based on the acetolactate synthase (ALS) gene was established, a target gene which had been used previously in rice and Arabidopsis thaliana. Expression of recombinases RAD51 and RAD54 had been shown to improve gene targeting in A. thaliana and positive-negative (P-N) selection allows the routine production of targeted mutants without DSB induction in rice. We implemented these approaches in barley and analysed gene targeting with the ALS gene in wild type and RAD51 and RAD54 transgenic lines. In addition, P-N selection was tested. In contrast to the high gene targeting efficiencies obtained in the absence of DSB induction in A. thaliana or rice, not one single gene targeting event was obtained in barley. These data suggest that gene targeting efficiencies are very low in barley and can substantially differ between different plants, even at the same target locus. They also suggest that the amount of labour and time would become unreasonably high to use these methods as a tool in routine applications. This is particularly true since DSB induction offers efficient alternatives. Barley, unlike rice and A. thaliana has a large, complex genome, suggesting that genome size or complexity could be the reason for the low efficiencies. We discuss to what extent transformation methods, genome size or genome complexity could contribute to the striking differences in the gene targeting efficiencies between barley, rice and A. thaliana.
Collapse
Affiliation(s)
| | | | - Bernd Reiss
- Plant DNA Recombination Group, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| |
Collapse
|
32
|
Mojica FJ, Montoliu L. On the Origin of CRISPR-Cas Technology: From Prokaryotes to Mammals. Trends Microbiol 2016; 24:811-820. [DOI: 10.1016/j.tim.2016.06.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/02/2016] [Accepted: 06/10/2016] [Indexed: 12/21/2022]
|
33
|
Abstract
Clustered regularly-interspaced short palindromic repeat (CRISPR) sequences cooperate with CRISPR-associated (Cas) proteins to form the basis of CRISPR-Cas adaptive immune systems in prokaryotes. For more than 20 years, these systems were of interest only to specialists, mainly molecular microbiologists, who tried to understand the properties of this unique defense mechanism. In 2012, the potential of CRISPR-Cas systems was uncovered and these were presented as genome-editing tools with an outstanding capacity to trigger targeted genetic modifications that can be applied to virtually any organism. Shortly thereafter, in early 2013, these tools were shown to efficiently drive specific modification of mammalian genomes. This review attempts to summarize, in a comprehensive manner, the key events and milestones that brought CRISPR-Cas technology from prokaryotes to mammals.
Collapse
Affiliation(s)
- Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain; Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain
| | - Lluis Montoliu
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; CIBERER, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
34
|
Watanabe K, Breier U, Hensel G, Kumlehn J, Schubert I, Reiss B. Stable gene replacement in barley by targeted double-strand break induction. J Exp Bot 2016; 67:1433-45. [PMID: 26712824 PMCID: PMC4762383 DOI: 10.1093/jxb/erv537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Gene targeting is becoming an important tool for precision genome engineering in plants. During gene replacement, a variant of gene targeting, transformed DNA integrates into the genome by homologous recombination (HR) to replace resident sequences. We have analysed gene targeting in barley (Hordeum vulgare) using a model system based on double-strand break (DSB) induction by the meganuclease I-SceI and a transgenic, artificial target locus. In the plants we obtained, the donor construct was inserted at the target locus by homology-directed DNA integration in at least two transformants obtained in a single experiment and was stably inherited as a single Mendelian trait. Both events were produced by one-sided integration. Our data suggest that gene replacement can be achieved in barley with a frequency suitable for routine application. The use of a codon-optimized nuclease and co-transfer of the nuclease gene together with the donor construct are probably the components important for efficient gene targeting. Such an approach, employing the recently developed synthetic nucleases/nickases that allow DSB induction at almost any sequence of a genome of interest, sets the stage for precision genome engineering as a routine tool even for important crops such as barley.
