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DGK and DZHK position paper on genome editing: basic science applications and future perspective. Basic Res Cardiol 2021; 116:2. [PMID: 33449167 PMCID: PMC7810637 DOI: 10.1007/s00395-020-00839-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
For a long time, gene editing had been a scientific concept, which was limited to a few applications. With recent developments, following the discovery of TALEN zinc-finger endonucleases and in particular the CRISPR/Cas system, gene editing has become a technique applicable in most laboratories. The current gain- and loss-of function models in basic science are revolutionary as they allow unbiased screens of unprecedented depth and complexity and rapid development of transgenic animals. Modifications of CRISPR/Cas have been developed to precisely interrogate epigenetic regulation or to visualize DNA complexes. Moreover, gene editing as a clinical treatment option is rapidly developing with first trials on the way. This article reviews the most recent progress in the field, covering expert opinions gathered during joint conferences on genome editing of the German Cardiac Society (DGK) and the German Center for Cardiovascular Research (DZHK). Particularly focusing on the translational aspect and the combination of cellular and animal applications, the authors aim to provide direction for the development of the field and the most frequent applications with their problems.
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Tomaselli D, Mautone N, Mai A, Rotili D. Recent advances in epigenetic proteolysis targeting chimeras (Epi-PROTACs). Eur J Med Chem 2020; 207:112750. [DOI: 10.1016/j.ejmech.2020.112750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 01/03/2023]
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Teli B, Purohit J, Rashid MM, Jailani AAK, Chattopadhyay A. Omics Insight on Fusarium Head Blight of Wheat for Translational Research Perspective. Curr Genomics 2020; 21:411-428. [PMID: 33093804 PMCID: PMC7536796 DOI: 10.2174/1389202921999200620222631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/28/2020] [Accepted: 05/13/2020] [Indexed: 01/11/2023] Open
Abstract
In the scenario of global warming and climate change, an outbreak of new pests and pathogens has become a serious concern owing to the rapid emergence of arms races, their epidemic infection, and the ability to break down host resistance, etc. Fusarium head blight (FHB) is one such evidence that depredates major cereals throughout the world. The symptomatological perplexity and aetiological complexity make this disease very severe, engendering significant losses in the yield. Apart from qualitative and quantitative losses, mycotoxin production solemnly deteriorates the grain quality in addition to life endangerment of humans and animals after consumption of toxified grains above the permissible limit. To minimize this risk, we must be very strategic in designing sustainable management practices constituting cultural, biological, chemical, and host resistance approaches. Even though genetic resistance is the most effective and environmentally safe strategy, a huge genetic variation and unstable resistance response limit the holistic deployment of resistance genes in FHB management. Thus, the focus must shift towards the editing of susceptible (S) host proteins that are soft targets of newly evolving effector molecules, which ultimately could be exploited to repress the disease development process. Hence, we must understand the pathological, biochemical, and molecular insight of disease development in a nutshell. In the present time, the availability of functional genomics, proteomics, and metabolomics information on host-pathogen interaction in FHB have constructed various networks which helped in understanding the pathogenesis and coherent host response(s). So now translation of this information for designing of host defense in the form of desirable resistant variety/genotype is the next step. The insights collected and presented in this review will be aiding in the understanding of the disease and apprise a solution to the multi-faceted problems which are related to FHB resistance in wheat and other cereals to ensure global food safety and food security.
