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Sandip Vora D, Manoj Bhandari S, Sundar D. DNA shape features improve prediction of CRISPR/Cas9 activity. Methods 2024:S1046-2023(24)00102-6. [PMID: 38641083 DOI: 10.1016/j.ymeth.2024.04.012] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine learning models have been proposed for the prediction of Cas9 activity at unintended sites, yet feature engineering plays a major role in the outcome of the predictors. This study evaluates the improvement in the performance of similar predictors upon inclusion of epigenetic and DNA shape feature groups in the conventionally used sequence-based Cas9 target and off-target datasets. The approach involved the utilization of neural networks trained on a diverse range of parameters, allowing us to systematically assess the performance increase for the meticulously designed datasets- (i) sequence only, (ii) sequence and epigenetic features, and (iii) sequence, epigenetic and DNA shape feature datasets. The addition of DNA shape information significantly improved predictive performance, evaluated by Akaike and Bayesian information criteria. The evaluation of individual feature importance by permutation and LIME-based methods also indicates that not only sequence features like mismatches and nucleotide composition, but also base pairing parameters like opening and stretch, that are indicative of distortion in the DNA-RNA hybrid in the presence of mismatches, influence model outcomes.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Sakshi Manoj Bhandari
- Department of Mathematics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India; School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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2
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Calbry J, Goudounet G, Charlot F, Guyon-Debast A, Perroud PF, Nogué F. The SpRY Cas9 variant release the PAM sequence constraint for genome editing in the model plant Physcomitrium patens. Transgenic Res 2024; 33:67-74. [PMID: 38573428 PMCID: PMC11021247 DOI: 10.1007/s11248-024-00381-1] [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: 08/25/2023] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Genome editing via CRISPR/Cas has enabled targeted genetic modifications in various species, including plants. The requirement for specific protospacer-adjacent motifs (PAMs) near the target gene, as seen with Cas nucleases like SpCas9, limits its application. PAMless SpCas9 variants, designed with a relaxed PAM requirement, have widened targeting options. However, these so-call PAMless SpCas9 still show variation of editing efficiency depending on the PAM and their efficiency lags behind the native SpCas9. Here we assess the potential of a PAMless SpCas9 variant for genome editing in the model plant Physcomitrium patens. For this purpose, we developed a SpRYCas9i variant, where expression was optimized, and tested its editing efficiency using the APT as a reporter gene. We show that the near PAMless SpRYCas9i effectively recognizes specific PAMs in P. patens that are not or poorly recognized by the native SpCas9. Pattern of mutations found using the SpRYCas9i are similar to the ones found with the SpCas9 and we could not detect off-target activity for the sgRNAs tested in this study. These findings contribute to advancing versatile genome editing techniques in plants.
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Affiliation(s)
- Julie Calbry
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Guillaume Goudounet
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Florence Charlot
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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3
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Hermantara R, Richmond L, Taqi AF, Chilaka S, Jeantet V, Guerrini I, West K, West A. Improving CRISPR-Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration. J Biomed Sci 2024; 31:32. [PMID: 38532479 DOI: 10.1186/s12929-024-01020-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR-Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency. METHOD Here we report the development of a multicolour fluorescence assay for studying CRISPR-Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR-Cas9 strategies. RESULT We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration. CONCLUSION Our results highlight the need for a more stringent assessment of CRISPR-Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
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Affiliation(s)
- Rio Hermantara
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
| | - Laura Richmond
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Aqeel Faisal Taqi
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sabari Chilaka
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Valentine Jeantet
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ileana Guerrini
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katherine West
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Adam West
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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4
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Hoogstraten CA, Koenderink JB, van Straaten CE, Scheer-Weijers T, Smeitink JAM, Schirris TJJ, Russel FGM. Pyruvate dehydrogenase is a potential mitochondrial off-target for gentamicin based on in silico predictions and in vitro inhibition studies. Toxicol In Vitro 2024; 95:105740. [PMID: 38036072 DOI: 10.1016/j.tiv.2023.105740] [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: 07/10/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
During the drug development process, organ toxicity leads to an estimated failure of one-third of novel chemical entities. Drug-induced toxicity is increasingly associated with mitochondrial dysfunction, but identifying the underlying molecular mechanisms remains a challenge. Computational modeling techniques have proven to be a good tool in searching for drug off-targets. Here, we aimed to identify mitochondrial off-targets of the nephrotoxic drugs tenofovir and gentamicin using different in silico approaches (KRIPO, ProBis and PDID). Dihydroorotate dehydrogenase (DHODH) and pyruvate dehydrogenase (PDH) were predicted as potential novel off-target sites for tenofovir and gentamicin, respectively. The predicted targets were evaluated in vitro, using (colorimetric) enzymatic activity measurements. Tenofovir did not inhibit DHODH activity, while gentamicin potently reduced PDH activity. In conclusion, the use of in silico methods appeared a valuable approach in predicting PDH as a mitochondrial off-target of gentamicin. Further research is required to investigate the contribution of PDH inhibition to overall renal toxicity of gentamicin.
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Affiliation(s)
- Charlotte A Hoogstraten
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Jan B Koenderink
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Carolijn E van Straaten
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Tom Scheer-Weijers
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Jan A M Smeitink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Khondrion BV, Nijmegen 6525 EX, the Netherlands
| | - Tom J J Schirris
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Frans G M Russel
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands.
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5
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Luo Y, Chen Y, Xie H, Zhu W, Zhang G. Interpretable CRISPR/Cas9 off-target activities with mismatches and indels prediction using BERT. Comput Biol Med 2024; 169:107932. [PMID: 38199209 DOI: 10.1016/j.compbiomed.2024.107932] [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: 08/11/2023] [Revised: 12/25/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
Off-target effects of CRISPR/Cas9 can lead to suboptimal genome editing outcomes. Numerous deep learning-based approaches have achieved excellent performance for off-target prediction; however, few can predict the off-target activities with both mismatches and indels between single guide RNA (sgRNA) and target DNA sequence pair. In addition, data imbalance is a common pitfall for off-target prediction. Moreover, due to the complexity of genomic contexts, generating an interpretable model also remains challenged. To address these issues, firstly we developed a BERT-based model called CRISPR-BERT for enhancing the prediction of off-target activities with both mismatches and indels. Secondly, we proposed an adaptive batch-wise class balancing strategy to combat the noise exists in imbalanced off-target data. Finally, we applied a visualization approach for investigating the generalizable nucleotide position-dependent patterns of sgRNA-DNA pair for off-target activity. In our comprehensive comparison to existing methods on five mismatches-only datasets and two mismatches-and-indels datasets, CRISPR-BERT achieved the best performance in terms of AUROC and PRAUC. Besides, the visualization analysis demonstrated how implicit knowledge learned by CRISPR-BERT facilitates off-target prediction, which shows potential in model interpretability. Collectively, CRISPR-BERT provides an accurate and interpretable framework for off-target prediction, further contributes to sgRNA optimization in practical use for improved target specificity in CRISPR/Cas9 genome editing. The source code is available at https://github.com/BrokenStringx/CRISPR-BERT.
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Affiliation(s)
- Ye Luo
- College of Engineering, Shantou University, Shantou, 515063, China
| | - Yaowen Chen
- College of Engineering, Shantou University, Shantou, 515063, China
| | - HuanZeng Xie
- College of Engineering, Shantou University, Shantou, 515063, China
| | - Wentao Zhu
- College of Engineering, Shantou University, Shantou, 515063, China
| | - Guishan Zhang
- College of Engineering, Shantou University, Shantou, 515063, China.
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6
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Le Huy B, Bui Thi Phuong H, Luong Xuan H. Advantages and disadvantages of RNA therapeutics. Prog Mol Biol Transl Sci 2024; 203:151-164. [PMID: 38359996 DOI: 10.1016/bs.pmbts.2023.12.016] [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: 02/17/2024]
Abstract
RNA therapeutics is an innovative and rapidly evolving field at the forefront of medical research and biotechnology. Recently, many studies have shown that diverse RNA types play important roles in cells. Besides the protein translation coding, they also express and regulate a variety of cellular pathways. Indeed, along with the research and studies, many drugs and vaccines were developed from RNAs, including both coding and non-coding RNA. Some cases were approved to be medicines or under clinical trial. After years of use and application, they have shown a bright opportunity to prevent and treat many fatal and rare diseases with many strong points, such as fast production and long-term effects. Besides, they still have some drawbacks that need to be overcome, like stability or delivery to become the new generation of medicine. Therefore, this chapter focuses on providing an overview of the advantages and disadvantages of RNA therapeutics as well as some crucial points for future development.
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Affiliation(s)
- Binh Le Huy
- Center for High Technology Development, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam; School of Chemical Engineering-Hanọi University of Science and Technology, Hanoi, Vietnam
| | | | - Huy Luong Xuan
- Faculty of Pharmacy, PHENIKAA University, Hanoi, Vietnam; PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi, Vietnam.
