1
|
Sui Z, Wu Q, Geng J, Xiao J, Huang D. CRISPR/Cas9-mediated efficient white genome editing in the black soldier fly Hermetia illucens. Mol Genet Genomics 2024; 299:5. [PMID: 38315256 DOI: 10.1007/s00438-023-02088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/17/2023] [Indexed: 02/07/2024]
Abstract
The CRISPR/Cas9 system is the most straightforward genome-editing technology to date, enabling genetic engineering in many insects, including the black soldier fly, Hermetia illucens. The white gene plays a significant role in the multifarious life activities of insects, especially the pigmentation of the eyes. In this study, the white gene of H. illucens (Hiwhite) was cloned, identified, and bioinformatically analysed for the first time. Using quantitative real-time polymerase chain reaction (qPCR), we found that the white gene was expressed in the whole body of the adult flies, particularly in Malpighian tubules and compound eyes. Furthermore, we utilised CRISPR/Cas9-mediated genome-editing technology to successfully generate heritable Hiwhite mutants using two single guide RNAs. During Hiwhite genome editing, we determined the timing, method, and needle-pulling parameters for embryo microinjection by observing early embryonic developmental features. We used the CasOT program to obtain highly specific guide RNAs (gRNAs) at the genome-wide level. According to the phenotypes of Hiwhite knockout strains, the pigmentation of larval stemmata, imaginal compound eyes, and ocelli differed from those of the wild type. These phenotypes were similar to those observed in other insects harbouring white gene mutations. In conclusion, our results described a detailed white genome editing process in black soldier flies, which lays a solid foundation for intensive research on the pigmentation pathway of the eyes and provides a methodological basis for further genome engineering applications in black soldier flies.
Collapse
Affiliation(s)
- Zhuoxiao Sui
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qi Wu
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jin Geng
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jinhua Xiao
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Dawei Huang
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| |
Collapse
|
2
|
Tiwari PK, Ko TH, Dubey R, Chouhan M, Tsai LW, Singh HN, Chaubey KK, Dayal D, Chiang CW, Kumar S. CRISPR/Cas9 as a therapeutic tool for triple negative breast cancer: from bench to clinics. Front Mol Biosci 2023; 10:1214489. [PMID: 37469704 PMCID: PMC10352522 DOI: 10.3389/fmolb.2023.1214489] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a third-generation genome editing method that has revolutionized the world with its high throughput results. It has been used in the treatment of various biological diseases and infections. Various bacteria and other prokaryotes such as archaea also have CRISPR/Cas9 systems to guard themselves against bacteriophage. Reportedly, CRISPR/Cas9-based strategy may inhibit the growth and development of triple-negative breast cancer (TNBC) via targeting the potentially altered resistance genes, transcription, and epigenetic regulation. These therapeutic activities could help with the complex issues such as drug resistance which is observed even in TNBC. Currently, various methods have been utilized for the delivery of CRISPR/Cas9 into the targeted cell such as physical (microinjection, electroporation, and hydrodynamic mode), viral (adeno-associated virus and lentivirus), and non-viral (liposomes and lipid nano-particles). Although different models have been developed to investigate the molecular causes of TNBC, but the lack of sensitive and targeted delivery methods for in-vivo genome editing tools limits their clinical application. Therefore, based on the available evidences, this review comprehensively highlighted the advancement, challenges limitations, and prospects of CRISPR/Cas9 for the treatment of TNBC. We also underscored how integrating artificial intelligence and machine learning could improve CRISPR/Cas9 strategies in TNBC therapy.