Collapse
Affiliation(s)
- Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany
| | - Ulrike Breier
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany Faculty of Science and Central European Institute of Technology, Masaryk University, 61137 Brno, Czech Republic
| | - Bernd Reiss
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany
| |
Collapse
|
35
|
Butler NM, Baltes NJ, Voytas DF, Douches DS. Geminivirus-Mediated Genome Editing in Potato (Solanum tuberosum L.) Using Sequence-Specific Nucleases. Front Plant Sci 2016; 7:1045. [PMID: 27493650 PMCID: PMC4955380 DOI: 10.3389/fpls.2016.01045] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/04/2016] [Indexed: 05/17/2023]
Abstract
Genome editing using sequence-specific nucleases (SSNs) is rapidly being developed for genetic engineering in crop species. The utilization of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems (CRISPR/Cas) for inducing double-strand breaks facilitates targeting of virtually any sequence for modification. Targeted mutagenesis via non-homologous end-joining (NHEJ) has been demonstrated extensively as being the preferred DNA repair pathway in plants. However, gene targeting via homologous recombination (HR) remains more elusive but could be a powerful tool for directed DNA repair. To overcome barriers associated with gene targeting, a geminivirus replicon (GVR) was used to deliver SSNs targeting the potato ACETOLACTATE SYNTHASE1 (ALS1) gene and repair templates designed to incorporate herbicide-inhibiting point mutations within the ALS1 locus. Transformed events modified with GVRs held point mutations that were capable of supporting a reduced herbicide susceptibility phenotype, while events transformed with conventional T-DNAs held no detectable mutations and were similar to wild-type. Regeneration of transformed events improved detection of point mutations that supported a stronger reduced herbicide susceptibility phenotype. These results demonstrate the use of geminiviruses for delivering genome editing reagents in plant species, and a novel approach to gene targeting in a vegetatively propagated species.
Collapse
Affiliation(s)
- Nathaniel M. Butler
- Department of Plant, Soils and Microbial Sciences, Michigan State University, East LansingMI, USA
| | - Nicholas J. Baltes
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, MinneapolisMN, USA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, MinneapolisMN, USA
| | - David S. Douches
- Department of Plant, Soils and Microbial Sciences, Michigan State University, East LansingMI, USA
- *Correspondence: David S. Douches,
| |
Collapse
|
36
|
Abstract
Phytophthora sojae is an oomycete pathogen of soybean. As a result of its economic importance, P. sojae has become a model for the study of oomycete genetics, physiology and pathology. The lack of efficient techniques for targeted mutagenesis and gene replacement have long hampered genetic studies of pathogenicity in Phytophthora species. Here, we describe a CRISPR/Cas9 system enabling rapid and efficient genome editing in P. sojae. Using the RXLR effector gene Avr4/6 as a target, we observed that, in the absence of a homologous template, the repair of Cas9-induced DNA double-strand breaks (DSBs) in P. sojae was mediated by non-homologous end-joining (NHEJ), primarily resulting in short indels. Most mutants were homozygous, presumably as a result of gene conversion triggered by Cas9-mediated cleavage of non-mutant alleles. When donor DNA was present, homology-directed repair (HDR) was observed, which resulted in the replacement of Avr4/6 with the NPT II gene. By testing the specific virulence of several NHEJ mutants and HDR-mediated gene replacements in soybean, we have validated the contribution of Avr4/6 to recognition by soybean R gene loci, Rps4 and Rps6, but also uncovered additional contributions to resistance by these two loci. Our results establish a powerful tool for the study of functional genomics in Phytophthora, which provides new avenues for better control of this pathogen.