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7
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Wang Z, Yuan H, Yang L, Ma L, Zhang Y, Deng J, Li X, Xiao W, Li Z, Qiu J, Ouyang H, Pang D. Decreasing predictable DNA off-target effects and narrowing editing windows of adenine base editors by fusing human Rad18 protein variant. Int J Biol Macromol 2023; 253:127418. [PMID: 37848112 DOI: 10.1016/j.ijbiomac.2023.127418] [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: 03/15/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Adenine base editors, enabling targeted A-to-G conversion in genomic DNA, have enormous potential in therapeutic applications. However, the currently used adenine base editors are limited by wide editing windows and off-target effects in genetic therapy. Here, we report human e18 protein, a RING type E3 ubiquitin ligase variant, fusing with adenine base editors can significantly improve the preciseness and narrow the editing windows compared with ABEmax and ABE8e by diminishing the abundance of base editor protein. As a proof of concept, ABEmax-e18 and ABE8e-e18 dramatically decrease Cas9-dependent and Cas9-independent off-target effects than traditional adenine base editors. Moreover, we utilized ABEmax-e18 to establish syndactyly mouse models and achieve accurate base conversion at human PCSK9 locus in HepG2 cells which exhibited its potential in genetic therapy. Furthermore, a truncated version of base editors-RING (ABEmax-RING or AncBE4max-RING), which fusing the 63 amino acids of e18 protein RING domain to the C terminal of ABEmax or AncBE4max, exhibited similar effect compared to ABEmax-e18 or AncBE4max-e18.In summary, the e18 or RING protein fused with base editors strengthens the precise toolbox in gene modification and maybe works well with various base editing tools with a more applicable to precise genetic therapies in the future.
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Affiliation(s)
- Ziru Wang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Hongming Yuan
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
| | - Lin Yang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lerong Ma
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiacheng Deng
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xueyuan Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wenyu Xiao
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiazhang Qiu
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hongsheng Ouyang
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
| | - Daxin Pang
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
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8
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Hu Y, Liu L, Jiang Q, Fang W, Chen Y, Hong Y, Zhai X. CRISPR/Cas9: a powerful tool in colorectal cancer research. J Exp Clin Cancer Res 2023; 42:308. [PMID: 37993945 PMCID: PMC10664500 DOI: 10.1186/s13046-023-02901-z] [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: 09/14/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant cancers worldwide and seriously threatens human health. The clustered regulatory interspaced short palindromic repeat/CRISPR-associate nuclease 9 (CRISPR/Cas9) system is an adaptive immune system of bacteria or archaea. Since its introduction, research into various aspects of treatment approaches for CRC has been accelerated, including investigation of the oncogenes, tumor suppressor genes (TSGs), drug resistance genes, target genes, mouse model construction, and especially in genome-wide library screening. Furthermore, the CRISPR/Cas9 system can be utilized for gene therapy for CRC, specifically involving in the molecular targeted drug delivery or targeted knockout in vivo. In this review, we elucidate the mechanism of the CRISPR/Cas9 system and its comprehensive applications in CRC. Additionally, we discussed the issue of off-target effects associated with CRISPR/Cas9, which serves to restrict its practical application. Future research on CRC should in-depth and systematically utilize the CRISPR/Cas9 system thereby achieving clinical practice.
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Affiliation(s)
- Yang Hu
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Liang Liu
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qi Jiang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Weiping Fang
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Yazhu Chen
- West China Hospital of Sichuan University, Chengdu, 610044, China.
| | - Yuntian Hong
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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9
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Zha MJ, Cai CE, He PM. Outlook on the Security and Potential Improvements of CRISPR-Cas9. Mol Biotechnol 2023; 65:1729-1736. [PMID: 36881252 DOI: 10.1007/s12033-023-00708-z] [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: 10/19/2022] [Accepted: 02/19/2023] [Indexed: 03/08/2023]
Abstract
Gene editing technology is regarded as a good news to save patients with genetic diseases because of its significant function of specifically changing genetic information. From zinc-finger proteins to transcription activator-like effector protein nucleases gene editing tools are constantly updated. At the same time, scientists are constantly developing a variety of new gene editing therapy strategies, in order to promote gene editing therapy from various aspects and realize the maturity of the technology as soon as possible. In 2016, CRISPR-Cas9-mediated CAR-T therapy was the first to enter the clinical trial stage, indicating that the use of CRISPR-Cas system as the blade of the genetic lancet to save patients is officially on the schedule. The first challenge to achieve this exciting goal is to improve the security of the technology. This review will introduce the gene security issues faced by the CRISPR system as a clinical treatment tool, the current safer delivery methods and the newly developed CRISPR editing tools with higher precision. Many reviews summarize the means of improving the security of gene editing therapy and the comprehensive delivery method, while few articles focus on the threat of gene editing to the genomic security of the treatment target. Therefore, this review focuses on the risks brought by gene editing therapy to the patient genome, which provides a broader perspective for exploring and improving the security of gene editing therapy from two aspects of delivery system and CRISPR editing tools.
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Affiliation(s)
- Min-Jun Zha
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
| | - Chun-Er Cai
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Pei-Min He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
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10
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Mangeat T, Gracia M, Pichard A, Poty S, Martineau P, Robert B, Deshayes E. Fc-engineered monoclonal antibodies to reduce off-target liver uptake. EJNMMI Res 2023; 13:81. [PMID: 37697076 PMCID: PMC10495296 DOI: 10.1186/s13550-023-01030-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Radiolabeled-antibodies usually display non-specific liver accumulation that may impair image analysis and antibody biodistribution. Here, we investigated whether Fc silencing influenced antibody biodistribution. We compared recombinant 89Zr-labeled antibodies (human IgG1 against different targets) with wild-type Fc and with mutated Fc (LALAPG triple mutation to prevent binding to Fc gamma receptors; FcγR). After antibody injection in mice harboring xenografts of different tumor cell lines or of immortalized human myoblasts, we analyzed antibody biodistribution by PET-CT and conventional biodistribution analysis. RESULTS Accumulation in liver was strongly reduced and tumor-specific targeting was increased for the antibodies with mutated Fc compared with wild-type Fc. CONCLUSION Antibodies with reduced binding to FcγR display lower liver accumulation and better tumor-to-liver ratios. These findings need to be taken into account to improve antibody-based theragnostic approaches.
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Affiliation(s)
- Tristan Mangeat
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France
| | - Matthieu Gracia
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France
| | - Alexandre Pichard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France
| | - Sophie Poty
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France
| | - Pierre Martineau
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France
| | - Bruno Robert
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France.
- Institut de Recherche en Cancérologie de Montpellier (IRCM), 124 Avenue des Apothicaires, 34090, Montpellier, France.
| | - Emmanuel Deshayes
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université de Montpellier, ICM, 34298, Montpellier, France.
- Institut Régional du Cancer de Montpellier (ICM), Service de Médecine Nucléaire, 34298, Montpellier, France.
- Institut de Recherche en Cancérologie de Montpellier (IRCM), 124 Avenue des Apothicaires, 34090, Montpellier, France.
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11
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Green JR, Mahalingaiah PKS, Gopalakrishnan SM, Liguori MJ, Mittelstadt SW, Blomme EAG, Van Vleet TR. Off-target pharmacological activity at various kinases: Potential functional and pathological side effects. J Pharmacol Toxicol Methods 2023; 123:107468. [PMID: 37553032 DOI: 10.1016/j.vascn.2023.107468] [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: 03/23/2023] [Revised: 06/16/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
In drug discovery, during the lead optimization and candidate characterization stages, novel small molecules are frequently evaluated in a battery of in vitro pharmacology assays to identify potential unintended, off-target interactions with various receptors, transporters, ion channels, and enzymes, including kinases. Furthermore, these screening panels may also provide utility at later stages of development to provide a mechanistic understanding of unexpected safety findings. Here, we present a compendium of the most likely functional and pathological outcomes associated with interaction(s) to a panel of 95 kinases based on an extensive curation of the scientific literature. This panel of kinases was designed by AbbVie based on safety-related data extracted from the literature, as well as from over 20 years of institutional knowledge generated from discovery efforts. For each kinase, the scientific literature was reviewed using online databases and the most often reported functional and pathological effects were summarized. This work should serve as a practical guide for small molecule drug discovery scientists and clinical investigators to predict and/or interpret adverse effects related to pharmacological interactions with these kinases.
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Affiliation(s)
- Jonathon R Green
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
| | | | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Michael J Liguori
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Scott W Mittelstadt
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Eric A G Blomme
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Terry R Van Vleet
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
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12
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Hoogstraten CA, Jacobs MME, de Boer G, van de Wal MAE, Koopman WJH, Smeitink JAM, Russel FGM, Schirris TJJ. Metabolic impact of genetic and chemical ADP/ATP carrier inhibition in renal proximal tubule epithelial cells. Arch Toxicol 2023; 97:1927-1941. [PMID: 37154957 PMCID: PMC10256673 DOI: 10.1007/s00204-023-03510-7] [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: 12/05/2022] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Mitochondrial dysfunction is pivotal in drug-induced acute kidney injury (AKI), but the underlying mechanisms remain largely unknown. Transport proteins embedded in the mitochondrial inner membrane form a significant class of potential drug off-targets. So far, most transporter-drug interactions have been reported for the mitochondrial ADP/ATP carrier (AAC). Since it remains unknown to what extent AAC contributes to drug-induced mitochondrial dysfunction in AKI, we here aimed to better understand the functional role of AAC in the energy metabolism of human renal proximal tubular cells. To this end, CRISPR/Cas9 technology was applied to generate AAC3-/- human conditionally immortalized renal proximal tubule epithelial cells. This AAC3-/- cell model was characterized with respect to mitochondrial function and morphology. To explore whether this model could provide first insights into (mitochondrial) adverse drug effects with suspicion towards AAC-mediated mechanisms, wild-type and knockout cells were exposed to established AAC inhibitors, after which cellular metabolic activity and mitochondrial respiratory capacity were measured. Two AAC3-/- clones showed a significant reduction in ADP import and ATP export rates and mitochondrial mass, without influencing overall morphology. AAC3-/- clones exhibited reduced ATP production, oxygen consumption rates and metabolic spare capacity was particularly affected, mainly in conditions with galactose as carbon source. Chemical AAC inhibition was stronger compared to genetic inhibition in AAC3-/-, suggesting functional compensation by remaining AAC isoforms in our knockout model. In conclusion, our results indicate that ciPTEC-OAT1 cells have a predominantly oxidative phenotype that was not additionally activated by switching energy source. Genetic inhibition of AAC3 particularly impacted mitochondrial spare capacity, without affecting mitochondrial morphology, suggesting an important role for AAC in maintaining the metabolic spare respiration.
