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Ma S, Zhang T, Wang R, Wang P, Liu Y, Chang J, Wang A, Lan X, Sun L, Sun H, Shi R, Lu W, Liu D, Zhang N, Hu W, Wang X, Xing W, Jia L, Xia Q. High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori. Genome Res 2024; 34:134-144. [PMID: 38191205 PMCID: PMC10903940 DOI: 10.1101/gr.278297.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR-Cas9-induced library in a nonmodel multicellular organism, Bombyx mori We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multipurpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollutant cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, as well as a powerful resource for identifying the potential of key candidate genes for improving various economic traits. This study also shows the effectiveness, practicality, and convenience of large-scale mutant libraries in other nonmodel organisms.
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Affiliation(s)
- Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China;
| | - Tong Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ruolin Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Pan Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Yue Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jiasong Chang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China
| | - Aoming Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xinhui Lan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Le Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Hao Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Run Shi
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Wei Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Dan Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Na Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Wenbo Hu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xiaogang Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
- China Chongqing Key Laboratory of Chinese Medicine & Health Science, Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Weiqing Xing
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ling Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China;
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Abstract
The CRISPR/Cas9 genome editing system has been one of the greatest scientific discoveries in the last decade. The highly efficient and precise editing ability of this technology is of great therapeutic value and benefits the basic sciences as an advantageous research tool. In recent years, forward genetic screens using CRISPR technology have been widely adopted, with genome-wide or pathway-focused screens leading to important and novel discoveries. CRISPR screens have been used primarily in cancer biology, virology, and basic cell biology, but they have rarely been applied to diabetes research. A potential reason for this is that diabetes-related research can be more complicated, often involving cross talk between multiple organs or cell types. Nevertheless, many questions can still be reduced to the study of a single cell type if assays are carefully designed. Here we review the application of CRISPR screen technology and provide perspective on how it can be used in diabetes research.
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Affiliation(s)
- Peng Yi
- Section for Islet Cell and Regenerative Biology, and CRISPR Screen Core Laboratory, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Noelle Morrow
- Section for Islet Cell and Regenerative Biology, and CRISPR Screen Core Laboratory, Joslin Diabetes Center, Harvard Medical School, Boston, MA
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Paraskevopoulos M, McGuigan AP. Application of CRISPR screens to investigate mammalian cell competition. Brief Funct Genomics 2021; 20:135-147. [PMID: 33782689 DOI: 10.1093/bfgp/elab020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 11/14/2022] Open
Abstract
Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control mechanism that facilitates the removal of suboptimal cells from both adult and embryonic tissues. Cell competition, however, can also be hijacked by transformed cells to acquire a 'super-competitor' status and outcompete the normal epithelium to establish a precancerous field. To date, many genetic drivers of cell competition have been identified predominately through studies in Drosophila. Especially during the last couple of years, ethylmethanesulfonate-based genetic screens have been instrumental to our understanding of the molecular regulators behind some of the most common competition mechanisms in Drosophila, namely competition due to impaired ribosomal function (or anabolism) and mechanical sensitivity. Despite recent findings in Drosophila and in mammalian models of cell competition, the drivers of mammalian cell competition remain largely elusive. Since the discovery of CRISPR/Cas9, its use in functional genomics has been indispensable to uncover novel cancer vulnerabilities. We envision that CRISPR/Cas9 screens will enable systematic, genome-scale probing of mammalian cell competition to discover novel mutations that not only trigger cell competition but also identify novel molecular components that are essential for the recognition and elimination of less fit cells. In this review, we summarize recent contributions that further our understanding of the molecular mechanisms of cell competition by genetic screening in Drosophila, and provide our perspective on how similar and novel screening strategies made possible by whole-genome CRISPR/Cas9 screening can advance our understanding of mammalian cell competition in the future.
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Safari F, Sharifi M, Farajnia S, Akbari B, Karimi Baba Ahmadi M, Negahdaripour M, Ghasemi Y. The interaction of phages and bacteria: the co-evolutionary arms race. Crit Rev Biotechnol 2019; 40:119-137. [PMID: 31793351 DOI: 10.1080/07388551.2019.1674774] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the dawn of life, bacteria and phages are locked in a constant battle and both are perpetually changing their tactics to overcome each other. Bacteria use various strategies to overcome the invading phages, including adsorption inhibition, restriction-modification (R/E) systems, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, abortive infection (Abi), etc. To counteract, phages employ intelligent tactics for the nullification of bacterial defense systems, such as accessing host receptors, evading R/E systems, and anti-CRISPR proteins. Intense knowledge about the details of these defense pathways is the basis for their broad utilities in various fields of research from microbiology to biotechnology. Hence, in this review, we discuss some strategies used by bacteria to inhibit phage infections as well as phage tactics to circumvent bacterial defense systems. In addition, the application of these strategies will be described as a lesson learned from bacteria and phage combats. The ecological factors that affect the evolution of bacterial immune systems is the other issue represented in this review.
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Affiliation(s)
- Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Sharifi
- Department of Emergency Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Van Damme P, Robberecht W, Van Den Bosch L. Modelling amyotrophic lateral sclerosis: progress and possibilities. Dis Model Mech 2018; 10:537-549. [PMID: 28468939 PMCID: PMC5451175 DOI: 10.1242/dmm.029058] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder that primarily affects the motor system and presents with progressive muscle weakness. Most patients survive for only 2-5 years after disease onset, often due to failure of the respiratory muscles. ALS is a familial disease in ∼10% of patients, with the remaining 90% developing sporadic ALS. Over the past decade, major advances have been made in our understanding of the genetics and neuropathology of ALS. To date, around 20 genes are associated with ALS, with the most common causes of typical ALS associated with mutations in SOD1, TARDBP, FUS and C9orf72. Advances in our understanding of the genetic basis of ALS have led to the creation of different models of this disease. The molecular pathways that have emerged from these systems are more heterogeneous than previously anticipated, ranging from protein aggregation and defects in multiple key cellular processes in neurons, to dysfunction of surrounding non-neuronal cells. Here, we review the different model systems used to study ALS and discuss how they have contributed to our current knowledge of ALS disease mechanisms. A better understanding of emerging disease pathways, the detrimental effects of the various gene mutations and the causes underlying motor neuron denegation in sporadic ALS will accelerate progress in the development of novel treatments. Summary: In this Review, Ludo Van Den Bosch and colleagues discuss the different model systems for studying ALS and how they have contributed to our current understanding of the etiology and pathology of this neurodegenerative disease.
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Affiliation(s)
- Philip Van Damme
- KU Leuven, University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB - Center of Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, B-3000 Leuven, Belgium
| | - Wim Robberecht
- KU Leuven, University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, B-3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- KU Leuven, University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium .,VIB - Center of Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium
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Lu XJ, Sun HM, Xu Y, Yu X, Gu B. The applications and advances of CRISPR-Cas9 in medical research. Brief Funct Genomics 2017; 16:1-3. [PMID: 28132023 DOI: 10.1093/bfgp/elw036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiao-Jie Lu
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong-Mei Sun
- Department of Anesthesiology, Jiangsu Huai'an Maternity and Children Hospital, Huai'an, China
| | - Yong Xu
- Department of Nephrology,, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Xi Yu
- Department of Gastroenterology, Longgang District Central Hospital of Shenzhen, Longgang District, Shenzhen, Guangdong, China
| | - Biao Gu
- Department of Thoracic Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
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