Collapse
Affiliation(s)
- Yufeng Fang
- Interdisciplinary PhD Program in Genetics, Bioinformatics & Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brett M Tyler
- Interdisciplinary PhD Program in Genetics, Bioinformatics & Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| |
Collapse
|
37
|
Weinreuter M, Kreusser MM, Beckendorf J, Schreiter FC, Leuschner F, Lehmann LH, Hofmann KP, Rostosky JS, Diemert N, Xu C, Volz HC, Jungmann A, Nickel A, Sticht C, Gretz N, Maack C, Schneider MD, Gröne HJ, Müller OJ, Katus HA, Backs J. CaM Kinase II mediates maladaptive post-infarct remodeling and pro-inflammatory chemoattractant signaling but not acute myocardial ischemia/reperfusion injury. EMBO Mol Med 2015; 6:1231-45. [PMID: 25193973 PMCID: PMC4287929 DOI: 10.15252/emmm.201403848] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CaMKII was suggested to mediate ischemic myocardial injury and adverse cardiac remodeling. Here, we investigated the roles of different CaMKII isoforms and splice variants in ischemia/reperfusion (I/R) injury by the use of new genetic CaMKII mouse models. Although CaMKIIδC was upregulated 1 day after I/R injury, cardiac damage 1 day after I/R was neither affected in CaMKIIδ-deficient mice, CaMKIIδ-deficient mice in which the splice variants CaMKIIδB and C were re-expressed, nor in cardiomyocyte-specific CaMKIIδ/γ double knockout mice (DKO). In contrast, 5 weeks after I/R, DKO mice were protected against extensive scar formation and cardiac dysfunction, which was associated with reduced leukocyte infiltration and attenuated expression of members of the chemokine (C-C motif) ligand family, in particular CCL3 (macrophage inflammatory protein-1α, MIP-1α). Intriguingly, CaMKII was sufficient and required to induce CCL3 expression in isolated cardiomyocytes, indicating a cardiomyocyte autonomous effect. We propose that CaMKII-dependent chemoattractant signaling explains the effects on post-I/R remodeling. Taken together, we demonstrate that CaMKII is not critically involved in acute I/R-induced damage but in the process of post-infarct remodeling and inflammatory processes.
Collapse
Affiliation(s)
- Martin Weinreuter
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Michael M Kreusser
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Jan Beckendorf
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Friederike C Schreiter
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Florian Leuschner
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Lorenz H Lehmann
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Kai P Hofmann
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Julia S Rostosky
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Nathalie Diemert
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Chang Xu
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Hans Christian Volz
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Andreas Jungmann
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | | | - Carsten Sticht
- Medical Research Center, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Norbert Gretz
- Medical Research Center, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Christoph Maack
- Department of Cardiology, Saarland University, Homburg, Germany
| | - Michael D Schneider
- British Heart Foundation Centre of Research Excellence, Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Hermann-Josef Gröne
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | - Oliver J Müller
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Hugo A Katus
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Johannes Backs
- Research Unit Cardiac Epigenetics, Department of Cardiology, University of Heidelberg, Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| |
Collapse
|
38
|
Aravalli RN, Belcher JD, Steer CJ. Liver-targeted gene therapy: Approaches and challenges. Liver Transpl 2015; 21:718-37. [PMID: 25824605 PMCID: PMC9353592 DOI: 10.1002/lt.24122] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 03/06/2015] [Accepted: 03/14/2015] [Indexed: 12/15/2022]
Abstract
The liver plays a major role in many inherited and acquired genetic disorders. It is also the site for the treatment of certain inborn errors of metabolism that do not directly cause injury to the liver. The advancement of nucleic acid-based therapies for liver maladies has been severely limited because of the myriad untoward side effects and methodological limitations. To address these issues, research efforts in recent years have been intensified toward the development of targeted gene approaches using novel genetic tools, such as zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats as well as various nonviral vectors such as Sleeping Beauty transposons, PiggyBac transposons, and PhiC31 integrase. Although each of these methods uses a distinct mechanism of gene modification, all of them are dependent on the efficient delivery of DNA and RNA molecules into the cell. This review provides an overview of current and emerging therapeutic strategies for liver-targeted gene therapy and gene repair.