Collapse
Affiliation(s)
- Prashant Kumar Tiwari
- Biological and Bio-Computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Tin-Hsien Ko
- Department of Orthopedics, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Mandeep Chouhan
- Biological and Bio-Computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei City, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei City, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei City, Taiwan
| | - Himanshu Narayan Singh
- Department of Systems Biology, Columbia University Irving Medical Centre, New York, NY, United States
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Deen Dayal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Chih-Wei Chiang
- Department of Orthopedics, Taipei Medical University Hospital, Taipei City, Taiwan
- Department of Orthopedic Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan
| | - Sanjay Kumar
- Biological and Bio-Computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| |
Collapse
|
3
|
Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies. Genes (Basel) 2020; 11:genes11050473. [PMID: 32349249 PMCID: PMC7290804 DOI: 10.3390/genes11050473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Inherited retinal dystrophies are an assorted group of rare diseases that collectively account for the major cause of visual impairment of genetic origin worldwide. Besides clinically, these vision loss disorders present a high genetic and allelic heterogeneity. To date, over 250 genes have been associated to retinal dystrophies with reported causative variants of every nature (nonsense, missense, frameshift, splice-site, large rearrangements, and so forth). Except for a fistful of mutations, most of them are private and affect one or few families, making it a challenge to ratify the newly identified candidate genes or the pathogenicity of dubious variants in disease-associated loci. A recurrent option involves altering the gene in in vitro or in vivo systems to contrast the resulting phenotype and molecular imprint. To validate specific mutations, the process must rely on simulating the precise genetic change, which, until recently, proved to be a difficult endeavor. The rise of the CRISPR/Cas9 technology and its adaptation for genetic engineering now offers a resourceful suite of tools to alleviate the process of functional studies. Here we review the implementation of these RNA-programmable Cas9 nucleases in culture-based and animal models to elucidate the role of novel genes and variants in retinal dystrophies.
Collapse
|
4
|
Gerashchenkov GA, Rozhnova NA, Kuluev BR, Kiryanova OY, Gumerova GR, Knyazev AV, Vershinina ZR, Mikhailova EV, Chemeris DA, Matniyazov RT, Baimiev AK, Gubaidullin IM, Baimiev AK, Chemeris AV. Design of Guide RNA for CRISPR/Cas Plant Genome Editing. Mol Biol 2020. [DOI: 10.1134/s0026893320010069] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
5
|
Torres-Perez R, Garcia-Martin JA, Montoliu L, Oliveros JC, Pazos F. WeReview: CRISPR Tools-Live Repository of Computational Tools for Assisting CRISPR/Cas Experiments. Bioengineering (Basel) 2019; 6:E63. [PMID: 31349743 PMCID: PMC6783853 DOI: 10.3390/bioengineering6030063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/23/2022] Open
Abstract
Computational tools are essential in the process of designing a CRISPR/Cas experiment for the targeted modification of an organism's genome. Among other functionalities, these tools facilitate the design of a guide-RNA (gRNA) for a given nuclease that maximizes its binding to the intended genomic site, while avoiding binding to undesired sites with similar sequences in the genome of the organism of interest (off-targets). Due to the popularity of this methodology and the rapid pace at which it evolves and changes, new computational tools show up constantly. This rapid turnover, together with the intrinsic high death-rate of bioinformatics tools, mean that many of the published tools become unavailable at some point. Consequently, the traditional ways to inform the community about the landscape of available tools, i.e., reviews in the scientific literature, are not adequate for this fast-moving field. To overcome these limitations, we have developed "WeReview: CRISPR Tools," a live, on-line, user-updatable repository of computational tools to assist researchers in designing CRISPR/Cas experiments. In its web site users can find an updated comprehensive list of tools and search for those fulfilling their specific needs, as well as proposing modifications to the data associated with the tools or the incorporation of new ones.
Collapse
Affiliation(s)
- Rafael Torres-Perez
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
| | | | - Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
- Rare Diseases Networking Biomedical Research Centre (CIBERER-ISCIII), 28049 Madrid, Spain
| | - Juan C Oliveros
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain.
| | - Florencio Pazos
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain.
| |
Collapse
|
6
|
Uniyal AP, Mansotra K, Yadav SK, Kumar V. An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. 3 Biotech 2019; 9:223. [PMID: 31139538 PMCID: PMC6529479 DOI: 10.1007/s13205-019-1760-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/13/2019] [Indexed: 12/26/2022] Open
Abstract
A large number of computational tools have been documented in recent years for identification of target-specific valid single-guide (sg) RNAs (18-20 nucleotide long sequence) that is an important component for the efficient utilization of the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated Protein) system. Despite optimization of Cas9, other major concerns are on-target efficiency and off-target activity that depend upon the sequence(s) of target-specific sgRNA(s). However, a very little attention has been paid for identification of the best-hit sgRNA for precise targeting as well as minimizing the off-target effects. The aim of this present work is to offer comparative insight into existing CRISPR software tools with their unique features (including targeted genome) and utilities. These available web tools were found to be designed based upon only a few limited mathematical models. Among all these available web tools, three (Benchling, Desktop and CRISPR-P) have been curated as exclusively available for plant genome-editing purpose. These three software tools have been comprehensively described and analyzed with single same target enquiry from two randomly selected genes (IDM2 and IDM3 from Arabidopsis thaliana). Interestingly, all these selected tools generated different results (sgRNAs) even for the same query. In fact, the sequence of sgRNA is considered an important parameter to determine the efficiency and specificity of sgRNAs for precise genome editing. Thus, there is an urgent requirement to pay attention for a validated sgRNA-designing tool for precise DNA editing in plants. In conclusion, this work will encourage building up a consensus for developing a universal valid sgRNA designing for different organisms including plants.
