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Zhang G, Luo Y, Dai X, Dai Z. Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities. Brief Bioinform 2023; 24:bbad333. [PMID: 37775147 DOI: 10.1093/bib/bbad333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023] Open
Abstract
In silico design of single guide RNA (sgRNA) plays a critical role in clustered regularly interspaced, short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. Continuous efforts are aimed at improving sgRNA design with efficient on-target activity and reduced off-target mutations. In the last 5 years, an increasing number of deep learning-based methods have achieved breakthrough performance in predicting sgRNA on- and off-target activities. Nevertheless, it is worthwhile to systematically evaluate these methods for their predictive abilities. In this review, we conducted a systematic survey on the progress in prediction of on- and off-target editing. We investigated the performances of 10 mainstream deep learning-based on-target predictors using nine public datasets with different sample sizes. We found that in most scenarios, these methods showed superior predictive power on large- and medium-scale datasets than on small-scale datasets. In addition, we performed unbiased experiments to provide in-depth comparison of eight representative approaches for off-target prediction on 12 publicly available datasets with various imbalanced ratios of positive/negative samples. Most methods showed excellent performance on balanced datasets but have much room for improvement on moderate- and severe-imbalanced datasets. This study provides comprehensive perspectives on CRISPR/Cas9 sgRNA on- and off-target activity prediction and improvement for method development.
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Affiliation(s)
- Guishan Zhang
- College of Engineering, Shantou University, Shantou 515063, China
| | - Ye Luo
- College of Engineering, Shantou University, Shantou 515063, China
| | - Xianhua Dai
- School of Cyber Science and Technology, Sun Yat-sen University, Shenzhen 518107, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, 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
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2
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Ma S, Zhou M, Xu Y, Gu X, Zou M, Abudushalamu G, Yao Y, Fan X, Wu G. Clinical application and detection techniques of liquid biopsy in gastric cancer. Mol Cancer 2023; 22:7. [PMID: 36627698 PMCID: PMC9832643 DOI: 10.1186/s12943-023-01715-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
Gastric cancer (GC) is one of the most common tumors worldwide and the leading cause of tumor-related mortality. Endoscopy and serological tumor marker testing are currently the main methods of GC screening, and treatment relies on surgical resection or chemotherapy. However, traditional examination and treatment methods are more harmful to patients and less sensitive and accurate. A minimally invasive method to respond to GC early screening, prognosis monitoring, treatment efficacy, and drug resistance situations is urgently needed. As a result, liquid biopsy techniques have received much attention in the clinical application of GC. The non-invasive liquid biopsy technique requires fewer samples, is reproducible, and can guide individualized patient treatment by monitoring patients' molecular-level changes in real-time. In this review, we introduced the clinical applications of circulating tumor cells, circulating free DNA, circulating tumor DNA, non-coding RNAs, exosomes, and proteins, which are the primary markers in liquid biopsy technology in GC. We also discuss the current limitations and future trends of liquid biopsy technology as applied to early clinical biopsy technology.
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Affiliation(s)
- Shuo Ma
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Meiling Zhou
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Yanhua Xu
- grid.452743.30000 0004 1788 4869Department of Laboratory Medicine, Northern Jiangsu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225000 Jiangsu China
| | - Xinliang Gu
- grid.440642.00000 0004 0644 5481Department of Laboratory Medicine, Medical School, Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001 Jiangsu China
| | - Mingyuan Zou
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Gulinaizhaer Abudushalamu
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Yuming Yao
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Xiaobo Fan
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Guoqiu Wu
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009 Jiangsu China
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3
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Kretzmer C, Narasimhan RL, Lal RD, Balassi V, Ravellette J, Kotekar Manjunath AK, Koshy JJ, Viano M, Torre S, Zanda VM, Kumravat M, Saldanha KMR, Chandranpillai H, Nihad I, Zhong F, Sun Y, Gustin J, Borgschulte T, Liu J, Razafsky D. De novo assembly and annotation of the CHOZN® GS -/- genome supports high-throughput genome-scale screening. Biotechnol Bioeng 2022; 119:3632-3646. [PMID: 36073082 PMCID: PMC9825924 DOI: 10.1002/bit.28226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/20/2022] [Accepted: 08/28/2022] [Indexed: 01/11/2023]
Abstract
Chinese hamster ovary (CHO) cells have been used as the industry standard for the production of therapeutic monoclonal antibodies for several decades. Despite significant improvements in commercial-scale production processes and media, the CHO cell has remained largely unchanged. Due to the cost and complexity of whole-genome sequencing and gene-editing it has been difficult to obtain the tools necessary to improve the CHO cell line. With the advent of next-generation sequencing and the discovery of the CRISPR/Cas9 system it has become more cost effective to sequence and manipulate the CHO genome. Here, we provide a comprehensive de novo assembly and annotation of the CHO-K1 based CHOZN® GS-/- genome. Using this platform, we designed, built, and confirmed the functionality of a whole genome CRISPR guide RNA library that will allow the bioprocessing community to design a more robust CHO cell line leading to the production of life saving medications in a more cost-effective manner.
