1
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Zhang X, Blumenthal RM, Cheng X. Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins. Curr Opin Struct Biol 2024; 87:102836. [PMID: 38754172 DOI: 10.1016/j.sbi.2024.102836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
C2H2 zinc-finger (ZF) proteins form the largest family of DNA-binding transcription factors coded by mammalian genomes. In a typical DNA-binding ZF module, there are twelve residues (numbered from -1 to -12) between the last zinc-coordinating cysteine and the first zinc-coordinating histidine. The established C2H2-ZF "recognition code" suggests that residues at positions -1, -4, and -7 recognize the 5', central, and 3' bases of a DNA base-pair triplet, respectively. Structural studies have highlighted that additional residues at positions -5 and -8 also play roles in specific DNA recognition. The presence of bulky and either charged or polar residues at these five positions determines specificity for given DNA bases: guanine is recognized by arginine, lysine, or histidine; adenine by asparagine or glutamine; thymine or 5-methylcytosine by glutamate; and unmodified cytosine by aspartate. This review discusses recent structural characterizations of C2H2-ZFs that add to our understanding of the principles underlying the C2H2-ZF recognition code.
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Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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2
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Li J, Wei Q, Cheng Y, Kong D, Kong Z, Ke Y, Dang X, Zhu JK, Shimada H, Miki D. Cas12a-mediated gene targeting by sequential transformation strategy in Arabidopsis thaliana. BMC PLANT BIOLOGY 2024; 24:665. [PMID: 38997669 PMCID: PMC11241819 DOI: 10.1186/s12870-024-05375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024]
Abstract
Gene targeting (GT) allows precise manipulation of genome sequences, such as knock-ins and sequence substitutions, but GT in seed plants remains a challenging task. Engineered sequence-specific nucleases (SSNs) are known to facilitate GT via homology-directed repair (HDR) in organisms. Here, we demonstrate that Cas12a and a temperature-tolerant Cas12a variant (ttCas12a) can efficiently establish precise and heritable GT at two loci in Arabidopsis thaliana (Arabidopsis) through a sequential transformation strategy. As a result, ttCas12a showed higher GT efficiency than unmodified Cas12a. In addition, the efficiency of transcriptional and translational enhancers for GT via sequential transformation strategy was also investigated. These enhancers and their combinations were expected to show an increase in GT efficiency in the sequential transformation strategy, similar to previous reports of all-in-one strategies, but only a maximum twofold increase was observed. These results indicate that the frequency of double strand breaks (DSBs) at the target site is one of the most important factors determining the efficiency of genetic GT in plants. On the other hand, a higher frequency of DSBs does not always lead to higher efficiency of GT, suggesting that some additional factors are required for GT via HDR. Therefore, the increase in DSB can no longer be expected to improve GT efficiency, and a new strategy needs to be established in the future. This research opens up a wide range of applications for precise and heritable GT technology in plants.
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Affiliation(s)
- Jing Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Wei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiqiu Cheng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe Kong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongping Ke
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Dang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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3
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Zhang X, Blumenthal RM, Cheng X. Keep Fingers on the CpG Islands. EPIGENOMES 2024; 8:23. [PMID: 38920624 PMCID: PMC11202855 DOI: 10.3390/epigenomes8020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/31/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
The post-genomic era has ushered in the extensive application of epigenetic editing tools, allowing for precise alterations of gene expression. The use of reprogrammable editors that carry transcriptional corepressors has significant potential for long-term epigenetic silencing for the treatment of human diseases. The ideal scenario involves precise targeting of a specific genomic location by a DNA-binding domain, ensuring there are no off-target effects and that the process yields no genetic remnants aside from specific epigenetic modifications (i.e., DNA methylation). A notable example is a recent study on the mouse Pcsk9 gene, crucial for cholesterol regulation and expressed in hepatocytes, which identified synthetic zinc-finger (ZF) proteins as the most effective DNA-binding editors for silencing Pcsk9 efficiently, specifically, and persistently. This discussion focuses on enhancing the specificity of ZF-array DNA binding by optimizing interactions between specific amino acids and DNA bases across three promoters containing CpG islands.
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Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Robert M. Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA;
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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4
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Allemailem KS, Almatroudi A, Rahmani AH, Alrumaihi F, Alradhi AE, Alsubaiyel AM, Algahtani M, Almousa RM, Mahzari A, Sindi AAA, Dobie G, Khan AA. Recent Updates of the CRISPR/Cas9 Genome Editing System: Novel Approaches to Regulate Its Spatiotemporal Control by Genetic and Physicochemical Strategies. Int J Nanomedicine 2024; 19:5335-5363. [PMID: 38859956 PMCID: PMC11164216 DOI: 10.2147/ijn.s455574] [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: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
The genome editing approach by clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) is a revolutionary advancement in genetic engineering. Owing to its simple design and powerful genome-editing capability, it offers a promising strategy for the treatment of different infectious, metabolic, and genetic diseases. The crystal structure of Streptococcus pyogenes Cas9 (SpCas9) in complex with sgRNA and its target DNA at 2.5 Å resolution reveals a groove accommodating sgRNA:DNA heteroduplex within a bilobate architecture with target recognition (REC) and nuclease (NUC) domains. The presence of a PAM is significantly required for target recognition, R-loop formation, and strand scission. Recently, the spatiotemporal control of CRISPR/Cas9 genome editing has been considerably improved by genetic, chemical, and physical regulatory strategies. The use of genetic modifiers anti-CRISPR proteins, cell-specific promoters, and histone acetyl transferases has uplifted the application of CRISPR/Cas9 as a future-generation genome editing tool. In addition, interventions by chemical control, small-molecule activators, oligonucleotide conjugates and bioresponsive delivery carriers have improved its application in other areas of biological fields. Furthermore, the intermediation of physical control by using heat-, light-, magnetism-, and ultrasound-responsive elements attached to this molecular tool has revolutionized genome editing further. These strategies significantly reduce CRISPR/Cas9's undesirable off-target effects. However, other undesirable effects still offer some challenges for comprehensive clinical translation using this genome-editing approach. In this review, we summarize recent advances in CRISPR/Cas9 structure, mechanistic action, and the role of small-molecule activators, inhibitors, promoters, and physical approaches. Finally, off-target measurement approaches, challenges, future prospects, and clinical applications are discussed.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arwa Essa Alradhi
- General Administration for Infectious Disease Control, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Amal M Alsubaiyel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca 21955, Saudi Arabia
| | - Rand Mohammad Almousa
- Department of Education, General Directorate of Education, Qassim 52361, Saudi Arabia
| | - Ali Mahzari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Gasim Dobie
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Gizan 82911, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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5
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Rahimi A, Sameei P, Mousavi S, Ghaderi K, Hassani A, Hassani S, Alipour S. Application of CRISPR/Cas9 System in the Treatment of Alzheimer's Disease and Neurodegenerative Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04143-2. [PMID: 38639864 DOI: 10.1007/s12035-024-04143-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Alzheimer's, Parkinson's, and Huntington's are some of the most common neurological disorders, which affect millions of people worldwide. Although there have been many treatments for these diseases, there are still no effective treatments to treat or completely stop these disorders. Perhaps the lack of proper treatment for these diseases can be related to various reasons, but the poor results related to recent clinical research also prompted doctors to look for new treatment approaches. In this regard, various researchers from all over the world have provided many new treatments, one of which is CRISPR/Cas9. Today, the CRISPR/Cas9 system is mostly used for genetic modifications in various species. In addition, by using the abilities available in the CRISPR/Cas9 system, researchers can either remove or modify DNA sequences, which in this way can establish a suitable and useful treatment method for the treatment of genetic diseases that have undergone mutations. We conducted a non-systematic review of articles and study results from various databases, including PubMed, Medline, Web of Science, and Scopus, in recent years. and have investigated new treatment methods in neurodegenerative diseases with a focus on Alzheimer's disease. Then, in the following sections, the treatment methods were classified into three groups: anti-tau, anti-amyloid, and anti-APOE regimens. Finally, we discussed various applications of the CRISPR/Cas-9 system in Alzheimer's disease. Today, using CRISPR/Cas-9 technology, scientists create Alzheimer's disease models that have a more realistic phenotype and reveal the processes of pathogenesis; following the screening of defective genes, they establish treatments for this disease.