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Affiliation(s)
- Charlotte A Hoogstraten
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Maaike M E Jacobs
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Guido de Boer
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Melissa A E van de Wal
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Werner J H Koopman
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Jan A M Smeitink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Khondrion BV, Nijmegen, 6525 EX, The Netherlands
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.
| | - Tom J J Schirris
- Department of Pharmacology and Toxicology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
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13
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Deventer MH, Persson M, Laus A, Pottie E, Cannaert A, Tocco G, Gréen H, Stove CP. Off-target activity of NBOMes and NBOMe analogs at the µ opioid receptor. Arch Toxicol 2023; 97:1367-1384. [PMID: 36853332 DOI: 10.1007/s00204-023-03465-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
New psychoactive substances (NPS) are introduced on the illicit drug market at a rapid pace. Their molecular targets are often inadequately elucidated, which contributes to the delayed characterization of their pharmacological effects. Inspired by earlier findings, this study set out to investigate the µ opioid receptor (MOR) activation potential of a large set of psychedelics, substances which typically activate the serotonin (5-HT2A) receptor as their target receptor. We observed that some substances carrying the N-benzyl phenethylamine (NBOMe) structure activated MOR, as confirmed by both the NanoBiT® βarr2 recruitment assay and the G protein-based AequoScreen® Ca2+ release assay. The use of two orthogonal systems proved beneficial as some aspecific, receptor independent effects were found for various analogs when using the Ca2+ release assay. The specific 'off-target' effects at MOR could be blocked by the opioid antagonist naloxone, suggesting that these NBOMes occupy the same common opioid binding pocket as conventional opioids. This was corroborated by molecular docking, which revealed the plausibility of multiple interactions of 25I-NBOMe with MOR, similar to those observed for opioids. Additionally, structure-activity relationship findings seen in vitro were rationalized in silico for two 25I-NBOMe isomers. Overall, as MOR activity of these psychedelics was only noticed at high concentrations, we consider it unlikely that for the tested compounds there will be a relevant opioid toxicity in vivo at physiologically relevant concentrations. However, small modifications to the original NBOMe structure may result in a panel of more efficacious and potent MOR agonists, potentially exhibiting a dual MOR/5-HT2A activation potential.
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Affiliation(s)
- Marie H Deventer
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Mattias Persson
- Department of Forensic Genetic and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Antonio Laus
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Eline Pottie
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Annelies Cannaert
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Henrik Gréen
- Department of Forensic Genetic and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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14
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Kwon J, Kim M, Hwang W, Jo A, Hwang GH, Jung M, Kim UG, Cui G, Kim H, Eom JH, Hur JK, Lee J, Kim Y, Kim JS, Bae S, Lee JK. Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches. Genome Biol 2023; 24:4. [PMID: 36627653 PMCID: PMC9832775 DOI: 10.1186/s13059-022-02842-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
We present a novel genome-wide off-target prediction method named Extru-seq and compare it with cell-based (GUIDE-seq), in vitro (Digenome-seq), and in silico methods using promiscuous guide RNAs with large numbers of valid off-target sites. Extru-seq demonstrates a high validation rate and retention of information about the intracellular environment, both beneficial characteristics of cell-based methods. Extru-seq also shows a low miss rate and could easily be performed in clinically relevant cell types with little optimization, which are major positive features of the in vitro methods. In summary, Extru-seq shows beneficial features of cell-based and in vitro methods.
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Affiliation(s)
| | | | - Woochang Hwang
- Department of Pre-Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| | - Anna Jo
- Toolgen, Seoul, Republic of Korea
| | - Gue-Ho Hwang
- Department of Chemistry, Hanyang University, Seoul, Republic of Korea
| | | | | | - Gang Cui
- Department of Ophthalmology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Heonseok Kim
- Department of Medicine, Division of Oncology, Stanford University, Stanford, USA
| | - Joon-Ho Eom
- National Institute of Food and Drug Safety Evaluation, Cheongju, Republic of Korea
| | - Junho K Hur
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Junwon Lee
- Department of Ophthalmology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Sangsu Bae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
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15
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Sanders BR, Townsend SE, Ford ML, Graves JL, Thomas MD. Reporting off-target effects of recombinant engineering using the pORTMAGE system. J Microbiol Methods 2023; 204:106627. [PMID: 36436701 PMCID: PMC9839536 DOI: 10.1016/j.mimet.2022.106627] [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: 08/15/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
pORTMAGE recombineering is a simple technique for incorporation of novel point mutations into bacterial genomes that eliminates off-target effects. Here we inserted point mutations into the cusS gene from Escherichia coli, then, using Illumina sequencing, report genetic variants in all mutant strains. Several off-site mutations were found at high frequency. Low frequency mutations also show high heterogeneity. This means that it is essential for studies to report all off-target effects and acknowledge the effect that this may have on resultant phenotypes.
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Affiliation(s)
| | | | - Maria L Ford
- North Carolina Agricultural and Technical State University, USA
| | - Joseph L Graves
- North Carolina Agricultural and Technical State University, USA
| | - Misty D Thomas
- North Carolina Agricultural and Technical State University, USA.
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16
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Kim D. Profiling Genome-Wide Specificity of dCpf1 Cytidine Base Editors Using Digenome-Seq. Methods Mol Biol 2023; 2606:33-40. [PMID: 36592306 DOI: 10.1007/978-1-0716-2879-9_4] [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] [Indexed: 01/03/2023]
Abstract
Digenome-seq is a powerful approach for determining the genome-wide specificity of programmable nuclease including CRISPR-Cas9 and CRISPR-Cpf1 (also known as Cas12a) and programmable deaminase including cytosine base editors (CBEs) and adenine base editors (ABEs). To define the genome-wide specificity of dLbCpf1-BE (also known as dLbCas12a-BE), genomic DNA is first incubated with dLbCpf1-BE, which induces C-to-U conversion at on-target and off-target sites, and then treated with a mixture of E. coli uracil DNA glycosylase (UDG) and Endonuclease VIII, which creates single-strand breaks (SSBs) by removing uracil in vitro. Digested genomic DNA is subjected to WGS, and then sequencing reads are aligned to the reference genome, resulting in straight alignments at on-target and off-target sites. The in vitro cleavage sites related to the straight alignments can be identified using the Digenome-seq computer tool.
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Affiliation(s)
- Daesik Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
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17
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Wani AK, Akhtar N, Singh R, Prakash A, Raza SHA, Cavalu S, Chopra C, Madkour M, Elolimy A, Hashem NM. Genome centric engineering using ZFNs, TALENs and CRISPR-Cas9 systems for trait improvement and disease control in Animals. Vet Res Commun 2023; 47:1-16. [PMID: 35781172 DOI: 10.1007/s11259-022-09967-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 04/26/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023]
Abstract
Livestock is an essential life commodity in modern agriculture involving breeding and maintenance. The farming practices have evolved mainly over the last century for commercial outputs, animal welfare, environment friendliness, and public health. Modifying genetic makeup of livestock has been proposed as an effective tool to create farmed animals with characteristics meeting modern farming system goals. The first technique used to produce transgenic farmed animals resulted in random transgene insertion and a low gene transfection rate. Therefore, genome manipulation technologies have been developed to enable efficient gene targeting with a higher accuracy and gene stability. Genome editing (GE) with engineered nucleases-Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) regulates the targeted genetic alterations to facilitate multiple genomic modifications through protein-DNA binding. The application of genome editors indicates usefulness in reproduction, animal models, transgenic animals, and cell lines. Recently, CRISPR/Cas system, an RNA-dependent genome editing tool (GET), is considered one of the most advanced and precise GE techniques for on-target modifications in the mammalian genome by mediating knock-in (KI) and knock-out (KO) of several genes. Lately, CRISPR/Cas9 tool has become the method of choice for genome alterations in livestock species due to its efficiency and specificity. The aim of this review is to discuss the evolution of engineered nucleases and GETs as a powerful tool for genome manipulation with special emphasis on its applications in improving economic traits and conferring resistance to infectious diseases of animals used for food production, by highlighting the recent trends for maintaining sustainable livestock production.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Road, CB# 7260, 3093 Genetic Medicine, Chapel Hill, NC, 27599-2760, USA
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P -ta 1Decembrie 10, 410073, Oradea, Romania
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Mahmoud Madkour
- Animal Production Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Ahmed Elolimy
- Animal Production Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Nesrein M Hashem
- Department of Animal and Fish Production, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, 21545, Egypt.
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18
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Yang Z, Fu Y, Zhao J, Zhang F, Li S, Zhao M, Wen W, Zhang L, Cheng T, Zhang J, Zhang X. Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing. Genomics Proteomics Bioinformatics 2022:S1672-0229(22)00168-1. [PMID: 36549468 DOI: 10.1016/j.gpb.2022.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 11/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
A series of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) systems have been engineered for genome editing. The most widely used Cas9 is SpCas9 from Streptococcus pyogenes and SaCas9 from Staphylococcus aureus. However, a comparison of their detailed gene editing outcomes is still lacking. By characterizing the editing outcomes of 11 sites in human induced pluripotent stem cells (iPSCs) and K562 cells, we found that SaCas9 could edit the genome with greater efficiencies than SpCas9. We also compared the effects of spacer lengths of single-guide RNAs (sgRNAs; 18-21 nt for SpCas9 and 19-23 nt for SaCas9) and found that the optimal spacer lengths were 20 nt and 21 nt for SpCas9 and SaCas9, respectively. However, the optimal spacer length for a particular sgRNA was 18-21 nt for SpCas9 and 21-22 nt for SaCas9. Furthermore, SpCas9 exhibited a more substantial bias than SaCas9 for nonhomologous end-joining (NHEJ) +1 insertion at the fourth nucleotide upstream of the protospacer adjacent motif (PAM), indicating a characteristic of a staggered cut. Accordingly, editing with SaCas9 led to higher efficiencies of NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertion or homology-directed repair (HDR)-mediated adeno-associated virus serotype 6 (AAV6) donor knock-in. Finally, GUIDE-seq analysis revealed that SaCas9 exhibited significantly reduced off-target effects compared with SpCas9. Our work indicates the superior performance of SaCas9 to SpCas9 in transgene integration-based therapeutic gene editing and the necessity to identify the optimal spacer length to achieve desired editing results.