Collapse
Affiliation(s)
- Rajagopal N. Aravalli
- Department of Radiology, University of Minnesota Medical School, Minneapolis, MN 54455
| | - John D. Belcher
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 54455
| | - Clifford J. Steer
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 54455,Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN 54455
| |
Collapse
|
39
|
Wendeler E, Zobell O, Chrost B, Reiss B. Recombination products suggest the frequent occurrence of aberrant gene replacement in the moss Physcomitrella patens. Plant J 2015; 81:548-558. [PMID: 25557140 DOI: 10.1111/tpj.12749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/20/2014] [Accepted: 12/11/2014] [Indexed: 06/04/2023]
Abstract
In gene replacement, a variant of gene targeting, transformed DNA integrates into the genome by homologous recombination (HR) to replace resident sequences. Gene replacement in the moss Physcomitrella patens is extremely efficient, but often large amounts of additional DNA are integrated at the target locus. A detailed analysis of recombination junctions of PpCOL2 gene knockout mutants shows that the integrated DNA can be highly rearranged. Our data suggest that the replaced sequences were excised by HR and became integrated back into the genome by non-homologous end-joining (NHEJ). RAD51-mediated strand-invasion and subsequent strand-exchange is central to the two-end invasion pathway, the major gene replacement pathway in yeast. In this pathway, integration is initiated by the free ends of a single replacement vector-derived donor molecule which then integrates as an entity. Gene replacement in P. patens is entirely RAD51-dependent suggesting the existence of a pathway mechanistically similar to two-end invasion. However, invasion of the two ends does not seem to be stringently coordinated in P. patens. Actually, often only one fragment end became integrated by HR, or one-sided integration of two independent donor fragments occurred simultaneously leading to a double-strand break that is subsequently sealed by NHEJ and thus causes the observed rearrangements.
Collapse
Affiliation(s)
- Edelgard Wendeler
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | | | | | | |
Collapse
|
40
|
Hu G, Leal M, Lin Q, Affolter T, Sapra P, Bates B, Damelin M. Phenotype of TPBG Gene Replacement in the Mouse and Impact on the Pharmacokinetics of an Antibody-Drug Conjugate. Mol Pharm 2014; 12:1730-7. [PMID: 25423493 DOI: 10.1021/mp5006323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The use of predictive preclinical models in drug discovery is critical for compound selection, optimization, preclinical to clinical translation, and strategic decision-making. Trophoblast glycoprotein (TPBG), also known as 5T4, is the therapeutic target of several anticancer agents currently in clinical development, largely due to its high expression in tumors and low expression in normal adult tissues. In this study, mice were engineered to express human TPBG under endogenous regulatory sequences by replacement of the murine Tpbg coding sequence. The gene replacement was considered functional since the hTPBG knockin (hTPBG-KI) mice did not exhibit clinical observations or histopathological phenotypes that are associated with Tpbg gene deletion, except in rare instances. The expression of hTPBG in certain epithelial cell types and in different microregions of the brain and spinal cord was consistent with previously reported phenotypes and expression patterns. In pharmacokinetic studies, the exposure of a clinical-stage anti-TPBG antibody-drug conjugate (ADC), A1mcMMAF, was lower in hTPBG-KI versus wild-type animals, which was evidence of target-related increased clearance in hTPBG-KI mice. Thus, the hTPBG-KI mice constitute an improved system for pharmacology studies with current and future TPBG-targeted therapies and can generate more precise pharmacokinetic and pharmacodynamic data. In general the strategy of employing gene replacement to improve pharmacokinetic assessments should be broadly applicable to the discovery and development of ADCs and other biotherapeutics.