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Affiliation(s)
- Araz Rahimi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Parsa Sameei
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Sana Mousavi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Kimia Ghaderi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Amin Hassani
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Sepideh Hassani
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University Medical Sciences (UMSU), Urmia, Iran.
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran.
| | - Shahriar Alipour
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran.
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University Medical Sciences (UMSU), Urmia, Iran.
- Department of Clinical Biochemistry and Applied Cell Sciences, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran.
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Ping N, Hara-Kuge S, Yagi Y, Kazama T, Nakamura T. Translational enhancement of target endogenous mRNA in mammalian cells using programmable RNA-binding pentatricopeptide repeat proteins. Sci Rep 2024; 14:251. [PMID: 38167853 PMCID: PMC10762265 DOI: 10.1038/s41598-023-50776-z] [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: 07/31/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
Programmable protein scaffolds are invaluable in the development of genome engineering tools. The pentatricopeptide repeat (PPR) protein is an attractive platform for RNA manipulation because of its programmable RNA-binding selectivity, which is determined by the combination of amino acid species at three specific sites in the PPR motif. Translation is a key RNA regulatory step that determines the final gene expression level and is involved in various human diseases. In this study, designer PPR protein was used to develop a translational enhancement technique by fusion with the translation initiation factor eIF4G. The results showed that the PPR-eIF4G fusion protein could activate the translation of endogenous c-Myc and p53 mRNAs and control cell fate, indicating that PPR-based translational enhancement is a versatile technique applicable to various endogenous mRNAs in mammalian cells. In addition, the translational enhancement was dependent on both the target position and presence of eIF4G, suggesting the presence of an unknown translation activation mechanism.
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Affiliation(s)
- Ning Ping
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Sayuri Hara-Kuge
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | | | - Tomohiko Kazama
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Takahiro Nakamura
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
- EditForce, Inc., Fukuoka, 819-0395, Japan.
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7
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Wal P, Aziz N, Singh CP, Rasheed A, Tyagi LK, Agrawal A, Wal A. Current Landscape of Gene Therapy for the Treatment of Cardiovascular Disorders. Curr Gene Ther 2024; 24:356-376. [PMID: 38288826 DOI: 10.2174/0115665232268840231222035423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 07/16/2024]
Abstract
Cardiovascular disorders (CVD) are the primary cause of death worldwide. Multiple factors have been accepted to cause cardiovascular diseases; among them, smoking, physical inactivity, unhealthy eating habits, age, and family history are flag-bearers. Individuals at risk of developing CVD are suggested to make drastic habitual changes as the primary intervention to prevent CVD; however, over time, the disease is bound to worsen. This is when secondary interventions come into play, including antihypertensive, anti-lipidemic, anti-anginal, and inotropic drugs. These drugs usually undergo surgical intervention in patients with a much higher risk of heart failure. These therapeutic agents increase the survival rate, decrease the severity of symptoms and the discomfort that comes with them, and increase the overall quality of life. However, most individuals succumb to this disease. None of these treatments address the molecular mechanism of the disease and hence are unable to halt the pathological worsening of the disease. Gene therapy offers a more efficient, potent, and important novel approach to counter the disease, as it has the potential to permanently eradicate the disease from the patients and even in the upcoming generations. However, this therapy is associated with significant risks and ethical considerations that pose noteworthy resistance. In this review, we discuss various methods of gene therapy for cardiovascular disorders and address the ethical conundrum surrounding it.
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Affiliation(s)
- Pranay Wal
- PSIT-Pranveer Singh Institute of Technology (Pharmacy), NH-19, Kanpur, Uttar Pradesh, 209305, India
| | - Namra Aziz
- PSIT-Pranveer Singh Institute of Technology (Pharmacy), NH-19, Kanpur, Uttar Pradesh, 209305, India
| | | | - Azhar Rasheed
- PSIT-Pranveer Singh Institute of Technology (Pharmacy), NH-19, Kanpur, Uttar Pradesh, 209305, India
| | - Lalit Kumar Tyagi
- Department of Pharmacy, Lloyd Institute of Management and Technology, Plot No.-11, Knowledge Park-II, Greater Noida, Uttar Pradesh, 201306, India
| | - Ankur Agrawal
- School of Pharmacy, Jai Institute of Pharmaceutical Sciences and Research, Gwalior, MP, India
| | - Ankita Wal
- PSIT-Pranveer Singh Institute of Technology (Pharmacy), NH-19, Kanpur, Uttar Pradesh, 209305, India
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8
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Huang HW, Shivatare VS, Tseng TH, Wong CH. Cell-based production of Fc-GlcNAc and Fc-alpha-2,6 sialyl glycan enriched antibody with improved effector functions through glycosylation pathway engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572280. [PMID: 38187613 PMCID: PMC10769250 DOI: 10.1101/2023.12.18.572280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Glycosylation of antibody plays an important role in Fc-mediated killing of tumor cells and virus-infected cells through effector functions such as antibody-dependent cellular cytotoxicity (ADCC), antibody dependent cell-mediated phagocytosis (ADCP) and vaccinal effect. Previous studies showed that therapeutical humanized antibodies with α2-6 sialyl complex type (SCT) glycan attached to Fc-Asn297 exhibited optimal binding to the Fc receptors on effector cells associated with ADCC, ADCP and vaccinal effect. However, the production of antibodies with homogeneous Fc-SCT needs multiple in vitro enzymatic and purification steps. In this study, we report two different approaches to shorten the processes to produce SCT-enriched antibodies. First, we expressed a bacterial endoglycosidase in GNT1-KO EXPI293 cells to trim all N -glycans to mono-GlcNAc glycoforms for in vitro transglycosylation to generate homogeneous SCT antibody. Second, we engineered the glycosylation pathway of HEK293 cells through knockout of the undesired glycosyltransferases and expression of the desired glycosyltransferases to produce SCT enriched antibodies with similar binding affinity to Fc receptors and ADCC activity to homogenous SCT antibody.
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9
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Xu Z, Chen S, Wu W, Wen Y, Cao H. Type I CRISPR-Cas-mediated microbial gene editing and regulation. AIMS Microbiol 2023; 9:780-800. [PMID: 38173969 PMCID: PMC10758571 DOI: 10.3934/microbiol.2023040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
There are six major types of CRISPR-Cas systems that provide adaptive immunity in bacteria and archaea against invasive genetic elements. The discovery of CRISPR-Cas systems has revolutionized the field of genetics in many organisms. In the past few years, exploitations of the most abundant class 1 type I CRISPR-Cas systems have revealed their great potential and distinct advantages to achieve gene editing and regulation in diverse microorganisms in spite of their complicated structures. The widespread and diversified type I CRISPR-Cas systems are becoming increasingly attractive for the development of new biotechnological tools, especially in genetically recalcitrant microbial strains. In this review article, we comprehensively summarize recent advancements in microbial gene editing and regulation by utilizing type I CRISPR-Cas systems. Importantly, to expand the microbial host range of type I CRISPR-Cas-based applications, these structurally complicated systems have been improved as transferable gene-editing tools with efficient delivery methods for stable expression of CRISPR-Cas elements, as well as convenient gene-regulation tools with the prevention of DNA cleavage by obviating deletion or mutation of the Cas3 nuclease. We envision that type I CRISPR-Cas systems will largely expand the biotechnological toolbox for microbes with medical, environmental and industrial importance.