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Affiliation(s)
- Zhixue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yawen Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Juanjuan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Siang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Jianping Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Xiaobing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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Zhang H, Chen J, Gao J, Zhang Q, Liu X, Han Z. New insights into transmission pathways and possible off-target effects of insecticidal dsRNA released by treated plants. Pestic Biochem Physiol 2022; 188:105281. [PMID: 36464336 DOI: 10.1016/j.pestbp.2022.105281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
RNAi has shown great potential in controlling pests and pathogens, and dsRNA-based pesticides have been used in different ways. Due to off-target effects, the transmission pathways and possible impacts of dsRNA on non-target organisms after release should be researched. Here, we tested pathways of dsRNA transmission through the rice-hopper-spider food chain and their efficiency for triggering RNAi. The results revealed five new pathways by which plants transfer dsRNA into the environment through the food chain. We found that ingestion of the tissues or guttation droplets of treated plant could trigger both targeted and off-target RNAi both in consumers and predators. Ingestion of consumer hoppers could also result in localized RNAi in the midguts of the predator spiders. Trace amounts of dsRNA were detected in plant root excretions and in hopper honeydew. Cutting the root tips dramatically increased the levels of dsRNA in root excretions. Host shifting experiments proved that hoppers could transfer a trace amount of dsRNA via vomit. With specially designed dsRNAs, we showed that dsRNA sharing matching sequences of 29 bp or 32 bp in length with non-target genes could trigger off-target RNAi, but that dsRNA sharing 13 bp matching sequences could not. We conclude that field-released pesticidal dsRNA could be transmitted via the hydrophilic transport system in plants, and that this may pose a safety risk to non-target animal consumers that are closely related to target pests. Rational use of pesticidal dsRNAs should involve careful consideration of dsRNA design to manage the biosafety risk.
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Affiliation(s)
- Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Jing Gao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaolong Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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20
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Li S, Liu L, Sun W, Zhou X, Zhou H. A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants. Genome Biol 2022; 23:51. [PMID: 35139891 PMCID: PMC8826654 DOI: 10.1186/s13059-022-02618-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
Background The high-activity adenine base editors (ABEs), engineered with the recently-developed tRNA adenosine deaminases (TadA8e and TadA9), show robust base editing activity but raise concerns about off-target effects. Results In this study, we perform a comprehensive evaluation of ABE8e- and ABE9-induced DNA and RNA mutations in Oryza sativa. Whole-genome sequencing analysis of plants transformed with four ABEs, including SpCas9n-TadA8e, SpCas9n-TadA9, SpCas9n-NG-TadA8e, and SpCas9n-NG-TadA9, reveal that ABEs harboring TadA9 lead to a higher number of off-target A-to-G (A>G) single-nucleotide variants (SNVs), and that those harboring CRISPR/SpCas9n-NG lead to a higher total number of off-target SNVs in the rice genome. An analysis of the T-DNAs carrying the ABEs indicates that the on-target mutations could be introduced before and/or after T-DNA integration into plant genomes, with more off-target A>G SNVs forming after the ABEs had integrated into the genome. Furthermore, we detect off-target A>G RNA mutations in plants with high expression of ABEs but not in plants with low expression of ABEs. The off-target A>G RNA mutations tend to cluster, while off-target A>G DNA mutations rarely clustered. Conclusion Our findings that Cas proteins, TadA variants, temporal expression of ABEs, and expression levels of ABEs contribute to ABE specificity in rice provide insight into the specificity of ABEs and suggest alternative ways to increase ABE specificity besides engineering TadA variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02618-w.
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Affiliation(s)
- Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China.,Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Wenxian Sun
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Zhejiang, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China.
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21
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Park SH, Lee CM, Bao G. Identification and Validation of CRISPR/Cas9 Off-Target Activity in Hematopoietic Stem and Progenitor Cells. Methods Mol Biol 2022; 2429:281-306. [PMID: 35507169 PMCID: PMC10972534 DOI: 10.1007/978-1-0716-1979-7_19] [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] [Indexed: 06/14/2023]
Abstract
Targeted genome editing in hematopoietic stem and progenitor cells (HSPCs) using CRISPR/Cas9 can potentially provide a permanent cure for hematologic diseases. However, the utility of CRISPR/Cas9 systems for therapeutic genome editing can be compromised by their off-target effects. In this chapter, we outline the procedures for CRISPR/Cas9 off-target identification and validation in HSPCs. This method is broadly applicable to diverse CRISPR/Cas9 systems and cell types. Using this protocol, researchers can perform computational prediction and experimental identification of potential off-target sites followed by off-target activity quantification by next-generation sequencing.
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Affiliation(s)
- So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ciaran M Lee
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA.
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22
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Dhanjal JK, Vora D, Radhakrishnan N, Sundar D. Computational Approaches for Designing Highly Specific and Efficient sgRNAs. Methods Mol Biol 2022; 2349:147-166. [PMID: 34718995 DOI: 10.1007/978-1-0716-1585-0_8] [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] [Indexed: 01/05/2024]
Abstract
The easily programmable CRISPR/Cas9 system has found applications in biomedical research as well as microbial and crop applications, due to its ability to create site-specific edits. This powerful and flexible system has also been modified to enable inducible gene regulation, epigenome modifications and high-throughput screens. Designing efficient and specific guides for the nuclease is a key step and also a major challenge in effective application. This chapter describes rules for sgRNA design and important features to consider while touching upon bioinformatics advances in predicting efficient guides. Computational tools that suggest improved guides, depending on application, or predict off-targets have also been mentioned and compared.
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Affiliation(s)
- Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Dhvani Vora
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Navaneethan Radhakrishnan
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
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23
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Slesarenko YS, Lavrov AV, Smirnikhina SA. Off-target effects of base editors: what we know and how we can reduce it. Curr Genet 2021. [PMID: 34515826 DOI: 10.1007/s00294-021-01211-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
The recently discovered CRISPR-Cas9 modification, base editors (BEs), is considered as one of the most promising tools for correcting disease-causing mutations in humans, since it allows point substitutions to be edited without generating double-stranded DNA breaks, and, therefore, with a significant decrease in non-specific activity. Until recently, this method was considered the safest, but at the same time, it is quite effective. However, recent studies of non-specific activity of BEs revealed that some of them lead to the formation of a huge number of off-targets in both DNA and RNA, occurring due to the nature of the Cas9-fused proteins used. In this review article, we have considered and combined data from numerous studies about the most commonly used and more described in detail APOBEC-based BEs and Target-AID version of CBE, as well as ABE7 and ABE8 with their basic modifications into TadA to improve BEs' specificity. In our opinion, modern advances in molecular genetics make it possible to dramatically reduce the off-target activity of base editors due to introducing mutations into the domains of deaminases or inhibition of Cas9 by anti-CRISPR proteins, which returns BEs to the leading position in genome editing technologies.
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24
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McConnell H, Andrews TD, Field MA. Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants. PeerJ 2021; 9:e11774. [PMID: 34316407 PMCID: PMC8286708 DOI: 10.7717/peerj.11774] [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: 07/01/2020] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Background Pharmacogenetic variation is important to drug responses through diverse and complex mechanisms. Predictions of the functional impact of missense pharmacogenetic variants primarily rely on the degree of sequence conservation between species as a primary discriminator. However, idiosyncratic or off-target drug-variant interactions sometimes involve effects that are peripheral or accessory to the central systems in which a gene functions. Given the importance of sequence conservation to functional prediction tools-these idiosyncratic pharmacogenetic variants may violate the assumptions of predictive software commonly used to infer their effect. Methods Here we exhaustively assess the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants contained in the Pharmacogenomics Knowledgebase (PharmGKB) repository. We categorize PharmGKB entries into sub-classes to catalog likely off-target interactions, such that we may compare predictions across different variant annotations. Results As previously demonstrated, functional inference tools perform variably across the complete set of PharmGKB variants, with large numbers of variants incorrectly classified as 'benign'. However, we find substantial differences amongst PharmGKB variant sub-classes, particularly in variants known to cause off-target, type B adverse drug reactions, that are largely unrelated to the main pharmacological action of the drug. Specifically, variants associated with off-target effects (hence referred to as off-target variants) were most often incorrectly classified as 'benign'. These results highlight the importance of understanding the underlying mechanism of pharmacogenetic variants and how variants associated with off-target effects will ultimately require new predictive algorithms. Conclusion In this work we demonstrate that functional inference tools perform poorly on pharmacogenetic variants, particularly on subsets enriched for variants causing off-target, type B adverse drug reactions. We describe how to identify variants associated with off-target effects within PharmGKB in order to generate a training set of variants that is needed to develop new algorithms specifically for this class of variant. Development of such tools will lead to more accurate functional predictions and pave the way for the increased wide-spread adoption of pharmacogenetics in clinical practice.