Collapse
Affiliation(s)
| | - Mauricio Leal
- §Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Pearl River, New York 10965, United States
| | - Qingcong Lin
- ∥Global Biotherapeutic Technologies, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | | | - Puja Sapra
- #Oncology Research Unit, Pfizer Inc., Pearl River, New York 10965, United States
| | - Brian Bates
- ∥Global Biotherapeutic Technologies, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Marc Damelin
- #Oncology Research Unit, Pfizer Inc., Pearl River, New York 10965, United States
| |
Collapse
|
41
|
Amato P, Tachibana M, Sparman M, Mitalipov S. Three-parent in vitro fertilization: gene replacement for the prevention of inherited mitochondrial diseases. Fertil Steril 2014; 101:31-5. [PMID: 24382342 DOI: 10.1016/j.fertnstert.2013.11.030] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/14/2013] [Accepted: 11/18/2013] [Indexed: 11/26/2022]
Abstract
The exchange of nuclear genetic material between oocytes and embryos offers a novel reproductive option for the prevention of inherited mitochondrial diseases. Mitochondrial dysfunction has been recognized as a significant cause of a number of serious multiorgan diseases. Tissues with a high metabolic demand, such as brain, heart, muscle, and central nervous system, are often affected. Mitochondrial disease can be due to mutations in mitochondrial DNA or in nuclear genes involved in mitochondrial function. There is no curative treatment for patients with mitochondrial disease. Given the lack of treatments and the limitations of prenatal and preimplantation diagnosis, attention has focused on prevention of transmission of mitochondrial disease through germline gene replacement therapy. Because mitochondrial DNA is strictly maternally inherited, two approaches have been proposed. In the first, the nuclear genome from the pronuclear stage zygote of an affected woman is transferred to an enucleated donor zygote. A second technique involves transfer of the metaphase II spindle from the unfertilized oocyte of an affected woman to an enucleated donor oocyte. Our group recently reported successful spindle transfer between human oocytes, resulting in blastocyst development and embryonic stem cell derivation, with very low levels of heteroplasmy. In this review we summarize these novel assisted reproductive techniques and their use to prevent transmission of mitochondrial disorders. The promises and challenges are discussed, focusing on their potential clinical application.
Collapse
Affiliation(s)
- Paula Amato
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon.
| | - Masahito Tachibana
- Department of Obstetrics and Gynecology, South Miyagi Medical Center, Miyagi, Japan
| | - Michelle Sparman
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon
| | - Shoukhrat Mitalipov
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon
| |
Collapse
|
42
|
de Val N, McMurray MA, Lam LH, Hsiung CCS, Bertin A, Nogales E, Thorner J. Native cysteine residues are dispensable for the structure and function of all five yeast mitotic septins. Proteins 2013; 81:1964-79. [PMID: 23775754 DOI: 10.1002/prot.24345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/30/2013] [Accepted: 05/31/2013] [Indexed: 01/19/2023]
Abstract
Budding yeast septins assemble into hetero-octamers and filaments required for cytokinesis. Solvent-exposed cysteine (Cys) residues provide sites for attaching substituents useful in assessing assembly kinetics and protein interactions. To introduce Cys at defined locations, site-directed mutagenesis was used, first, to replace the native Cys residues in Cdc3 (C124 C253 C279), Cdc10 (C266), Cdc11 (C43 C137 C138), Cdc12 (C40 C278), and Shs1 (C29 C148) with Ala, Ser, Val, or Phe. When plasmid-expressed, each Cys-less septin mutant rescued the cytokinesis defects caused by absence of the corresponding chromosomal gene. When integrated and expressed from its endogenous promoter, the same mutants were fully functional, except Cys-less Cdc12 mutants (which were viable, but exhibited slow growth and aberrant morphology) and Cdc3(C124V C253V C279V) (which was inviable). No adverse phenotypes were observed when certain pairs of Cys-less septins were co-expressed as the sole source of these proteins. Cells grew less well when three Cys-less septins were co-expressed, suggesting some reduction in fitness. Nonetheless, cells chromosomally expressing Cys-less Cdc10, Cdc11, and Cdc12, and expressing Cys-less Cdc3 from a plasmid, grew well at 30°C. Moreover, recombinant Cys-less septins--or where one of the Cys-less septins contained a single Cys introduced at a new site--displayed assembly properties in vitro indistinguishable from wild-type.