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Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yongqi Wen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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Khlidj Y. What did CRISPR-Cas9 accomplish in its first 10 years? Biochem Med (Zagreb) 2023; 33:030601. [PMID: 37545694 PMCID: PMC10373057 DOI: 10.11613/bm.2023.030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/01/2023] [Indexed: 08/08/2023] Open
Abstract
It's been 10 years now from the debut of clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) era in which gene engineering has never been so accessible, precise and efficient. This technology, like a refined surgical procedure, has offered the ability of removing different types of disease causing mutations and restoring key proteins activity with ease of outperforming the previous resembling methods: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Additionally, CRISPR-Cas9 systems can systematically introduce genetic sequences to the specific sites in the human genome allowing to stimulate desired functions such as anti-tumoral and anti-infectious faculties. The present brief review provides an updated resume of CRISPR-Cas9's top achievements from its first appearance to the current date focusing on the breakthrough research including in vitro, in vivo and human studies. This enables the evaluation of the previous phase 'the proof-of-concept phase' and marks the beginning of the next phase which will probably bring a spate of clinical trials.
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11
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Li L, Vasan L, Kartono B, Clifford K, Attarpour A, Sharma R, Mandrozos M, Kim A, Zhao W, Belotserkovsky A, Verkuyl C, Schmitt-Ulms G. Advances in Recombinant Adeno-Associated Virus Vectors for Neurodegenerative Diseases. Biomedicines 2023; 11:2725. [PMID: 37893099 PMCID: PMC10603849 DOI: 10.3390/biomedicines11102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors are gene therapy delivery tools that offer a promising platform for the treatment of neurodegenerative diseases. Keeping up with developments in this fast-moving area of research is a challenge. This review was thus written with the intention to introduce this field of study to those who are new to it and direct others who are struggling to stay abreast of the literature towards notable recent studies. In ten sections, we briefly highlight early milestones within this field and its first clinical success stories. We showcase current clinical trials, which focus on gene replacement, gene augmentation, or gene suppression strategies. Next, we discuss ongoing efforts to improve the tropism of rAAV vectors for brain applications and introduce pre-clinical research directed toward harnessing rAAV vectors for gene editing applications. Subsequently, we present common genetic elements coded by the single-stranded DNA of rAAV vectors, their so-called payloads. Our focus is on recent advances that are bound to increase treatment efficacies. As needed, we included studies outside the neurodegenerative disease field that showcased improved pre-clinical designs of all-in-one rAAV vectors for gene editing applications. Finally, we discuss risks associated with off-target effects and inadvertent immunogenicity that these technologies harbor as well as the mitigation strategies available to date to make their application safer.
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Affiliation(s)
- Leyao Li
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Lakshmy Vasan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Bryan Kartono
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Kevan Clifford
- Institute of Medical Science, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Centre for Addiction and Mental Health (CAMH), 250 College St., Toronto, ON M5T 1R8, Canada
| | - Ahmadreza Attarpour
- Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Raghav Sharma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Matthew Mandrozos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ain Kim
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Wenda Zhao
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ari Belotserkovsky
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Claire Verkuyl
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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12
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Peroni E, Randi ML, Rosato A, Cagnin S. Acute myeloid leukemia: from NGS, through scRNA-seq, to CAR-T. dissect cancer heterogeneity and tailor the treatment. J Exp Clin Cancer Res 2023; 42:259. [PMID: 37803464 PMCID: PMC10557350 DOI: 10.1186/s13046-023-02841-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a malignant blood cancer with marked cellular heterogeneity due to altered maturation and differentiation of myeloid blasts, the possible causes of which are transcriptional or epigenetic alterations, impaired apoptosis, and excessive cell proliferation. This neoplasm has a high rate of resistance to anticancer therapies and thus a high risk of relapse and mortality because of both the biological diversity of the patient and intratumoral heterogeneity due to the acquisition of new somatic changes. For more than 40 years, the old gold standard "one size fits all" treatment approach included intensive chemotherapy treatment with anthracyclines and cytarabine.The manuscript first traces the evolution of the understanding of the pathology from the 1970s to the present. The enormous strides made in its categorization prove to be crucial for risk stratification, enabling an increasingly personalized diagnosis and treatment approach.Subsequently, we highlight how, over the past 15 years, technological advances enabling single cell RNA sequencing and T-cell modification based on the genomic tools are affecting the classification and treatment of AML. At the dawn of the new millennium, the advent of high-throughput next-generation sequencing technologies has enabled the profiling of patients evidencing different facets of the same disease, stratifying risk, and identifying new possible therapeutic targets that have subsequently been validated. Currently, the possibility of investigating tumor heterogeneity at the single cell level, profiling the tumor at the time of diagnosis or after treatments exist. This would allow the identification of underrepresented cellular subclones or clones resistant to therapeutic approaches and thus responsible for post-treatment relapse that would otherwise be difficult to detect with bulk investigations on the tumor biopsy. Single-cell investigation will then allow even greater personalization of therapy to the genetic and transcriptional profile of the tumor, saving valuable time and dangerous side effects. The era of personalized medicine will take a huge step forward through the disclosure of each individual piece of the complex puzzle that is cancer pathology, to implement a "tailored" therapeutic approach based also on engineered CAR-T cells.
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Affiliation(s)
- Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy.
| | - Maria Luigia Randi
- First Medical Clinic, Department of Medicine-DIMED, University of Padua, Padua, Italy
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, 35131, Italy
- CIR-Myo Myology Center, University of Padova, Padova, 35131, Italy
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13
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Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X. Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic Acids Res 2023; 51:8447-8462. [PMID: 37439339 PMCID: PMC10484683 DOI: 10.1093/nar/gkad594] [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: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12-15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1-ZF7 and ZF3-ZF11 in complex with DNA that incorporates the CORE sequence together with either 3' downstream or 5' upstream motifs. Like conventional tandem ZF array proteins, ZF1-ZF7 follow the right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three base pairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9-ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1-ZF7 and ZF8-ZF11 to residues at the two positions -6 and -5 within each finger, with small residues for ZF1-ZF7 and bulkier and polar/charged residues for ZF8-ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine-guanine and glutamine-adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9-ZF11. The differences between ZF1-ZF7 and ZF8-ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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14
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Bestas B, Wimberger S, Degtev D, Madsen A, Rottner AK, Karlsson F, Naumenko S, Callahan M, Touza JL, Francescatto M, Möller CI, Badertscher L, Li S, Cerboni S, Selfjord N, Ericson E, Gordon E, Firth M, Chylinski K, Taheri-Ghahfarokhi A, Bohlooly-Y M, Snowden M, Pangalos M, Nuttall B, Akcakaya P, Sienski G, Maresca M. A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo. Nat Commun 2023; 14:5474. [PMID: 37673883 PMCID: PMC10482872 DOI: 10.1038/s41467-023-41240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes.
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Affiliation(s)
- Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dmitrii Degtev
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Alexandra Madsen
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Antje K Rottner
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Sergey Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - Megan Callahan
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Julia Liz Touza
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Margherita Francescatto
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Carl Ivar Möller
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Niklas Selfjord
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Elke Ericson
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | | | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Snowden
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Barrett Nuttall
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Grzegorz Sienski
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
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15
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Yin G, Wang XH, Sun Y. Recent advances in CRISPR-Cas system for the treatment of genetic hearing loss. AMERICAN JOURNAL OF STEM CELLS 2023; 12:37-50. [PMID: 37736272 PMCID: PMC10509501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023]
Abstract
Genetic hearing loss has emerged as a significant public health concern that demands attention. Among the various treatment strategies, gene therapy based on gene editing technology is considered the most promising approach for addressing genetic hearing loss by repairing or eliminating mutated genes. The advent of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has revolutionized gene therapy through its remarkable gene editing capabilities. This system has been extensively employed in mammalian gene editing and is currently being evaluated through clinical trials. Against this backdrop, this review aims to provide an overview of recent advances in utilizing the CRISPR-Cas system to treat genetic hearing loss. Additionally, we delve into the primary challenges and prospects associated with the current application of this system in addressing genetic hearing loss.