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Affiliation(s)
- Hannah McConnell
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - T Daniel Andrews
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Smithfield, Australia.,Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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25
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Sledzinski P, Dabrowska M, Nowaczyk M, Olejniczak M. Paving the way towards precise and safe CRISPR genome editing. Biotechnol Adv 2021; 49:107737. [PMID: 33785374 DOI: 10.1016/j.biotechadv.2021.107737] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
As the possibilities of CRISPR-Cas9 technology have been revealed, we have entered a new era of research aimed at increasing its specificity and safety. This stage of technology development is necessary not only for its wider application in the clinic but also in basic research to better control the process of genome editing. Research during the past eight years has identified some factors influencing editing outcomes and led to the development of highly specific endonucleases, modified guide RNAs and computational tools supporting experiments. More recently, large-scale experiments revealed a previously overlooked feature: Cas9 can generate reproducible mutation patterns. As a result, it has become apparent that Cas9-induced double-strand break (DSB) repair is nonrandom and can be predicted to some extent. Here, we review the present state of knowledge regarding the specificity and safety of CRISPR-Cas9 technology to define gRNA, protein and target-related problems and solutions. These issues include sequence-specific off-target effects, immune responses, genetic variation and chromatin accessibility. We present new insights into the role of DNA repair in genome editing and define factors influencing editing outcomes. In addition, we propose practical guidelines for increasing the specificity of editing and discuss novel perspectives in improvement of this technology.
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Affiliation(s)
- Pawel Sledzinski
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Mateusz Nowaczyk
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland.
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26
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Wang Q, Chen F, Liu P, Mu Y, Sun S, Yuan X, Shang P, Ji B. Scaffold-based analysis of nonpeptide oncogenic FTase inhibitors using multiple similarity matching, binding affinity scoring and enzyme inhibition assay. J Mol Graph Model 2021; 105:107898. [PMID: 33784524 DOI: 10.1016/j.jmgm.2021.107898] [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: 12/23/2020] [Revised: 02/25/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Oncogenic protein farnesyltransferase (FTase) is a key enzyme responsible for the lipid modification of a large and important number of proteins including Ras, which has been recognized as a druggable target of diverse cancers. Here, we report a systematic scaffold-based analysis to investigate the affinity, selectivity and cross-reactivity of nonpeptide inhibitors across ontology-enriched, disease-associated FTase mutants, by integrating multiple similarity matching, binding affinity scoring and enzyme inhibition assay. It is revealed that nonpeptide inhibitors are generally insensitive to FTase mutations; many of them cannot definitely select for wild-type target over mutant enzymes. Therefore, off-target is observed as a common phenomenon for the untargeted consequence of targeted therapies with FTase inhibition. This is not unexpected if considering that the enzyme active site is highly conserved in composition, configuration and function. The off-target, on the one hand, causes nonpeptide inhibitors with adverse drug reactions and, on the other hand, makes the inhibitors as promising candidates for the new use of old drugs. To practice the latter, a number of unexpected mutant-inhibitor interactions involved in cancer signaling pathways are uncovered in the created profile, from which several nonpeptide inhibitors are identified as insensitive to a drug-resistant mutation. Structural analysis suggests that the inhibitor ligands can bind to the mutant active site in a similar manner with wild-type target, although their nonbonded interactions appear to be impaired moderately upon the mutation.
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Affiliation(s)
- Qifei Wang
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Fei Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Peng Liu
- Department of Chest Surgery, Ningyang First People's Hospital, Taian, 271400, China
| | - Yushu Mu
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Shibin Sun
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Xulong Yuan
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Pan Shang
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Bo Ji
- Department of Chest Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China.
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27
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Zhang G, Zeng T, Dai Z, Dai X. Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks. Comput Struct Biotechnol J 2021; 19:1445-1457. [PMID: 33841753 PMCID: PMC8010402 DOI: 10.1016/j.csbj.2021.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 is a preferred genome editing tool and has been widely adapted to ranges of disciplines, from molecular biology to gene therapy. A key prerequisite for the success of CRISPR/Cas9 is its capacity to distinguish between single guide RNAs (sgRNAs) on target and homologous off-target sites. Thus, optimized design of sgRNAs by maximizing their on-target activity and minimizing their potential off-target mutations are crucial concerns for this system. Several deep learning models have been developed for comprehensive understanding of sgRNA cleavage efficacy and specificity. Although the proposed methods yield the performance results by automatically learning a suitable representation from the input data, there is still room for the improvement of accuracy and interpretability. Here, we propose novel interpretable attention-based convolutional neural networks, namely CRISPR-ONT and CRISPR-OFFT, for the prediction of CRISPR/Cas9 sgRNA on- and off-target activities, respectively. Experimental tests on public datasets demonstrate that our models significantly yield satisfactory results in terms of accuracy and interpretability. Our findings contribute to the understanding of how RNA-guide Cas9 nucleases scan the mammalian genome. Data and source codes are available at https://github.com/Peppags/CRISPRont-CRISPRofft.
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Affiliation(s)
- Guishan Zhang
- Key Laboratory of Digital Signal and Image Processing of Guangdong Provincial, College of Engineering, Shantou University, Shantou 515063, China.,School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian Zeng
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiming Dai
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-sen University, Guangzhou 510006, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou 510006, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
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28
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Gohil N, Bhattacharjee G, Lam NL, Perli SD, Singh V. CRISPR-Cas systems: Challenges and future prospects. Prog Mol Biol Transl Sci 2021; 180:141-151. [PMID: 33934835 DOI: 10.1016/bs.pmbts.2021.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The advancement gained over the past couple of decades in clustered regularly interspaced short palindromic repeats and CRISPR associated proteins (CRISPR-Cas) systems have revolutionized the field of synthetic biology, therapeutics, diagnostics and metabolic engineering. The technique has enabled the process of genome editing to be very precise, rapid, cost-effective and highly efficient which were the downfalls for the previously debuted zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) technologies. However, despite its great potential, challenges including off-target activity, method of delivery, ethical and regulatory issues still remain unresolved for the CRISPR-Cas systems. In this chapter, we present and point out the obstacles faced in implementation of the CRISPR-Cas system along with its future prospects.
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Affiliation(s)
- Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Navya Lavina Lam
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Samuel D Perli
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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29
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Abstract
The CRISPR/Cas systems have become the most widely used tool for genome editing in plants and beyond. However, CRISPR/Cas systems may cause unexpected off-target mutations due to sgRNA recognizing highly homologous DNA sequence elsewhere in the genome. Whole-genome sequencing (WGS) can be used to identify on- and off-target mutation. Here, we describe a pipeline of analyzing WGS data using a series of open source software for analysis of off-target mutations in CRISPR-edited rice plants. In this pipeline, the adapter is trimmed using SKEWER. Then, the cleaned reads are mapped to reference genome by applying BWA. To avoid mapping bias, the GATK is used to realign reads near indels (insertions and deletions) and recalibrate base quality controls. Whole-genome single nucleotide variations (SNVs) and indels are detected by LoFreq*, Mutect2, VarScan2, and Pindel. Last, SNVs and indels are compared with in silico off-target sites using Cas-OFFinder.
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30
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Abstract
The CRISPR-Cas system facilitates highly efficient genome editing; thus, it has been applied in many research fields such as biological science, medicine, and gene therapy. However, CRISPR nucleases can cleave off-target sites as well as on-target sites, causing unwanted mutations. Furthermore, after CRISPR treatments are delivered into cells or organisms, it is important to estimate the resulting mutation rates and to determine the patterns of mutations, but these tasks can be difficult. To address these issues, we have developed a tool for identifying potential off-target sites (Cas-OFFinder), a tool for designing CRISPR targets (Cas-Designer), and an assessment tool (Cas-Analyzer). These programs are all implemented on our website so that researchers can easily design CRISPR guide RNAs and assess the resulting mutations by simply clicking on the appropriate buttons; no login process is required.
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Affiliation(s)
- Gue-Ho Hwang
- Department of Chemistry, Hanyang University, Seoul, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea.
- Department of Chemistry, Seoul National University, Seoul, South Korea.
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, South Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea.
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31
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Abstract
CRISPR-associated nuclease (Cas) has been widely applied to modify the genomes of various cell types. As RNA-guided endonucleases, Cas enzymes can target different genomic sequences simply by changing the guide sequence of the CRISPR RNA (crRNA) or single guide RNA (sgRNA). Recent studies have demonstrated that DNA-RNA chimeric crRNA or sgRNA can efficiently guide the Cas9 protein for genome editing with reduced off-target effects. This chapter aims to describe a procedure for using chimeric RNA to modify the genomes of mammalian cells.
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Affiliation(s)
- Shuhan Lu
- Department of Pathology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ying Zhang
- Medical Research Institute, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Hao Yin
- Department of Pathology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
- Department of Urology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
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32
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Hazafa A, Mumtaz M, Farooq MF, Bilal S, Chaudhry SN, Firdous M, Naeem H, Ullah MO, Yameen M, Mukhtiar MS, Zafar F. CRISPR/Cas9: A powerful genome editing technique for the treatment of cancer cells with present challenges and future directions. Life Sci 2020; 263:118525. [PMID: 33031826 PMCID: PMC7533657 DOI: 10.1016/j.lfs.2020.118525] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 08/30/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Cancer is one of the most leading causes of death and a major public health problem, universally. According to accumulated data, annually, approximately 8.5 million people died because of the lethality of cancer. Recently, a novel RNA domain-containing endonuclease-based genome engineering technology, namely the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-9 (Cas9) have been proved as a powerful technique in the treatment of cancer cells due to its multifunctional properties including high specificity, accuracy, time reducing and cost-effective strategies with minimum off-target effects. The present review investigates the overview of recent studies on the newly developed genome-editing strategy, CRISPR/Cas9, as an excellent pre-clinical therapeutic option in the reduction and identification of new tumor target genes in the solid tumors. Based on accumulated data, we revealed that CRISPR/Cas9 significantly inhibited the robust tumor cell growth (breast, lung, liver, colorectal, and prostate) by targeting the oncogenes, tumor-suppressive genes, genes associated to therapies by inhibitors, genes associated to chemotherapies drug resistance, and suggested that CRISPR/Cas9 could be a potential therapeutic target in inhibiting the tumor cell growth by suppressing the cell-proliferation, metastasis, invasion and inducing the apoptosis during the treatment of malignancies in the near future. The present review also discussed the current challenges and barriers, and proposed future recommendations for a better understanding.