Collapse
Affiliation(s)
- Natalia de Val
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720-3202
| | | | | | | | | | | | | |
Collapse
|
43
|
Richter H, Lieberei R, Strnad M, Novák O, Gruz J, Rensing SA, von Schwartzenberg K. Polyphenol oxidases in Physcomitrella: functional PPO1 knockout modulates cytokinin-dependent development in the moss Physcomitrella patens. J Exp Bot 2012; 63:5121-35. [PMID: 22865913 PMCID: PMC3430990 DOI: 10.1093/jxb/ers169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Polyphenol oxidases (PPOs) are copper-binding enzymes of the plant secondary metabolism that oxidize polyphenols to quinones. Although PPOs are nearly ubiquitous in seed plants, knowledge on their evolution and function in other plant groups is missing. This study reports on the PPO gene family in the moss Physcomitrella patens (Hedw.) B.S.G. asan example for an early divergent plant. The P. patens PPO multigene family comprises 13 paralogues. Phylogenetic analyses suggest that plant PPOs evolved with the colonization of land and that PPO duplications within the monophyletic P. patens paralogue clade occurred after the separation of the moss and seed plant lineages. PPO functionality was demonstrated for recombinant PPO6. P. patens was analysed for phenolic compounds and six substances were detected intracellularly by LC-MS analysis: 4-hydroxybenzoic acid, p-cumaric acid, protocatechuic acid, salicylic acid, caffeic acid, and an ester of caffeic acid. Targeted PPO1 knockout (d|ppo1) plants were generated and plants lacking PPO1 exhibited only ~30% of the wild-type PPO activity in the culture medium, thus suggesting extracellular localization of PPO1, which is in contrast to the mostly plastidic PPO localization in seed plants. Further, d|ppo1 lines formed significantly more gametophores with a reduced areal plant size, which could be related to an increase of endogenously produced cytokinins and indicates an impact of PPO1 on plant development. d|ppo1 plants were less tolerant towards applied 4-methylcatechol compared to the wild type, which suggests a role of extracellular PPO1 in establishing appropriate conditions by the removal of inhibitory extracellular phenolic compounds.
Collapse
Affiliation(s)
- Hanna Richter
- University of Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, D-22609Hamburg, Germany
- University of Amsterdam, Swammerdam Institute for Life Sciences, Molecular Plant Pathology, PO Box 94215 1090 GEAmsterdam, The Netherlands
| | - Reinhard Lieberei
- University of Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, D-22609Hamburg, Germany
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany AS CR, v.v.i., Šlechtitelů 11, CZ-78371Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-78371Olomouc, Czech Republic
| | - Ondrej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany AS CR, v.v.i., Šlechtitelů 11, CZ-78371Olomouc, Czech Republic
| | - Jiri Gruz
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany AS CR, v.v.i., Šlechtitelů 11, CZ-78371Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-78371Olomouc, Czech Republic
| | - Stefan A. Rensing
- University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104Freiburg, Germany
- University of Freiburg, BIOSS Centre for Biological Signalling Studies, Hebelstr. 25, D-79104Freiburg, Germany
| | - Klaus von Schwartzenberg
- University of Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, D-22609Hamburg, Germany
- To whom correspondence should be addressed: E-mail:
| |
Collapse
|
44
|
Chiu CH, Lin WD, Huang SY, Lee YH. Effect of a C/EBP gene replacement on mitochondrial biogenesis in fat cells. Genes Dev 2004; 18:1970-5. [PMID: 15289464 PMCID: PMC514177 DOI: 10.1101/gad.1213104] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Accepted: 06/17/2004] [Indexed: 12/20/2022]
Abstract
CCAAT/enhancer-binding proteins, C/EBPalpha and C/EBPbeta, are required for fat cell differentiation and maturation. Previous studies showed that replacement of C/EBPalpha with C/EBPbeta, generating the beta/beta alleles in the mouse genome, prevents lipid accumulation in white adipose tissue (WAT). In this study, beta/beta mice lived longer and had higher energy expenditure than their control littermates due to increased WAT energy oxidation. The WAT of beta/beta mice was enriched with metabolically active, thermogenic mitochondria known for energy burning. The beta/beta allele exerted its effect through the elevated expression of the G protein alpha stimulatory subunit (Galphas) in WAT. Galphas, when overexpressed in fat-laden 3T3-L1 cells, stimulated mitochondrial biogenesis similar to that seen in the WAT of beta/beta mice, and effectively diminished the stored lipid pool.