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Affiliation(s)
- Ge Yin
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Xiao-Hui Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and RegenerationWuhan 430022, Hubei, China
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
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16
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Tsibulnikov S, Fayzullina D, Karlina I, Schroeder BA, Karpova O, Timashev P, Ulasov I. Ewing sarcoma treatment: a gene therapy approach. Cancer Gene Ther 2023; 30:1066-1071. [PMID: 37037906 PMCID: PMC10088695 DOI: 10.1038/s41417-023-00615-0] [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: 09/21/2022] [Revised: 02/07/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
Ewing sarcoma (ES) is an aggressive malignant tumor, characterized by non-random chromosomal translocations that produce fusion genes. Fusion genes and fusion protein products are promising targets for gene therapy. Therapeutic approaches and strategies vary based on target molecules (nucleotides, proteins) of interest. We present an extensive literature review of active molecules for gene therapy and methods of gene therapy delivery, both of which are necessary for successful treatment.
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Affiliation(s)
- Sergey Tsibulnikov
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Daria Fayzullina
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Irina Karlina
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Brett A Schroeder
- National Cancer Institute, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Olga Karpova
- Section of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Peter Timashev
- World-Class Research Centre "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
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17
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Rahimi A, Karimipoor M, Mahdian R, Alipour A, Hosseini S, Mohammadi M, Kaghazian H, Abbasi A, Shahsavarani H, Shokrgozar MA. Efficient CRISPR/Cas9-Mediated BAX Gene Ablation in CHO Cells To Impair Apoptosis and Enhance Recombinant Protein Production. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3388. [PMID: 37228627 PMCID: PMC10203183 DOI: 10.30498/ijb.2023.343428.3388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/25/2023] [Indexed: 05/27/2023]
Abstract
Background Despite recent advances in recombinant biotherapeutics production using CHO cells, their productivity remains lower than industrial needs, mainly due to apoptosis. Objectives Present study aimed to exploit CRISPR/Cas9 technology to specifically disrupt the BAX gene to attenuate apoptosis in recombinant Chinese hamster's ovary cells producing erythropoietin. Materials and Methods The STRING database was used to identify the key pro-apoptotic genes to be modified by CRISPR/Cas9 technique. The single guide RNAs (sgRNAs) targeting identified gene (BAX) were designed, and CHO cells were then transfected with vectors. Afterward, changes in the expression of the Bax gene and consequent production rates of erythropoietin were investigated in manipulated cells, even in the presence of an apoptosis inducer agent, oleuropein. Results BAX disruption significantly prolonged cell viability and increased proliferation rate in manipulated clones (152%, P-value = 0.0002). This strategy reduced the levels of Bax protein expression in manipulated cells by more than 4.3-fold (P-value <0.0001). The Bax-8 manipulated cells displayed higher threshold tolerance to the stress and consequence apoptosis compared to the control group. Also, they exhibited a higher IC50 compared to the control in the presence of oleuropein (5095 µM.ml-1 Vs. 2505 µM.ml-1). We found a significant increase in recombinant protein production levels in manipulated cells, even in the presence of 1,000 µM oleuropein compared to the control cell line (p-value=0.0002). Conclusions CRISPR/Cas9 assisted BAX gene ablation is promising to improve erythropoietin production in CHO cells via engineering anti-apoptotic genes. Therefore, exploiting genome editing tools such as CRISPR/Cas9 has been proposed to develop host cells that result in a safe, feasible, and robust manufacturing operation with a yield that meets the industrial requirements.
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Affiliation(s)
- Amirabbas Rahimi
- Laboratory of regenerative medicine and biomedical innovations, National Cell Bank Department, Pasteur Institute of Iran, Tehran, Iran
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | | | - Reza Mahdian
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Alipour
- Department of Nano-Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Saadi Hosseini
- Laboratory of regenerative medicine and biomedical innovations, National Cell Bank Department, Pasteur Institute of Iran, Tehran, Iran
| | - Marzieh Mohammadi
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Hooman Kaghazian
- Department of Research & Development, Production & Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Abdolrahim Abbasi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD
| | - Hosein Shahsavarani
- Department of Cell and Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Ali Shokrgozar
- Laboratory of regenerative medicine and biomedical innovations, National Cell Bank Department, Pasteur Institute of Iran, Tehran, Iran
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18
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Poletto E, Silva AO, Weinlich R, Martin PKM, Torres DC, Giugliani R, Baldo G. Ex vivo gene therapy for lysosomal storage disorders: future perspectives. Expert Opin Biol Ther 2023; 23:353-364. [PMID: 36920351 DOI: 10.1080/14712598.2023.2192348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Lysosomal storage disorders (LSD) are a group of monogenic rare diseases caused by pathogenic variants in genes that encode proteins related to lysosomal function. These disorders are good candidates for gene therapy for different reasons: they are monogenic, most of lysosomal proteins are enzymes that can be secreted and cross-correct neighboring cells, and small quantities of these proteins are able to produce clinical benefits in many cases. Ex vivo gene therapy allows for autologous transplant of modified cells from different sources, including stem cells and hematopoietic precursors. AREAS COVERED Here, we summarize the main gene therapy and genome editing strategies that are currently being used as ex vivo gene therapy approaches for lysosomal disorders, highlighting important characteristics, such as vectors used, strategies, types of cells that are modified and main results in different disorders. EXPERT OPINION Clinical trials are already ongoing, and soon approved therapies for LSD based on ex vivo gene therapy approaches should reach the market.
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Affiliation(s)
- Edina Poletto
- Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto alegre, Brazil
- Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Andrew Oliveira Silva
- Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Ricardo Weinlich
- Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Centro de Ensino e Pesquisa/Pesquisa Experimental, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Davi Coe Torres
- Centro de Ensino e Pesquisa/Pesquisa Experimental, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Roberto Giugliani
- Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto alegre, Brazil
- Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Guilherme Baldo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto alegre, Brazil
- Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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19
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Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH. Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533036. [PMID: 36993517 PMCID: PMC10055298 DOI: 10.1101/2023.03.17.533036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Traditional genome-editing reagents such as CRISPR-Cas9 achieve targeted DNA modification by introducing double-strand breaks (DSBs), thereby stimulating localized DNA repair by endogenous cellular repair factors. While highly effective at generating heterogenous knockout mutations, this approach suffers from undesirable byproducts and an inability to control product purity. Here we develop a system in human cells for programmable, DSB-free DNA integration using Type I CRISPR-associated transposons (CASTs). To adapt our previously described CAST systems, we optimized DNA targeting by the QCascade complex through a comprehensive assessment of protein design, and we developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase, TnsC, to genomic sites targeted by QCascade. After initial detection of plasmid-based transposition, we screened 15 homologous CAST systems from a wide range of bacterial hosts, identified a CAST homolog from Pseudoalteromonas that exhibited improved activity, and increased integration efficiencies through parameter optimization. We further discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, and we propose that this critical accessory factor functions to drive active disassembly of the post-transposition CAST complex, akin to its demonstrated role in Mu transposition. Our work highlights the ability to functionally reconstitute complex, multi-component machineries in human cells, and establishes a strong foundation to realize the full potential of CRISPR-associated transposons for human genome engineering.