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Affiliation(s)
- Abu Hazafa
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhammad Mumtaz
- Department of Chemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Fras Farooq
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shahid Bilal
- Department of Agronomy, Faculty of Agriculture, University of Agriculture, Faisalabad 38000, Pakistan
| | - Sundas Nasir Chaudhry
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Musfira Firdous
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Huma Naeem
- Department of Computer Science, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Obaid Ullah
- Department of Zoology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Muhammad Yameen
- Department of Biochemistry, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan.
| | - Muhammad Shahid Mukhtiar
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Fatima Zafar
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan
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33
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Höijer I, Johansson J, Gudmundsson S, Chin CS, Bunikis I, Häggqvist S, Emmanouilidou A, Wilbe M, den Hoed M, Bondeson ML, Feuk L, Gyllensten U, Ameur A. Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity. Genome Biol 2020; 21:290. [PMID: 33261648 PMCID: PMC7706270 DOI: 10.1186/s13059-020-02206-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 04/03/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging. Here, we present SMRT-OTS and Nano-OTS, two novel, amplification-free, long-read sequencing protocols for detection of gRNA-driven digestion of genomic DNA by Cas9 in vitro. RESULTS The methods are assessed using the human cell line HEK293, re-sequenced at 18x coverage using highly accurate HiFi SMRT reads. SMRT-OTS and Nano-OTS are first applied to three different gRNAs targeting HEK293 genomic DNA, resulting in a set of 55 high-confidence gRNA cleavage sites identified by both methods. Twenty-five of these sites are not reported by off-target prediction software, either because they contain four or more single nucleotide mismatches or insertion/deletion mismatches, as compared with the human reference. Additional experiments reveal that 85% of Cas9 cleavage sites are also found by other in vitro-based methods and that on- and off-target sites are detectable in gene bodies where short-reads fail to uniquely align. Even though SMRT-OTS and Nano-OTS identify several sites with previously validated off-target editing activity in cells, our own CRISPR-Cas9 editing experiments in human fibroblasts do not give rise to detectable off-target mutations at the in vitro-predicted sites. However, indel and structural variation events are enriched at the on-target sites. CONCLUSIONS Amplification-free long-read sequencing reveals Cas9 cleavage sites in vitro that would have been difficult to predict using computational tools, including in dark genomic regions inaccessible by short-read sequencing.
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Affiliation(s)
- Ida Höijer
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Josefin Johansson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sanna Gudmundsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA USA
| | | | - Ignas Bunikis
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Susana Häggqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anastasia Emmanouilidou
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- The Beijer laboratory and Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Wilbe
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marcel den Hoed
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- The Beijer laboratory and Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marie-Louise Bondeson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
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34
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Kleefeldt JM, Pozarska A, Nardiello C, Pfeffer T, Vadász I, Herold S, Seeger W, Morty RE. Commercially available transfection reagents and negative control siRNA are not inert. Anal Biochem 2020; 606:113828. [PMID: 32745542 DOI: 10.1016/j.ab.2020.113828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 04/07/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 01/17/2023]
Abstract
The transfection of synthetic small interfering (si)RNA into cultured cells forms the basis of studies that use RNA interference (commonly referred to as "gene knockdown") to study the impact of loss of gene or protein expression on a biological pathway or process. In these studies, mock transfections (with transfection reagents alone), and the use of synthetic negative control (apparently inert) siRNA are both essential negative controls. This report reveals that three widely-used transfection reagents (X-tremeGENE™, HiPerFect, and Lipofectamine® 2000) and five commercially-available control siRNA (from Ambion, Sigma, Santa Cruz, Cell Signaling Technology, and Qiagen) are not inert in cell-culture studies. Both transfection reagents and control siRNA perturbed steady-state mRNA and protein levels in primary mouse lung fibroblasts and in NIH/3T3 cells (a widely-used mouse embryonic fibroblast cell-line), using components of the canonical transforming growth factor-β signaling machinery as a model system. Furthermore, transfection reagents and control siRNA reduced the viability and proliferation of both lung fibroblasts and NIH/3T3 cells. These data collectively provide a cautionary note to investigators to carefully consider the impact of control interventions, such as mock transfections and control siRNA, in RNA interference studies with synthetic siRNA.
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Affiliation(s)
- Jan M Kleefeldt
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Agnieszka Pozarska
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Claudio Nardiello
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Tilman Pfeffer
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany
| | - István Vadász
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Werner Seeger
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Rory E Morty
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany.
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Zhao J, Fang H, Zhang D. Expanding application of CRISPR-Cas9 system in microorganisms. Synth Syst Biotechnol 2020; 5:269-276. [PMID: 32913902 PMCID: PMC7451738 DOI: 10.1016/j.synbio.2020.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 06/14/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 11/08/2022] Open
Abstract
The development of CRISPR-Cas9 based genetic manipulation tools represents a huge breakthrough in life sciences and has been stimulating research on metabolic engineering, synthetic biology, and systems biology. The CRISPR-Cas9 and its derivative tools are one of the best choices for precise genome editing, multiplexed genome editing, and reversible gene expression control in microorganisms. However, challenges remain for applying CRISPR-Cas9 in novel microorganisms, especially those industrial microorganism hosts that are intractable using traditional genetic manipulation tools. How to further extend CRISPR-Cas9 to these microorganisms is being an urgent matter. In this review, we first introduce the mechanism and application of CRISPR-Cas9, then discuss how to optimize CRISPR-Cas9 as genome editing tools, including but not limited to how to reduce off-target effects and Cas9 related toxicity, and how to increase on-target efficiency by optimizing crRNA and sgRNA design.
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Affiliation(s)
- Jing Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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Jenkinson S, Schmidt F, Rosenbrier Ribeiro L, Delaunois A, Valentin JP. A practical guide to secondary pharmacology in drug discovery. J Pharmacol Toxicol Methods 2020; 105:106869. [PMID: 32302774 DOI: 10.1016/j.vascn.2020.106869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 02/21/2020] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 01/29/2023]
Abstract
Secondary pharmacological profiling is increasingly applied in pharmaceutical drug discovery to address unwanted pharmacological side effects of drug candidates before entering the clinic. Regulators, drug makers and patients share a demand for deep characterization of secondary pharmacology effects of novel drugs and their metabolites. The scope of such profiling has therefore expanded substantially in the past two decades, leading to the implementation of broad in silico profiling methods and focused in vitro off-target screening panels, to identify liabilities, but also opportunities, as early as possible. The pharmaceutical industry applies such panels at all stages of drug discovery routinely up to early development. Nevertheless, target composition, screening technologies, assay formats, interpretation and scheduling of panels can vary significantly between companies in the absence of dedicated guidelines. To contribute towards best practices in secondary pharmacology profiling, this review aims to summarize the state-of-the art in this field. Considerations are discussed with respect to panel design, screening strategy, implementation and interpretation of the data, including regulatory perspectives. The cascaded, or integrated, use of in silico and off-target profiling allows to exploit synergies for comprehensive safety assessment of drug candidates.
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Affiliation(s)
- Stephen Jenkinson
- Drug Safety Research and Development, Pfizer Inc., La Jolla, CA 92121, United States of America.
| | - Friedemann Schmidt
- Sanofi, R&D Preclinical Safety, Industriepark Höchst, 65926 Frankfurt/Main, Germany
| | - Lyn Rosenbrier Ribeiro
- Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, SK10 4TG, United Kingdom
| | - Annie Delaunois
- UCB BioPharma SRL, Early Solutions, Development Science, Non-Clinical Safety, 1420 Braine L'Alleud, Walloon Region, Belgium
| | - Jean-Pierre Valentin
- UCB BioPharma SRL, Early Solutions, Development Science, Non-Clinical Safety, 1420 Braine L'Alleud, Walloon Region, Belgium
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Abstract
BACKGROUND The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis. In CRISPR/Cas, RNA guides Cas nuclease to the target site to perform DNA modification. RESULTS The performance of CRISPR/Cas depends on well-designed single guide RNA (sgRNA). However, the off-target effect of sgRNA leads to undesired mutations in genome and limits the use of CRISPR/Cas. Here, we present OffScan, a universal and fast CRISPR off-target detection tool. CONCLUSIONS OffScan is not limited by the number of mismatches and allows custom protospacer-adjacent motif (PAM), which is the target site by Cas protein. Besides, OffScan adopts the FM-index, which efficiently improves query speed and reduce memory consumption.