Collapse
Affiliation(s)
- Chih-Hsien Chiu
- Laboratory of Molecular Pathology, Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | | | | | | |
Collapse
|
45
|
Malynn BA, de Alboran IM, O'Hagan RC, Bronson R, Davidson L, DePinho RA, Alt FW. N-myc can functionally replace c-myc in murine development, cellular growth, and differentiation. Genes Dev 2000; 14:1390-9. [PMID: 10837031 PMCID: PMC316670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Members of the myc family of cellular oncogenes have been implicated as transcriptional regulators in pathways that govern cellular proliferation and death. In addition, N-myc and c-myc are essential for completion of murine embryonic development. However, the basis for the evolutionary conservation of myc gene family has remained unclear. To elucidate this issue, we have generated mice in which the endogenous c-myc coding sequences have been replaced with N-myc coding sequences. Strikingly, mice homozygous for this replacement mutation can survive into adulthood and reproduce. Moreover, when expressed from the c-myc locus, N-myc is similarly regulated and functionally complementary to c-myc in the context of various cellular growth and differentiation processes. Therefore, the myc gene family must have evolved, to a large extent, to facilitate differential patterns of expression.
Collapse
Affiliation(s)
- B A Malynn
- The Center for Blood Research, Boston, Massachusetts 02115 USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Paladini RD, Coulombe PA. The functional diversity of epidermal keratins revealed by the partial rescue of the keratin 14 null phenotype by keratin 16. J Cell Biol 1999; 146:1185-201. [PMID: 10477769 PMCID: PMC2169494 DOI: 10.1083/jcb.146.5.1185] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/1999] [Accepted: 08/02/1999] [Indexed: 11/22/2022] Open
Abstract
The type I epidermal keratins K14 and K16 are remarkably similar at the primary sequence level. While a structural function has been clearly defined for K14, we have proposed that a function of K16 may be to play a role in the process of keratinocyte activation that occurs after acute injury to stratified epithelia. To compare directly the functions of the two keratins we have targeted the expression of the human K16 cDNA to the progenitor basal layer of the epidermis of K14 null mice. Mice null for K14 blister extensively and die approximately 2 d after birth (Lloyd, C., Q.C. Yu, J. Cheng, K. Turksen, L. Degenstein, E. Hutton, and E. Fuchs. 1995. J. Cell Biol. 129:1329-1344). The skin of mice expressing K16 in the absence of K14 developed normally without evidence of blistering. However, as the mice aged they featured extensive alopecia, chronic epidermal ulcers in areas of frequent physical contact, and alterations in other stratified epithelia. Mice expressing a control K16-C14 cDNA also rescue the blistering phenotype of the K14 null mice with only a small percentage exhibiting minor alopecia. While K16 is capable of rescuing the blistering, phenotypic complementation in the resulting skin is incomplete due to the multiple age dependent anomalies. Despite their high sequence similarity, K16 and K14 are not functionally equivalent in the epidermis and other stratified epithelia and it is primarily the carboxy-terminal approximately 105 amino acids of K16 that define these differences.
Collapse
Affiliation(s)
- Rudolph D. Paladini
- Departments of Biological Chemistry and Dermatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Pierre A. Coulombe
- Departments of Biological Chemistry and Dermatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| |
Collapse
|