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Affiliation(s)
- George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Rebeca T King
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tyler S Halpin-Healy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Marcus I Hogan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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20
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Ugalde L, Fañanas S, Torres R, Quintana-Bustamante O, Río P. CRISPR/Cas9-mediated gene editing. A promising strategy in hematological disorders. Cytotherapy 2023; 25:277-285. [PMID: 36610813 DOI: 10.1016/j.jcyt.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/09/2022] [Accepted: 11/30/2022] [Indexed: 01/07/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has revolutionized the gene editing field, making it possible to interrupt, insert or replace a sequence of interest with high precision in the human genome. Its easy design and wide applicability open up a variety of therapeutic alternatives for the treatment of genetic diseases. Indeed, very promising approaches for the correction of hematological disorders have been developed in the recent years, based on the self-renewal and multipotent differentiation properties of hematopoietic stem and progenitor cells, which make this cell subset the ideal target for gene therapy purposes. This technology has been applied in different congenital blood disorders, such as primary immunodeficiencies, X-linked severe combined immunodeficiency, X-linked chronic granulomatous disease or Wiskott-Aldrich syndrome, and inherited bone marrow failure syndromes, such as Fanconi anemia, congenital amegakaryocytic thrombocytopenia or severe congenital neutropenia. Furthermore, CRISPR/Cas9-based gene editing has been implemented successfully as a novel therapy for cancer immunotherapy, by the development of promising strategies such as the use of oncolytic viruses or adoptive cellular therapy to the chimeric antigen receptor-T-cell therapy. Therefore, considering the variety of genes and mutations affected, we can take advantage of the different DNA repair mechanisms by CRISPR/Cas9 in different manners, from homology-directed repair to non-homologous-end-joining to the latest emerging technologies such as base and prime editing. Although the delivery systems into hematopoietic stem and progenitor cells are still the bottleneck of this technology, some of the advances in genome editing shown in this review have already reached a clinical stage and show very promising preliminary results.
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Affiliation(s)
- Laura Ugalde
- Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Sara Fañanas
- Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Raúl Torres
- Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; Molecular Cytogenetics Group, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Oscar Quintana-Bustamante
- Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Paula Río
- Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain.
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21
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Alamillo JM, López CM, Martínez Rivas FJ, Torralbo F, Bulut M, Alseekh S. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein and hairy roots: a perfect match for gene functional analysis and crop improvement. Curr Opin Biotechnol 2023; 79:102876. [PMID: 36621223 PMCID: PMC9923253 DOI: 10.1016/j.copbio.2022.102876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/21/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023]
Abstract
Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) gene editing has become a powerful tool in genome manipulation for crop improvement. Advances in omics technologies, including genomics, transcriptomics, and metabolomics, allow the identification of causal genes that can be used to improve crops. However, the functional validation of these genetic components remains a challenge due to the lack of efficient protocols for crop engineering. Hairy roots gene editing using CRISPR/Cas, coupled with omics analyses, provide a platform for rapid, precise, and cost-effective functional analysis of genes. Here, we describe common requirements for efficient crop genome editing, focused on the transformation of recalcitrant legumes, and highlight the great opportunities that gene editing in hairy roots offers for future crop improvement.
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Affiliation(s)
- Josefa M Alamillo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain.
| | - Cristina M López
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | | | - Fernando Torralbo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Mustafa Bulut
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Institute of Plants Systems Biology and Biotechnology, Plovdiv, Bulgaria.
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22
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Zhang W, Wang R, Kong D, Peng F, Chen M, Zeng W, Giaume F, He S, Zhang H, Wang Z, Kyozuka J, Zhu JK, Fornara F, Miki D. Precise and heritable gene targeting in rice using a sequential transformation strategy. CELL REPORTS METHODS 2023; 3:100389. [PMID: 36814841 PMCID: PMC9939429 DOI: 10.1016/j.crmeth.2022.100389] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/18/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023]
Abstract
Gene targeting (GT) is a powerful tool for modifying endogenous genomic sequences of interest, such as sequence replacement and gene knockin. Although the efficiency of GT is extremely low in higher plants, engineered sequence-specific nucleases (SSNs)-mediated double-strand breaks (DSBs) can improve GT frequency. We recently reported a CRISPR-Cas9-mediated approach for heritable GT in Arabidopsis, called the "sequential transformation" strategy. For efficient establishment of GT via the sequential transformation method, strong Cas9 activity and robust DSBs are required in the plant cells being infected with Agrobacterium carrying sgRNA and donor DNA. Accordingly, we generated two independent parental lines with maize Ubiquitin 1 promoter-driven Cas9 and established sequential transformation-mediated GT in the Japonica rice cultivar Oryza sativa Nipponbare. We achieved precise GFP knockin into the endogenous OsFTL1 and OsROS1a loci. We believe that our GT technology could be widely utilized in rice research and breeding applications.
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Affiliation(s)
- Wenxin Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fangnan Peng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Chen
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjie Zeng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Francesca Giaume
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Sheng He
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hui Zhang
- College of Life Science, Shanghai Normal University, Shanghai 200234, China
| | - Zhen Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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23
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Li T, Yang Y, Qi H, Cui W, Zhang L, Fu X, He X, Liu M, Li PF, Yu T. CRISPR/Cas9 therapeutics: progress and prospects. Signal Transduct Target Ther 2023; 8:36. [PMID: 36646687 PMCID: PMC9841506 DOI: 10.1038/s41392-023-01309-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/06/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene-editing technology is the ideal tool of the future for treating diseases by permanently correcting deleterious base mutations or disrupting disease-causing genes with great precision and efficiency. A variety of efficient Cas9 variants and derivatives have been developed to cope with the complex genomic changes that occur during diseases. However, strategies to effectively deliver the CRISPR system to diseased cells in vivo are currently lacking, and nonviral vectors with target recognition functions may be the focus of future research. Pathological and physiological changes resulting from disease onset are expected to serve as identifying factors for targeted delivery or targets for gene editing. Diseases are both varied and complex, and the choice of appropriate gene-editing methods and delivery vectors for different diseases is important. Meanwhile, there are still many potential challenges identified when targeting delivery of CRISPR/Cas9 technology for disease treatment. This paper reviews the current developments in three aspects, namely, gene-editing type, delivery vector, and disease characteristics. Additionally, this paper summarizes successful examples of clinical trials and finally describes possible problems associated with current CRISPR applications.
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Affiliation(s)
- Tianxiang Li
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Yanyan Yang
- grid.410645.20000 0001 0455 0905Department of Immunology, School of Basic Medicine, Qingdao University, 266021 Qingdao, People’s Republic of China
| | - Hongzhao Qi
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Weigang Cui
- grid.452710.5Department of Cardiology, People’s Hospital of Rizhao, No. 126 Taian Road, 276827 Rizhao, People’s Republic of China
| | - Lin Zhang
- Department of Microbiology, Linyi Center for Disease Control and Prevention, 276000 Linyi, People’s Republic of China
| | - Xiuxiu Fu
- grid.412521.10000 0004 1769 1119Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, 266000 Qingdao, People’s Republic of China
| | - Xiangqin He
- grid.412521.10000 0004 1769 1119Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, 266000 Qingdao, People’s Republic of China
| | - Meixin Liu
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Pei-feng Li
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021, Qingdao, People's Republic of China. .,Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, 266000, Qingdao, People's Republic of China.
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24
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Davies M, Jurynec MJ, Gomez-Alvarado F, Hu D, Feeley SE, Allen-Brady K, Tashjian RZ, Feeley BT. Current cellular and molecular biology techniques for the orthopedic surgeon-scientist. J Shoulder Elbow Surg 2023; 32:e11-e22. [PMID: 35988889 DOI: 10.1016/j.jse.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/27/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Michael Davies
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Jurynec
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
| | - Francisco Gomez-Alvarado
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Hu
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Sonali E Feeley
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Kristina Allen-Brady
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Robert Z Tashjian
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.
| | - Brian T Feeley
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
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25
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Lee SK, Kim YG. Construction of a Z-DNA-Specific Recombinant Nuclease Zαα-FOK for Conformation Studies. Methods Mol Biol 2023; 2651:143-155. [PMID: 36892765 DOI: 10.1007/978-1-0716-3084-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Development of FokI-based engineered nucleases has been a platform technology that enables creation of novel sequence-specific nucleases as well as structure-specific nucleases. Z-DNA-specific nucleases have been constructed by fusing a Z-DNA-binding domain to the nuclease domain of FokI (FN). In particular, Zαα, an engineered Z-DNA-binding domain with a high affinity, is an ideal fusion partner to generate a highly efficient Z-DNA-specific cutter. Here, we describe construction, expression, and purification of Zαα-FOK (Zαα-FN) nuclease in detail. In addition, Z-DNA-specific cleavage is demonstrated by the use of Zαα-FOK.