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Affiliation(s)
- Corey Kretzmer
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - Rajagopalan Lakshmi Narasimhan
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Rahul Deva Lal
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Vincent Balassi
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - James Ravellette
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - Ajaya Kumar Kotekar Manjunath
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Jesvin Joy Koshy
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Marta Viano
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Serena Torre
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Valeria M. Zanda
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Mausam Kumravat
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Keith Metelo Raul Saldanha
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Harikrishnan Chandranpillai
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Ifra Nihad
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Fei Zhong
- Life Science Bioinformatics, IT, MilliporeSigmaSt. LouisMissouriUSA
| | - Yi Sun
- Bioinformatics, IT R&D Applications, MilliporeSigmaSt. LouisMissouriUSA
| | - Jason Gustin
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | | | - Jiajian Liu
- Life Science Bioinformatics, IT, MilliporeSigmaSt. LouisMissouriUSA
| | - David Razafsky
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
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Ma Y, Sun W, Zhao L, Yao M, Wu C, Su P, Yang L, Wang G. Generation of an mESC model with a human hemophilia B nonsense mutation via CRISPR/Cas9 technology. Stem Cell Res Ther 2022; 13:353. [PMID: 35883203 PMCID: PMC9327398 DOI: 10.1186/s13287-022-03036-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hemophilia B is a rare inherited genetic bleeding disorder caused by a deficiency or lack of coagulation factor IX, the gene for which (F9) is located on the X chromosome. Hemophilia B is currently incurable and the standard treatment is coagulation factor replacement therapy. Although gene therapy has the potential to cure hemophilia, significant barriers are still needed to be overcome, e.g., off-target effects and immunoreactivity, so new approaches must be explored. Nonsense mutations account for 8% of all the hemophilia B mutation types and can result in the development of coagulation factor inhibitors. In this study, CRISPR/Cas9 technology was used to construct a mouse embryonic stem cell model with a hemophilia B nonsense mutation (F9 c.223C > T) in humans to investigate the pathogenesis and treatment of nonsense mutations in hemophilia B. METHODS First, a donor plasmid with a mutation (F9 c.223 C > T) and sgRNAs were constructed. Second, both the donor plasmid and the px330-sgRNA were electroporated into mouse embryonic stem cell, and the mutant cells were then screened using puromycin and red fluorescence. Third, the mutant cell lines were tested for pluripotency and the ability to differentiate into three layers. Finally, the effect of mutation on gene function was studied in the differentiation system. RESULTS The mutant vector and effective sgRNA were constructed, and the mutant cell line was screened. This mutant cell line exhibited pluripotency and the ability to differentiate into three layers. This point mutation affects F9 expression at both the RNA and protein levels in the differentiation system. CONCLUSIONS The mutant cell line obtained in the current study had a single-base mutation rather than a base deletion or insertion in the exon, which is more similar to clinical cases. In addition, the mutant has the characteristics of mouse embryonic stem cells, and this point mutation affects F9 gene transcription and translation, which can be used as a disease model for studying the pathogenesis and treatment of hemophilia at the stem cell level.
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Affiliation(s)
- Yanchun Ma
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Wenwen Sun
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Lidong Zhao
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Mingze Yao
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi Province, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi Province, China
| | - Pengfei Su
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi Province, China
| | - Linhua Yang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
| | - Gang Wang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
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Dong C, Gou Y, Lian J. SgRNA engineering for improved genome editing and expanded functional assays. Curr Opin Biotechnol 2022; 75:102697. [PMID: 35217295 DOI: 10.1016/j.copbio.2022.102697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
Abstract
The CRISPR/Cas system has been established as the most powerful and practical genome engineering tool for both fundamental researches and biotechnological applications. Great efforts have been devoted to engineering the CRISPR system with better performance and novel functions. As an essential component, single guide RNAs (sgRNAs) have been extensively designed and engineered with desirable functions. This review highlights representative studies that optimize the sgRNA nucleotide sequences for improved genome editing performance (e.g. activity and specificity) as well as add extra aptamers and end extensions for expanded CRISPR-based functional assays (e.g. transcriptional regulation, genome imaging, and prime editor). The perspectives for further sgRNA engineering to establish more powerful and versatile CRISPR/Cas systems are also discussed.
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Affiliation(s)
- Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China.
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Konstantakos V, Nentidis A, Krithara A, Paliouras G. CRISPR-Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning. Nucleic Acids Res 2022; 50:3616-3637. [PMID: 35349718 PMCID: PMC9023298 DOI: 10.1093/nar/gkac192] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become a successful and promising technology for gene-editing. To facilitate its effective application, various computational tools have been developed. These tools can assist researchers in the guide RNA (gRNA) design process by predicting cleavage efficiency and specificity and excluding undesirable targets. However, while many tools are available, assessment of their application scenarios and performance benchmarks are limited. Moreover, new deep learning tools have been explored lately for gRNA efficiency prediction, but have not been systematically evaluated. Here, we discuss the approaches that pertain to the on-target activity problem, focusing mainly on the features and computational methods they utilize. Furthermore, we evaluate these tools on independent datasets and give some suggestions for their usage. We conclude with some challenges and perspectives about future directions for CRISPR-Cas9 guide design.
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Affiliation(s)
- Vasileios Konstantakos
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
| | - Anastasios Nentidis
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
- School of Informatics, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia Krithara
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
| | - Georgios Paliouras
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E & 27 Neapoleos Str, 15341 Athens, Greece
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Xie VC, Styles MJ, Dickinson BC. Methods for the directed evolution of biomolecular interactions. Trends Biochem Sci 2022; 47:403-416. [PMID: 35427479 PMCID: PMC9022280 DOI: 10.1016/j.tibs.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 02/06/2023]
Abstract
Noncovalent interactions between biomolecules such as proteins and nucleic acids coordinate all cellular processes through changes in proximity. Tools that perturb these interactions are and will continue to be highly valuable for basic and translational scientific endeavors. By taking cues from natural systems, such as the adaptive immune system, we can design directed evolution platforms that can generate proteins that bind to biomolecules of interest. In recent years, the platforms used to direct the evolution of biomolecular binders have greatly expanded the range of types of interactions one can evolve. Herein, we review recent advances in methods to evolve protein-protein, protein-RNA, and protein-DNA interactions.
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Affiliation(s)
| | - Matthew J Styles
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
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