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Affiliation(s)
- Yingbo Cui
- School of Computer, National University of Defense Technology, Changsha,, 410073 China
| | - Xiangke Liao
- School of Computer, National University of Defense Technology, Changsha,, 410073 China
| | - Shaoliang Peng
- National Supercomputing Center, Changsha, 410082 China
- College of Information Science and Engineering, Hunan University, Changsha, 410006 China
| | - Tao Tang
- School of Computer, National University of Defense Technology, Changsha,, 410073 China
| | - Chun Huang
- School of Computer, National University of Defense Technology, Changsha,, 410073 China
| | - Canqun Yang
- School of Computer, National University of Defense Technology, Changsha,, 410073 China
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Abstract
BACKGROUND CRISPR/Cas9 system, as the third-generation genome editing technology, has been widely applied in target gene repair and gene expression regulation. Selection of appropriate sgRNA can improve the on-target knockout efficacy of CRISPR/Cas9 system with high sensitivity and specificity. However, when CRISPR/Cas9 system is operating, unexpected cleavage may occur at some sites, known as off-target. Presently, a number of prediction methods have been developed to predict the off-target propensity of sgRNA at specific DNA fragments. Most of them use artificial feature extraction operations and machine learning techniques to obtain off-target scores. With the rapid expansion of off-target data and the rapid development of deep learning theory, the existing prediction methods can no longer satisfy the prediction accuracy at the clinical level. RESULTS Here, we propose a prediction method named CnnCrispr to predict the off-target propensity of sgRNA at specific DNA fragments. CnnCrispr automatically trains the sequence features of sgRNA-DNA pairs with GloVe model, and embeds the trained word vector matrix into the deep learning model including biLSTM and CNN with five hidden layers. We conducted performance verification on the data set provided by DeepCrispr, and found that the auROC and auPRC in the "leave-one-sgRNA-out" cross validation could reach 0.957 and 0.429 respectively (the Pearson value and spearman value could reach 0.495 and 0.151 respectively under the same settings). CONCLUSION Our results show that CnnCrispr has better classification and regression performance than the existing states-of-art models. The code for CnnCrispr can be freely downloaded from https://github.com/LQYoLH/CnnCrispr.
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Affiliation(s)
- Qiaoyue Liu
- Department of information and computing science, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiang Cheng
- Department of information and computing science, University of Science and Technology Beijing, Beijing, 100083, China
| | - Gan Liu
- Department of information and computing science, University of Science and Technology Beijing, Beijing, 100083, China
| | - Bohao Li
- Department of information and computing science, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiuqin Liu
- Department of information and computing science, University of Science and Technology Beijing, Beijing, 100083, China.
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Palve V, Liao Y, Remsing Rix LL, Rix U. Turning liabilities into opportunities: Off-target based drug repurposing in cancer. Semin Cancer Biol 2020; 68:209-229. [PMID: 32044472 DOI: 10.1016/j.semcancer.2020.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 09/17/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022]
Abstract
Targeted drugs and precision medicine have transformed the landscape of cancer therapy and significantly improved patient outcomes in many cases. However, as therapies are becoming more and more tailored to smaller patient populations and acquired resistance is limiting the duration of clinical responses, there is an ever increasing demand for new drugs, which is not easily met considering steadily rising drug attrition rates and development costs. Considering these challenges drug repurposing is an attractive complementary approach to traditional drug discovery that can satisfy some of these needs. This is facilitated by the fact that most targeted drugs, despite their implicit connotation, are not singularly specific, but rather display a wide spectrum of target selectivity. Importantly, some of the unintended drug "off-targets" are known anticancer targets in their own right. Others are becoming recognized as such in the process of elucidating off-target mechanisms that in fact are responsible for a drug's anticancer activity, thereby revealing potentially new cancer vulnerabilities. Harnessing such beneficial off-target effects can therefore lead to novel and promising precision medicine approaches. Here, we will discuss experimental and computational methods that are employed to specifically develop single target and network-based off-target repurposing strategies, for instance with drug combinations or polypharmacology drugs. By illustrating concrete examples that have led to clinical translation we will furthermore examine the various scientific and non-scientific factors that cumulatively determine the success of these efforts and thus can inform the future development of new and potentially lifesaving off-target based drug repurposing strategies for cancers that constitute important unmet medical needs.
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Affiliation(s)
- Vinayak Palve
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA.
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Abstract
Agriculture has benefited from various conventional techniques for plant breeding, including chemical- or radiation-induced mutagenesis, and to some extent from transgenesis. Genome editing techniques are likely to allow straightforward, cost-effective and efficient gene-specific modifications for identified genetic traits associated to agronomic interest. As for previous plant breeding techniques, genome editing techniques need an appraisal for unintended effects. Hence, an evaluation of potential specific risks associated with genome editing must be considered. The Scientific Committee of the High Council for biotechnology (HCB), using a broad theoretical and literature-based approach, identified three categories of points to consider in terms of hazards in health and environment, as compared to conventional breeding: (1) technical unintended effects related to effector persistence as well as risks associated with off-target modifications or other unintended genome modifications, (2) risks arising from the desired trait and its novelty in the plant, and (3) risks associated with the potential modification of plant breeding practices, owing to efficacy and technical ease-of-use of genome editing (acceleration), be it for single traits or for combined modifications (multiplex genome editing). Due to novelty, HCB also envisions the need for specific risk assessment and management.
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Affiliation(s)
- Marie-Bérengère Troadec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France.
- CHRU Brest, service de génétique, UF de cytogénétique, Brest, France.
- Scientific Committee of the High Council for biotechnology, Paris, France.
| | - Jean-Christophe Pagès
- Service de Biochimie et Biologie Moléculaire, Université François Rabelais de Tours, Tours, France
- INSERM, UMR 1016, Institut Cochin de Génétique Moléculaire, Paris, France
- INSERM U1031 STROMALab, Université Paul Sabatier Toulouse 3, Toulouse, France
- IFB Purpan, Service de biologie cellulaire, Toulouse, France
- Scientific Committee of the High Council for biotechnology, Paris, France
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Prykhozhij SV, Cordeiro-Santanach A, Caceres L, Berman JN. Genome Editing in Zebrafish Using High-Fidelity Cas9 Nucleases: Choosing the Right Nuclease for the Task. Methods Mol Biol 2020; 2115:385-405. [PMID: 32006412 DOI: 10.1007/978-1-0716-0290-4_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Indexed: 12/14/2022]
Abstract
Shortly after the development of the CRISPR/Cas9 system, it was recognized that it is prone to induce off-target mutations at significant frequencies. Therefore, there is a strong motivation to develop Cas9 enzymes with reduced off-target activity. Multiple rational design or selection approaches have been applied to develop several Cas9 versions with reduced off-target activities (high fidelity). To make these high-fidelity Cas9s available for model systems other than human cells and bacterial strains, as, for example, in zebrafish, new specialized expression vectors need to be developed. In this chapter, we focused on the HypaCas9 and HiFi Cas9 high-fidelity enzymes and incorporated the mutations of these Cas9 versions into a codon-optimized zebrafish Cas9 vector. This optimized vector was further improved by introducing an artificial polyadenine insert (A71) since polyadenylation is known to enhance mRNA translational efficiency. The Hypa-nCas9n and HiFi-nCas9n vectors were produced by single-site mutagenesis from pT3TS-nCas9n-A71 vector. We then tested the polyadenylated mRNAs for nCas9n, Hypa-nCas9n, HiFi-nCas9n, and HiFi-Cas9 protein for editing efficiency in five genome editing strategies and found that these high-fidelity Cas9 versions had different performances ranging from activity at 2-4 sites, where the wild-type nCas9n is active, indicating that these Cas9 versions have different sgRNA preferences. In summary, the developed new high-fidelity Cas9 vectors will enable researchers to perform much more accurate genome editing.
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Li J, Hong S, Chen W, Zuo E, Yang H. Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing. J Genet Genomics 2019; 46:513-521. [PMID: 31911131 DOI: 10.1016/j.jgg.2019.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.
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Affiliation(s)
- Jinjing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Shunyan Hong
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
| | - Erwei Zuo
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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43
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Mao S, Liu Y, Huang S, Huang X, Chi T. Site-directed RNA editing (SDRE): Off-target effects and their countermeasures. J Genet Genomics 2019; 46:531-535. [PMID: 31889638 DOI: 10.1016/j.jgg.2019.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/18/2019] [Revised: 10/08/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022]
Abstract
Site-directed RNA editing (SDRE) is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing. The past few years have witnessed a surge of interest in SDRE, with SDRE tools emerging at a breathtaking pace. However, off-target effects of SDRE remain a tough problem, which constitutes a major hurdle to their clinical applications. Here we discuss the diverse strategies for combating off-target editing, drawing lessons from the published studies as well as our ongoing research. Overall, SDRE is still at its infancy, with significant challenges and exciting opportunities ahead.
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Affiliation(s)
- Shaoshuai Mao
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajing Liu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shisheng Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingxu Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Tian Chi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Dong Y, Li H, Zhao L, Koopman P, Zhang F, Huang JX. Genome-Wide Off-Target Analysis in CRISPR-Cas9 Modified Mice and Their Offspring. G3 (Bethesda) 2019; 9:3645-51. [PMID: 31492696 DOI: 10.1534/g3.119.400503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The emergence of the CRISPR-Cas9 system has triggered a technical revolution in mammalian genome editing. Compared to traditional gene-targeting strategies, CRISPR-Cas9 technology offers a more efficient and cost-effective approach for generating genetically modified animal models. However, off-target cleavage in CRISPR-mediated genome editing is a major concern in the analysis of phenotypes as well as the selection of therapeutic targets. Here, we analyzed whole-genome sequencing (WGS) data from two knock-out (KO) mouse strains generated by using the CRISPR-Cas9 system targeting the Mmd and Paqr8 loci. A total of nine individuals were sequenced including two parents, four F1 offspring and three uninjected control mice. Using GATK and bcftools software, we identified two off-target events in the founder mice. The two CRISPR-Cas9-induced off-target events were predictable using Cas-OFFinder and were not passed on to the offspring that we investigated. In addition, our results indicated that the number of CRISPR-Cas9-induced mutations was not statistically distinguishable from the background de novo mutations (DNMs).