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Affiliation(s)
- Seul Ki Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, South Korea
| | - Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, South Korea.
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26
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Sharma P, Pandey A, Malviya R, Dey S, Karmakar S, Gayen D. Genome editing for improving nutritional quality, post-harvest shelf life and stress tolerance of fruits, vegetables, and ornamentals. Front Genome Ed 2023; 5:1094965. [PMID: 36911238 PMCID: PMC9998953 DOI: 10.3389/fgeed.2023.1094965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Agricultural production relies on horticultural crops, including vegetables, fruits, and ornamental plants, which sustain human life. With an alarming increase in human population and the consequential need for more food, it has become necessary for increased production to maintain food security. Conventional breeding has subsidized the development of improved verities but to enhance crop production, new breeding techniques need to be acquired. CRISPR-Cas9 system is a unique and powerful genome manipulation tool that can change the DNA in a precise way. Based on the bacterial adaptive immune system, this technique uses an endonuclease that creates double-stranded breaks (DSBs) at the target loci under the guidance of a single guide RNA. These DSBs can be repaired by a cellular repair mechanism that installs small insertion and deletion (indels) at the cut sites. When equated to alternate editing tools like ZFN, TALENs, and meganucleases, CRISPR- The cas-based editing tool has quickly gained fast-forward for its simplicity, ease to use, and low off-target effect. In numerous horticultural and industrial crops, the CRISPR technology has been successfully used to enhance stress tolerance, self-life, nutritional improvements, flavor, and metabolites. The CRISPR-based tool is the most appropriate one with the prospective goal of generating non-transgenic yields and avoiding the regulatory hurdles to release the modified crops into the market. Although several challenges for editing horticultural, industrial, and ornamental crops remain, this new novel nuclease, with its crop-specific application, makes it a dynamic tool for crop improvement.
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Affiliation(s)
- Punam Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Anuradha Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Rinku Malviya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Sharmistha Dey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | | | - Dipak Gayen
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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27
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Aliaga Goltsman DS, Alexander LM, Lin JL, Fregoso Ocampo R, Freeman B, Lamothe RC, Perez Rivas A, Temoche-Diaz MM, Chadha S, Nordenfelt N, Janson OP, Barr I, Devoto AE, Cost GJ, Butterfield CN, Thomas BC, Brown CT. Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes. Nat Commun 2022; 13:7602. [PMID: 36522342 PMCID: PMC9755519 DOI: 10.1038/s41467-022-35257-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. However, to further expand the therapeutic application of these tools there is a need for targetable systems that are small enough to be delivered efficiently. Here, we mined an extensive genome-resolved metagenomics database and identified families of uncharacterized RNA-guided, compact nucleases (between 450 and 1,050 aa). We report that Cas9d, a new CRISPR type II subtype, contains Zinc-finger motifs and high arginine content, features that we also found in nucleases related to HEARO effectors. These enzymes exhibit diverse biochemical characteristics and are broadly targetable. We show that natural Cas9d enzymes are capable of genome editing in mammalian cells with >90% efficiency, and further engineered nickase variants into the smallest base editors active in E. coli and human cells. Their small size, broad targeting potential, and translatability suggest that Cas9d and HEARO systems will enable a variety of genome editing applications.
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Affiliation(s)
| | | | - Jyun-Liang Lin
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA, 94608, USA
| | | | | | | | | | | | | | | | - Owen P Janson
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA, 94608, USA
| | - Ian Barr
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA, 94608, USA
| | - Audra E Devoto
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA, 94608, USA
| | - Gregory J Cost
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA, 94608, USA
| | | | - Brian C Thomas
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA, 94608, USA
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28
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Rahimi A, Karimipoor M, Mahdian R, Alipour A, Hosseini S, Kaghazian H, Abbasi A, Shahsavarani H, Shokrgozar MA. Targeting Caspase-3 Gene in rCHO Cell Line by CRISPR/Cas9 Editing Tool and Its Effect on Protein Production in Manipulated Cell Line. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2022; 21:e130236. [PMID: 36915405 PMCID: PMC10007989 DOI: 10.5812/ijpr-130236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/19/2022] [Accepted: 12/12/2022] [Indexed: 03/06/2023]
Abstract
Background Chinese hamster ovary (CHO) cells are the widely used mammalian cell host for biopharmaceutical manufacturing. During cell cultures, CHO cells lose viability mainly from apoptosis. Inhibiting cell death is useful because prolonging cell lifespans can direct to more productive cell culture systems for biotechnology requests. Objectives This study exploited a CRISPR/Cas9 technology to generate site-specific gene disruptions in the caspase-3 gene in the apoptosis pathway, which acts as an apoptotic regulator to extend cell viability in the CHO cell line. Methods The STRING database was used to identify the key pro-apoptotic genes to be modified by CRISPR/Cas9 system. The guide RNAs targeting the caspase-3 gene were designed, and vectors containing sgRNA and Cas9 were transfected into CHO cells that expressed erythropoietin as a heterologous protein. Indel formation was investigated by DNA sequencing. Caspase-3 expression was quantified by real-time PCR and western blot. The effect of editing the caspase-3 gene on the inhibition of apoptosis was also investigated by induction of apoptosis in manipulated cell lines by oleuropein. Finally, the erythropoietin production in the edited cells was compared to the control cells. Results The caspase-3 manipulation significantly prolongation of the cell viability and decreased the caspase-3 expression level of protein in manipulated CHO cells (more than 6-fold, P-value < 0.0001). Manipulated cells displayed higher threshold tolerance to apoptosis compared to the control cells when they were induced by oleuropein. They show a higher IC50 than the control ones (7271 µM/mL Vs. 5741 µM/mL). They also show a higher proliferation rate than the control cells in the presence of an apoptosis inducer (P-value < 0.0001). Furthermore, manipulated cell lines significantly produce more recombinant protein in the presence of 2,000 µM oleuropein compared to the control ones (P-value = 0.0021). Conclusions We understood that CRISPR/Cas9 could be effectively applied to suppress the expression of the caspase-3 gene and rescue CHO cells from apoptosis induced by cell stress and metabolites. The CRISPR/Cas9 system-assisted caspase-3 gene ablation can potentially increase erythropoietin yield in CHO cells.
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Affiliation(s)
- Amirabbas Rahimi
- Laboratory of Regenerative Medicine and Biomedical Innovations, Department of National Cell Bank, Pasteur Institute of Iran, Tehran, Iran
- Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Mahdian
- Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Alipour
- Department of Nano-Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Sadi Hosseini
- Laboratory of Regenerative Medicine and Biomedical Innovations, Department of National Cell Bank, Pasteur Institute of Iran, Tehran, Iran
| | - Hooman Kaghazian
- Department of Research & Development, Production & Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Abdolrahim Abbasi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hosein Shahsavarani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Corresponding Author: Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Mohammad Ali Shokrgozar
- Laboratory of Regenerative Medicine and Biomedical Innovations, Department of National Cell Bank, Pasteur Institute of Iran, Tehran, Iran
- Corresponding Author: Laboratory of Regenerative Medicine and Biomedical Innovations, Department of National Cell Bank, Pasteur Institute of Iran, 13169-43551, Tehran, Iran.