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Affiliation(s)
- Basavaraj Teli
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Jyotika Purohit
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Md Mahtab Rashid
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - A Abdul Kader Jailani
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Anirudha Chattopadhyay
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Purohit J, Chattopadhyay A, Teli B. Metagenomic Exploration of Plastic Degrading Microbes for Biotechnological Application. Curr Genomics 2020; 21:253-270. [PMID: 33071619 PMCID: PMC7521044 DOI: 10.2174/1389202921999200525155711] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Since the last few decades, the promiscuous and uncontrolled use of plastics led to the accumulation of millions of tons of plastic waste in the terrestrial and marine environment. It elevated the risk of environmental pollution and climate change. The concern arises more due to the reckless and unscientific disposal of plastics containing high molecular weight polymers, viz., polystyrene, polyamide, polyvinylchloride, polypropylene, polyurethane, and polyethylene, etc. which are very difficult to degrade. Thus, the focus is now paid to search for efficient, eco-friendly, low-cost waste management technology. Of them, degradation of non-degradable synthetic polymer using diverse microbial agents, viz., bacteria, fungi, and other extremophiles become an emerging option. So far, very few microbial agents and their secreted enzymes have been identified and characterized for plastic degradation, but with low efficiency. It might be due to the predominance of uncultured microbial species, which consequently remain unexplored from the respective plastic degrading milieu. To overcome this problem, metagenomic analysis of microbial population engaged in the plastic biodegradation is advisable to decipher the microbial community structure and to predict their biodegradation potential in situ. Advancements in sequencing technologies and bioinformatics analysis allow the rapid metagenome screening that helps in the identification of total microbial community and also opens up the scope for mining genes or enzymes (hydrolases, laccase, etc.) engaged in polymer degradation. Further, the extraction of the core microbial population and their adaptation, fitness, and survivability can also be deciphered through comparative metagenomic study. It will help to engineer the microbial community and their metabolic activity to speed up the degradation process.
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Affiliation(s)
- Jyotika Purohit
- 1Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, SK Nagar, (Guj.), India; 2Division of Plant Pathology, IARI, New Delhi, India; 3Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, (U.P.), India
| | - Anirudha Chattopadhyay
- 1Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, SK Nagar, (Guj.), India; 2Division of Plant Pathology, IARI, New Delhi, India; 3Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, (U.P.), India
| | - Basavaraj Teli
- 1Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, SK Nagar, (Guj.), India; 2Division of Plant Pathology, IARI, New Delhi, India; 3Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, (U.P.), India
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Chang Y, Shao J, Gao Y, Liu W, Gao Z, Hu Y, Chang H. Reporter gene knock-in into Marc-145 cells using CRISPR/Cas9-mediated homologous recombination. Biotechnol Lett 2020; 42:1317-1325. [PMID: 32185620 DOI: 10.1007/s10529-020-02860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Marc-145 cells (monkey embryonic kidney epithelial cells) play a critical role in the biotechnology industry as certain virus host cells. To investigate the expression of enhanced green fluorescent protein (eGFP) gene as a foreign gene in Marc-145 cells, which we developed an approach of foreign gene site-specific knock-in into Marc-145 cells by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) and putatively explored appropriate genomic recombination sites in Marc-145 cells. RESULTS Our study demonstrated that the specific homologous recombination (HR) site between the Rac GTPase activating protein 1 (RACGAP1) and the acid-sensing ion channel subunit 1 (ASIC1) genes of the 11th chromosome could be used as the target site of Cas9 for the generation of target gene knock-in into Marc-145 cells, by the insertion of the eGFP cassette into the specific HR site and subsequent expression. CONCLUSIONS Junction PCR, sequencing, Southern blot and fluorescence assay determined eGFP gene-specific knock-in HR site between the RACGAP1 and ASIC1 genes of the 11th chromosome, which was identified by the genomic safe harbours in Marc-145 cells. Our study encouraged a broader range of applications, such as Marc-145 cells development and engineering for virus adaption and yield increase in the vaccine biotechnology industry.
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Affiliation(s)
- Yanyan Chang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Junjun Shao
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Yuan Gao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Wei Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Zhan Gao
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Yonghao Hu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Huiyun Chang
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.