Collapse
Affiliation(s)
- Ajay Prakash Uniyal
- Department of Plant Sciences, School for Basic and Applied Sciences, Central University of Punjab, Bathinda, 161001 India
| | - Komal Mansotra
- Department of Plant Sciences, School for Basic and Applied Sciences, Central University of Punjab, Bathinda, 161001 India
| | | | - Vinay Kumar
- Department of Plant Sciences, School for Basic and Applied Sciences, Central University of Punjab, Bathinda, 161001 India
| |
Collapse
|
7
|
Hu Z, Ma D. The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications. Cancer Med 2018; 7:5217-5236. [PMID: 30589505 PMCID: PMC6198240 DOI: 10.1002/cam4.1501] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/14/2018] [Accepted: 03/21/2018] [Indexed: 12/14/2022] Open
Abstract
Cervical cancer is the third most common cancer in women worldwide, with concepts and knowledge about its prevention and treatment evolving rapidly. Human papillomavirus (HPV) has been identified as a major factor that leads to cervical cancer, although HPV infection alone cannot cause the disease. In fact, HPV-driven cancer is a small probability event because most infections are transient and could be cleared spontaneously by host immune system. With persistent HPV infection, decades are required for progression to cervical cancer. Therefore, this long time window provides golden opportunity for clinical intervention, and the fundament here is to elucidate the carcinogenic pattern and applicable targets during HPV-host interaction. In this review, we discuss the key factors that contribute to the persistence of HPV and cervical carcinogenesis, emerging new concepts and technologies for cancer interventions, and more urgently, how these concepts and technologies might lead to clinical precision medicine which could provide prediction, prevention, and early treatment for patients.
Collapse
Affiliation(s)
- Zheng Hu
- Department of Gynecological oncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd RoadYuexiu, GuangzhouGuangdongChina
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan, Hubei430030China
| | - Ding Ma
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan, Hubei430030China
| |
Collapse
|
8
|
Yan J, Chuai G, Zhou C, Zhu C, Yang J, Zhang C, Gu F, Xu H, Wei J, Liu Q. Benchmarking CRISPR on-target sgRNA design. Brief Bioinform 2018; 19:721-724. [PMID: 28203699 DOI: 10.1093/bib/bbx001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 12/26/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based gene editing has been widely implemented in various cell types and organisms. A major challenge in the effective application of the CRISPR system is the need to design highly efficient single-guide RNA (sgRNA) with minimal off-target cleavage. Several tools are available for sgRNA design, while limited tools were compared. In our opinion, benchmarking the performance of the available tools and indicating their applicable scenarios are important issues. Moreover, whether the reported sgRNA design rules are reproducible across different sgRNA libraries, cell types and organisms remains unclear. In our study, a systematic and unbiased benchmark of the sgRNA predicting efficacy was performed on nine representative on-target design tools, based on six benchmark data sets covering five different cell types. The benchmark study presented here provides novel quantitative insights into the available CRISPR tools.
Collapse
Affiliation(s)
- Jifang Yan
- School of Life Sciences, Tongji University, China
| | - Guohui Chuai
- School of Life Sciences, Tongji University, China
| | - Chi Zhou
- School of Life Sciences, Tongji University, China
| | - Chenyu Zhu
- School of Life Sciences, Tongji University, China
| | - Jing Yang
- School of Life Sciences, Tongji University, China
| | - Chao Zhang
- School of Life Sciences, Tongji University, China
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, China
| | - Han Xu
- Dana-Farber Cancer Institute, Harvard School of Public Health, USA
| | - Jia Wei
- R&D Information, Innovation Center China, AstraZeneca, Shanghai, China
| | - Qi Liu
- School of Life Sciences, Tongji University, China
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
9
|
Fernández A, Josa S, Montoliu L. A history of genome editing in mammals. Mamm Genome 2017; 28:237-246. [DOI: 10.1007/s00335-017-9699-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/31/2017] [Indexed: 12/28/2022]
|