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29
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Pal S, Dam S. CRISPR-Cas9: Taming protozoan parasites with bacterial scissor. J Parasit Dis 2022; 46:1204-1212. [PMID: 36457766 PMCID: PMC9606157 DOI: 10.1007/s12639-022-01534-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022] Open
Abstract
The invention of CRISPR-Cas9 technology has opened a new era in which genome manipulation has become precise, faster, cheap and more accurate than previous genome editing strategies. Despite the intricacies of the genomes associated with several protozoan parasites, CRISPR-Cas9 has made a substantial contribution to parasitology. The study of functional genomics through CRISPR-Cas9 mediated gene knockout, insertion, deletion and mutation has helped in understanding intrinsic parasite biology. The invention of CRISPR-dCas9 has helped in the programmable control of protozoan gene expression and epigenetic engineering. CRISPR and CRISPR-based alternatives will continue to thrive and may aid in the development of novel anti-protozoan strategies to tame the protozoan parasites in the imminent future.
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Affiliation(s)
- Suchetana Pal
- Department of Microbiology, The University of Burdwan, Burdwan, West Bengal 713104 India
| | - Somasri Dam
- Department of Microbiology, The University of Burdwan, Burdwan, West Bengal 713104 India
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30
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Zhang Z, Zeng W, Zhang W, Li J, Kong D, Zhang L, Wang R, Peng F, Kong Z, Ke Y, Zhang H, Kim C, Zhang H, Botella JR, Zhu JK, Miki D. Insights into the molecular mechanisms of CRISPR/Cas9-mediated gene targeting at multiple loci in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2203-2216. [PMID: 36106983 PMCID: PMC9706422 DOI: 10.1093/plphys/kiac431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Homologous recombination-mediated gene targeting (GT) enables precise sequence knockin or sequence replacement, and thus is a powerful tool for heritable precision genome engineering. We recently established a clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9)-mediated approach for heritable GT in Arabidopsis (Arabidopsis thaliana), but its broad utility was not tested, and the underlying molecular mechanism was unclear. Here, we achieved precise GT at 14 out of 27 tested endogenous target loci using the sequential transformation approach and obtained vector-free GT plants by backcrossing. Thus, the sequential transformation GT method provides a broadly applicable technology for precise genome manipulation. We show that our approach generates heritable GT in the egg cell or early embryo of T1 Arabidopsis plants. Analysis of imprecise GT events suggested that single-stranded transfer DNA (T-DNA)/VirD2 complexes produced during the Agrobacterium (Agrobacterium tumefaciens) transformation process may serve as the donor templates for homologous recombination-mediated repair in the GT process. This study provides new insights into the molecular mechanisms of CRISPR/Cas9-mediated GT in Arabidopsis.
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Affiliation(s)
- Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjie Zeng
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxin Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangnan Peng
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Kong
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongping Ke
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jose Ramón Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Allemailem KS, Alsahli MA, Almatroudi A, Alrumaihi F, Alkhaleefah FK, Rahmani AH, Khan AA. Current updates of CRISPR/Cas9-mediated genome editing and targeting within tumor cells: an innovative strategy of cancer management. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:1257-1287. [PMID: 36209487 PMCID: PMC9759771 DOI: 10.1002/cac2.12366] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 01/25/2023]
Abstract
Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR/Cas9), an adaptive microbial immune system, has been exploited as a robust, accurate, efficient and programmable method for genome targeting and editing. This innovative and revolutionary technique can play a significant role in animal modeling, in vivo genome therapy, engineered cell therapy, cancer diagnosis and treatment. The CRISPR/Cas9 endonuclease system targets a specific genomic locus by single guide RNA (sgRNA), forming a heteroduplex with target DNA. The Streptococcus pyogenes Cas9/sgRNA:DNA complex reveals a bilobed architecture with target recognition and nuclease lobes. CRISPR/Cas9 assembly can be hijacked, and its nanoformulation can be engineered as a delivery system for different clinical utilizations. However, the efficient and safe delivery of the CRISPR/Cas9 system to target tissues and cancer cells is very challenging, limiting its clinical utilization. Viral delivery strategies of this system may have many advantages, but disadvantages such as immune system stimulation, tumor promotion risk and small insertion size outweigh these advantages. Thus, there is a desperate need to develop an efficient non-viral physical delivery system based on simple nanoformulations. The delivery strategies of CRISPR/Cas9 by a nanoparticle-based system have shown tremendous potential, such as easy and large-scale production, combination therapy, large insertion size and efficient in vivo applications. This review aims to provide in-depth updates on Streptococcus pyogenic CRISPR/Cas9 structure and its mechanistic understanding. In addition, the advances in its nanoformulation-based delivery systems, including lipid-based, polymeric structures and rigid NPs coupled to special ligands such as aptamers, TAT peptides and cell-penetrating peptides, are discussed. Furthermore, the clinical applications in different cancers, clinical trials and future prospects of CRISPR/Cas9 delivery and genome targeting are also discussed.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | | | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health SciencesCollege of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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Khurana A, Sayed N, Singh V, Khurana I, Allawadhi P, Rawat PS, Navik U, Pasumarthi SK, Bharani KK, Weiskirchen R. A comprehensive overview of CRISPR/Cas 9 technology and application thereof in drug discovery. J Cell Biochem 2022; 123:1674-1698. [PMID: 36128934 DOI: 10.1002/jcb.30329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas technology possesses revolutionary potential to positively affect various domains of drug discovery. It has initiated a rise in the area of genetic engineering and its advantages range from classical science to translational medicine. These genome editing systems have given a new dimension to our capabilities to alter, detect and annotate specified gene sequences. Moreover, the ease, robustness and adaptability of the CRISPR/Cas9 technology have led to its extensive utilization in research areas in such a short period of time. The applications include the development of model cell lines, understanding disease mechanisms, discovering disease targets, developing transgenic animals and plants, and transcriptional modulation. Further, the technology is rapidly growing; hence, an overlook of progressive success is crucial. This review presents the current status of the CRISPR-Cas technology in a tailor-made format from its discovery to several advancements for drug discovery alongwith future trends associated with possibilities and hurdles including ethical concerns.
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Affiliation(s)
- Amit Khurana
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Hyderabad, Telangana, India
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Nilofer Sayed
- Department of Pharmacy, Pravara Rural Education Society's (P.R.E.S.'s) College of Pharmacy, Shreemati Nathibai Damodar Thackersey (SNDT) Women's University, Nashik, Maharashtra, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Isha Khurana
- Department of Pharmaceutical Chemistry, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pushkar Singh Rawat
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | | | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
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Novel AAV-mediated genome editing therapy improves health and survival in a mouse model of methylmalonic acidemia. PLoS One 2022; 17:e0274774. [PMID: 36126056 PMCID: PMC9488783 DOI: 10.1371/journal.pone.0274774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/04/2022] [Indexed: 11/19/2022] Open
Abstract
Methylmalonic acidemia (MMA) is an inborn error of metabolism mostly caused by mutations in the mitochondrial methylmalonyl-CoA mutase gene (MMUT). MMA patients suffer from frequent episodes of metabolic decompensation, which can be life threatening. To mimic both the dietary restrictions and metabolic decompensation seen in MMA patients, we developed a novel protein-controlled diet regimen in a Mmut deficient mouse model of MMA and demonstrated the therapeutic benefit of mLB-001, a nuclease-free, promoterless recombinant AAV GeneRideTM vector designed to insert the mouse Mmut into the endogenous albumin locus via homologous recombination. A single intravenous administration of mLB-001 to neonatal or adult MMA mice prevented body weight loss and mortality when challenged with a high protein diet. The edited hepatocytes expressed functional MMUT protein and expanded over time in the Mmut deficient mice, suggesting a selective growth advantage over the diseased cells. In mice with a humanized liver, treatment with a human homolog of mLB-001 resulted in site-specific genome editing and transgene expression in the transplanted human hepatocytes. Taken together, these findings support the development of hLB-001 that is currently in clinical trials in pediatric patients with severe forms of MMA.