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Xie C, Zhu F, Wang J, Zhang W, Bellanti JA, Li B, Brand D, Olsen N, Zheng SG. Off-Target Deletion of Conditional Dbc1 Allele in the Foxp3YFP-Cre Mouse Line under Specific Setting. Cells 2019; 8:cells8111309. [PMID: 31652947 PMCID: PMC6912351 DOI: 10.3390/cells8111309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 09/03/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
The Cre-LoxP conditional knockout strategy has been used extensively to study gene function in a specific cell-type. In this study, the authors tried to engineer mice in which the Dbc1 gene is conditionally knocked out in Treg cells. Unexpectedly, the conditional Dbc1 allele was completely deleted with a low frequency in some Foxp3YFP-Cre mice harboring floxed Dbc1 allele under specific settings. It was found that the germline recombination of floxed Dbc1 allele, which caused Dbc1 knock out mice, occurred in the male Foxp3YFP-Cre mice harboring floxed Dbc1 allele. Even though the authors documented that Foxp3 is expressed in the testis, the germline recombination was not caused by the germline expression of Cre, which was driven by the Foxp3 promoter. The germline recombination may be caused by the unspecific expression of Cre recombinase in the fetus, in which the floxed Dbc1 allele of some stem cells with development potential to germ cells may be recombined. Additionally, this study found that the floxed Dbc1 allele was recombined in non-T cells of some Foxp3Cre Dbc1fl mice, which need to be characterized. Our results also suggest that using male mice with a low frequency of recombined gene allele can reduce the risk of having full knock out mice.
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Affiliation(s)
- Chichu Xie
- Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China.
| | - Fangming Zhu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Science, Shanghai University, Shanghai 200025, China.
| | - Julie Wang
- Department of Internal Medicine, Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH 43210, USA.
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine UF Health Cancer Center, Gainesville, FL 32610, USA.
| | - Joseph A Bellanti
- Department of Pediatrics and Microbiology-Immunology, Georgetown University Medical Center, Washington, DC 20057, USA.
| | - Bin Li
- Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - David Brand
- Research Service, Memphis VA Medical Center, Memphis, TN 38104, USA.
| | - Nancy Olsen
- Department of Medicine, Penn State University Hershey College of Medicine, Hershey, PA 17033, USA.
| | - Song Guo Zheng
- Department of Internal Medicine, Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH 43210, USA.
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Song R, Zhai Q, Sun L, Huang E, Zhang Y, Zhu Y, Guo Q, Tian Y, Zhao B, Lu H. CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective. Appl Microbiol Biotechnol 2019; 103:6919-6932. [PMID: 31332488 PMCID: PMC6690858 DOI: 10.1007/s00253-019-10007-w] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [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: 05/24/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
Filamentous fungi play an important role in human health and industrial/agricultural production. With the increasing number of full genomes available for fungal species, the study of filamentous fungi has brought about a wider range of genetic manipulation opportunities. However, the utilization of traditional methods to study fungi is time consuming and laborious. Recent rapid progress and wide application of a versatile genome editing technology, i.e., the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-related nuclease 9) system, has revolutionized biological research and has many innovative applications in a wide range of fields showing great promise in research and application of filamentous fungi. In this review, we introduce the CRISPR/Cas9 genome editing technology focusing on its application in research of filamentous fungi and we discuss the general considerations of genome editing using CRISPR/Cas9 system illustrating vector construction, multiple editing strategies, technical consideration of different sizes of homology arms on genome editing efficiency, off-target effects, and different transformation methodologies. In addition, we discuss the challenges encountered using CRISPR/Cas9 technology and give the perspectives of future applications of CRISPR/Cas9 technology for basic research and practical application of filamentous fungi.
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Affiliation(s)
- Runjie Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qing Zhai
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, Tibet, China
| | - Lu Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Enxia Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yu Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanli Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingyun Guo
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province/State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China.
| | - Yanan Tian
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Baoyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hao Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Choi K, Shim J, Ko N, Park J. No excessive mutations in transcription activator-like effector nuclease-mediated α-1,3-galactosyltransferase knockout Yucatan miniature pigs. Asian-Australas J Anim Sci 2019; 33:360-372. [PMID: 31480150 PMCID: PMC6946973 DOI: 10.5713/ajas.19.0480] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Specific genomic sites can be recognized and permanently modified by genome editing. The discovery of endonucleases has advanced genome editing in pigs, attenuating xenograft rejection and cross-species disease transmission. However, off-target mutagenesis caused by these nucleases is a major barrier to putative clinical applications. Furthermore, off-target mutagenesis by genome editing has not yet been addressed in pigs. METHODS Here, we generated genetically inheritable α-1,3-galactosyltransferase (GGTA1) knockout Yucatan miniature pigs by combining transcription activator-like effector nuclease (TALEN) and nuclear transfer. For precise estimation of genomic mutations induced by TALEN in GGTA1 knockout pigs, we obtained the whole-genome sequence of the donor cells for use as an internal control genome. RESULTS In-depth whole-genome sequencing analysis demonstrated that TALEN-mediated GGTA1 knockout pigs had a comparable mutation rate to homologous recombination-treated pigs and wild-type strain controls. RNA sequencing analysis associated with genomic mutations revealed that TALEN-induced off-target mutations had no discernable effect on RNA transcript abundance. CONCLUSION Therefore, TALEN appears to be a precise and safe tool for generating genome-edited pigs, and the TALEN-mediated GGTA1 knockout Yucatan miniature pigs produced in this study can serve as a safe and effective organ and tissue resource for clinical applications.
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Affiliation(s)
| | - Joohyun Shim
- Optipharm Inc., Cheongju 28158, Korea.,Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Nayoung Ko
- Optipharm Inc., Cheongju 28158, Korea.,Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Joonghoon Park
- Department of International Agricultural Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea.,Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
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Aareskjold E, Grindheim AK, Hollås H, Goris M, Lillehaug JR, Vedeler A. Two tales of Annexin A2 knock-down: One of compensatory effects by antisense RNA and another of a highly active hairpin ribozyme. Biochem Pharmacol 2019; 166:253-263. [PMID: 31158338 DOI: 10.1016/j.bcp.2019.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/04/2019] [Accepted: 05/29/2019] [Indexed: 11/26/2022]
Abstract
Besides altering its own expression during cell transformation, Annexin A2 is upregulated during the progression of many cancer types and also plays key roles during viral infection and multiplication. Consequently, there has been great interest in Annexin A2 as a potential drug target. The successful design of efficient in vivo delivery systems constitutes an obstacle in full exploitation of antisense and RNA-cleaving technologies for the knock-down of specific targets. Efficiency is dependent on the method of delivery and accessibility of the target. Here, hairpin ribozymes and an antisense RNA against rat annexin A2 mRNA were tested for their efficiencies in a T7-driven coupled transcription/translation system. The most efficient ribozyme and antisense RNA were subsequently inserted into a retroviral vector under the control of a tRNA promoter, in a cassette inserted between retroviral Long Terminal Repeats for stable insertion into host DNA. The Phoenix package system based on defective retroviruses was used for virus-mediated gene transfer into PC12 cells. Cells infected with the ribozyme-containing particles died shortly after infection. However, the same ribozyme showed a very high catalytic effect in vitro in cell lysates, explained by its loose hinge helix 2 region. This principle can be transferred to other ribozymes, such as those designed to cleave the guide RNA in the CRISPR/Cas9 technology, as well as to target specific viral RNAs. Interestingly, efficient down-regulation of the expression of Annexin A2 by the antisense RNA resulted in up-regulation of Annexin A7 as a compensatory effect after several cell passages. Indeed, compensatory effects have previously been observed during gene knock-out, but not during knock-down of protein expression. This highlights the problems in interpreting the phenotypic effects of knocking down the expression of a protein. In addition, these data are highly relevant when considering the effects of the CRISPR/Cas9 approach.
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Affiliation(s)
- Elin Aareskjold
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Ann Kari Grindheim
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Hanne Hollås
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Marianne Goris
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Johan R Lillehaug
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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Abstract
The CRISPR/Cas technology has recently become the tool of choice for targeted genome modification in plants and beyond. Although CRSIPR/Cas offers a rapid and facile way of introducing changes at genomic loci of interest, its application is associated with off-targeting, i.e. introduction of unintended mutations at off-target sites within the genome, which has been reported frequently in the mammalian field. Here we summarise the current knowledge on the precision of CRISPR/Cas in plant systems and provide a summary of state-of the-art strategies for avoiding off-target mutations, as well as unintended on-target changes, in plants. These include using natural (e.g. Cas12a) or engineered (e.g. SpCas9-HF) CRISPR/Cas nucleases characterised by higher precision, as compared to the commonly used wild type SpCas9. In addition, we discuss the usage of CRISPR/Cas nucleases in the form of ribonucleoproteins (RNPs) as an option for reducing off-targeting in plants. Finally, we conclude that the most important factor for reducing CRISPR/Cas off-targeting remains careful selection of target sequences, for which we provide an overview of available online software tools and experimental guidance.
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Affiliation(s)
- Florian Hahn
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK.
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Abstract
Identification of the protein targets of bioactive small molecules is a routine challenge in chemical biology and phenotype-based drug discovery. Recent years have seen an explosion of approaches to meeting this challenge, but the traditional method of affinity pulldowns remains a practical choice in many contexts. This technique can be used as long as an affinity probe can be synthesized, usually with a crosslinking moiety to enable photo-affinity pulldowns. It can be applied to varied tissue types and can be performed with minimal specialized equipment. Here, we provide our protocol for photo-affinity pulldown experiments, with notes on making this method generally applicable to varied target identification challenges.
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Affiliation(s)
- Seung-Yong Seo
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Timothy W Corson
- Indiana University School of Medicine, Indianapolis, IN, United States.
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