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Josipović G, Tadić V, Klasić M, Zanki V, Bečeheli I, Chung F, Ghantous A, Keser T, Madunić J, Bošković M, Lauc G, Herceg Z, Vojta A, Zoldoš V. Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system. Nucleic Acids Res 2019; 47:9637-9657. [PMID: 31410472 PMCID: PMC6765142 DOI: 10.1093/nar/gkz709] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/15/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Establishing causal relationship between epigenetic marks and gene transcription requires molecular tools, which can precisely modify specific genomic regions. Here, we present a modular and extensible CRISPR/dCas9-based toolbox for epigenetic editing and direct gene regulation. It features a system for expression of orthogonal dCas9 proteins fused to various effector domains and includes a multi-gRNA system for simultaneous targeting dCas9 orthologs to up to six loci. The C- and N-terminal dCas9 fusions with DNMT3A and TET1 catalytic domains were thoroughly characterized. We demonstrated simultaneous use of the DNMT3A-dSpCas9 and TET1-dSaCas9 fusions within the same cells and showed that imposed cytosine hyper- and hypo-methylation altered level of gene transcription if targeted CpG sites were functionally relevant. Dual epigenetic manipulation of the HNF1A and MGAT3 genes, involved in protein N-glycosylation, resulted in change of the glycan phenotype in BG1 cells. Furthermore, simultaneous targeting of the TET1-dSaCas9 and VPR-dSpCas9 fusions to the HNF1A regulatory region revealed strong and persistent synergistic effect on gene transcription, up to 30 days following cell transfection, suggesting involvement of epigenetic mechanisms in maintenance of the reactivated state. Also, modulation of dCas9 expression effectively reduced off-target effects while maintaining the desired effects on target regions.
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Affiliation(s)
- Goran Josipović
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vanja Tadić
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Marija Klasić
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vladimir Zanki
- Department of Chemistry, Division of Biochemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ivona Bečeheli
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Felicia Chung
- Epigenetics group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Akram Ghantous
- Epigenetics group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia
| | - Josip Madunić
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Maria Bošković
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia
- Genos Glycoscience Research Laboratory, Borogajska cesta 83 h, 10000 Zagreb, Croatia
| | - Zdenko Herceg
- Epigenetics group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Aleksandar Vojta
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vlatka Zoldoš
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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Sandoval IM, Collier TJ, Manfredsson FP. Design and Assembly of CRISPR/Cas9 Lentiviral and rAAV Vectors for Targeted Genome Editing. Methods Mol Biol 2019; 1937:29-45. [PMID: 30706388 DOI: 10.1007/978-1-4939-9065-8_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR/Cas) system has emerged as an extremely useful tool for biological research and as a potential technology for gene therapy approaches. CRISPR/Cas mediated genome editing can be used to easily and efficiently modify endogenous genes in a large variety of cells and organisms. Furthermore, a modified version of the Cas9 nuclease has been developed that can be used for regulation of endogenous gene expression and labeling of genomic loci, among other applications. This chapter provides an introduction to the basis of the technology and a detail protocol for the most classic application: gene inactivation by CRISPR/Cas9 nuclease system from Streptococcus pyogenes. This workflow can be easily adapted for other CRISPR systems and applications.
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Affiliation(s)
- Ivette M Sandoval
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA.
- Mercy Health Saint Mary's, Grand Rapids, MI, USA.
| | - Timothy J Collier
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Mercy Health Saint Mary's, Grand Rapids, MI, USA
| | - Fredric P Manfredsson
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Mercy Health Saint Mary's, Grand Rapids, MI, USA
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Kumlehn J, Pietralla J, Hensel G, Pacher M, Puchta H. The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1127-1153. [PMID: 30387552 DOI: 10.1111/jipb.12734] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/30/2018] [Indexed: 05/18/2023]
Abstract
Since the discovery that nucleases of the bacterial CRISPR (clustered regularly interspaced palindromic repeat)-associated (Cas) system can be used as easily programmable tools for genome engineering, their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction, resulting in mutations by non-homologous recombination. Strategies for performing such experiments - from the design of guide RNA to the use of different transformation technologies - are evaluated. Furthermore, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNA-binding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.
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Affiliation(s)
- Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland OT Gatersleben, Germany
| | - Janine Pietralla
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland OT Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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Li R, Liu Y, Hou Y, Gan J, Wu P, Li C. 3D genome and its disorganization in diseases. Cell Biol Toxicol 2018; 34:351-365. [DOI: 10.1007/s10565-018-9430-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/26/2018] [Indexed: 01/25/2023]
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