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Mapook A, Hyde KD, Hassan K, Kemkuignou BM, Čmoková A, Surup F, Kuhnert E, Paomephan P, Cheng T, de Hoog S, Song Y, Jayawardena RS, Al-Hatmi AMS, Mahmoudi T, Ponts N, Studt-Reinhold L, Richard-Forget F, Chethana KWT, Harishchandra DL, Mortimer PE, Li H, Lumyong S, Aiduang W, Kumla J, Suwannarach N, Bhunjun CS, Yu FM, Zhao Q, Schaefer D, Stadler M. Ten decadal advances in fungal biology leading towards human well-being. FUNGAL DIVERS 2022; 116:547-614. [PMID: 36123995 PMCID: PMC9476466 DOI: 10.1007/s13225-022-00510-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/28/2022] [Indexed: 11/04/2022]
Abstract
Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.
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Affiliation(s)
- Ausana Mapook
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
- Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225 China
| | - Khadija Hassan
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
| | - Blondelle Matio Kemkuignou
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
| | - Adéla Čmoková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Frank Surup
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Brunswick, Germany
| | - Eric Kuhnert
- Centre of Biomolecular Drug Research (BMWZ), Institute for Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Pathompong Paomephan
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Department of Biotechnology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400 Thailand
| | - Tian Cheng
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, China
- Microbiology, Parasitology and Pathology Graduate Program, Federal University of Paraná, Curitiba, Brazil
| | - Yinggai Song
- Department of Dermatology, Peking University First Hospital, Peking University, Beijing, China
| | - Ruvishika S. Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Abdullah M. S. Al-Hatmi
- Center of Expertise in Mycology, Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nadia Ponts
- INRAE, UR1264 Mycology and Food Safety (MycSA), 33882 Villenave d’Ornon, France
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | | | - K. W. Thilini Chethana
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Dulanjalee L. Harishchandra
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Peter E. Mortimer
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Huili Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Saisamorm Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, 10300 Thailand
| | - Worawoot Aiduang
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Chitrabhanu S. Bhunjun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Feng-Ming Yu
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Yunnan Key Laboratory of Fungal Diversity and Green Development, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Qi Zhao
- Yunnan Key Laboratory of Fungal Diversity and Green Development, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Doug Schaefer
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Brunswick, Germany
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Park ME, Kim HU. Applications and prospects of genome editing in plant fatty acid and triacylglycerol biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:969844. [PMID: 36119569 PMCID: PMC9471015 DOI: 10.3389/fpls.2022.969844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/08/2022] [Indexed: 05/29/2023]
Abstract
Triacylglycerol (TAG), which is a neutral lipid, has a structure in which three molecules of fatty acid (FA) are ester-bonded to one molecule of glycerol. TAG is important energy source for seed germination and seedling development in plants. Depending on the FA composition of the TAG, it is used as an edible oil or industrial material for cosmetics, soap, and lubricant. As the demand for plant oil is rising worldwide, either the type of FA must be changed or the total oil content of various plants must be increased. In this review, we discuss the regulation of FA metabolism by Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, a recent genome-editing technology applicable to various plants. The development of plants with higher levels of oleic acid or lower levels of very long-chain fatty acids (VLCFAs) in seeds are discussed. In addition, the current status of research on acyltransferases, phospholipases, TAG lipases, and TAG synthesis in vegetative tissues is described. Finally, strategies for the application of CRISPR/Cas9 in lipid metabolism studies are mentioned.
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Affiliation(s)
- Mid-Eum Park
- Department of Molecular Biology, Sejong University, Seoul, South Korea
| | - Hyun Uk Kim
- Department of Molecular Biology, Sejong University, Seoul, South Korea
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
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Meena MR, Appunu C, Arun Kumar R, Manimekalai R, Vasantha S, Krishnappa G, Kumar R, Pandey SK, Hemaprabha G. Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits. Front Genet 2022; 13:854936. [PMID: 35991570 PMCID: PMC9382102 DOI: 10.3389/fgene.2022.854936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in sugarcane breeding have contributed significantly to improvements in agronomic traits and crop yield. However, the growing global demand for sugar and biofuel in the context of climate change requires further improvements in cane and sugar yields. Attempts to achieve the desired rates of genetic gain in sugarcane by conventional breeding means are difficult as many agronomic traits are genetically complex and polygenic, with each gene exerting small effects. Unlike those of many other crops, the sugarcane genome is highly heterozygous due to its autopolyploid nature, which further hinders the development of a comprehensive genetic map. Despite these limitations, many superior agronomic traits/genes for higher cane yield, sugar production, and disease/pest resistance have been identified through the mapping of quantitative trait loci, genome-wide association studies, and transcriptome approaches. Improvements in traits controlled by one or two loci are relatively easy to achieve; however, this is not the case for traits governed by many genes. Many desirable phenotypic traits are controlled by quantitative trait nucleotides (QTNs) with small and variable effects. Assembling these desired QTNs by conventional breeding methods is time consuming and inefficient due to genetic drift. However, recent developments in genomics selection (GS) have allowed sugarcane researchers to select and accumulate desirable alleles imparting superior traits as GS is based on genomic estimated breeding values, which substantially increases the selection efficiency and genetic gain in sugarcane breeding programs. Next-generation sequencing techniques coupled with genome-editing technologies have provided new vistas in harnessing the sugarcane genome to look for desirable agronomic traits such as erect canopy, leaf angle, prolonged greening, high biomass, deep root system, and the non-flowering nature of the crop. Many desirable cane-yielding traits, such as single cane weight, numbers of tillers, numbers of millable canes, as well as cane quality traits, such as sucrose and sugar yield, have been explored using these recent biotechnological tools. This review will focus on the recent advances in sugarcane genomics related to genetic gain and the identification of favorable alleles for superior agronomic traits for further utilization in sugarcane breeding programs.
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Affiliation(s)
- Mintu Ram Meena
- Regional Centre, ICAR-Sugarcane Breeding Institute, Karnal, India
- *Correspondence: Mintu Ram Meena, ; Chinnaswamy Appunu,
| | - Chinnaswamy Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Mintu Ram Meena, ; Chinnaswamy Appunu,
| | - R. Arun Kumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - S. Vasantha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - Ravinder Kumar
- Regional Centre, ICAR-Sugarcane Breeding Institute, Karnal, India
| | - S. K. Pandey
- Regional Centre, ICAR-Sugarcane Breeding Institute, Karnal, India
| | - G. Hemaprabha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
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Li X, Dong H, Guo X, Huang F, Xu X, Li N, Yang Y, Yao T, Feng Y, Liu Q. Mesophilic Argonaute-based isothermal detection of SARS-CoV-2. Front Microbiol 2022; 13:957977. [PMID: 35966688 PMCID: PMC9363790 DOI: 10.3389/fmicb.2022.957977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
Coronavirus disease (COVID-19), caused by SARS-CoV-2 infection and its mutations, has spread rapidly all over the world and still requires sensitive detection to distinguish mutations. CRISPR-based diagnosis has been regarded as a next-generation detection method; however, it has some limitations, such as the need for specific recognition sequences and multiple enzymes for multiplex detection. Therefore, research on the exploration and development of novel nucleases helps to promote specific and sensitive diagnoses. Prokaryotic Argonaute (Ago) proteins exert directed nuclease activity that can target any sequence. Recently, thermophilic Agos have been developed as new detection techniques achieving multiplexity for multiple targets using a single enzyme, as well as accurate recognition of single-base differential sequences. In this study, to overcome the requirement for high reaction temperature of thermophilic Ago-based methods, we expanded the mining of mesophilic Agos to achieve CRISPR-like isothermal detection, named mesophilic Ago-based isothermal detection method (MAIDEN). The principle of MAIDEN uses mesophilic Ago cleavage combined with reverse transcription, which can provide single-strand DNA as a substrate and allow cleavage of fluorescence probes to sense SARS-CoV-2 at moderate temperature. We first mined and optimized the mesophilic Ago and the fluorescence reporter system and then selected a compatible reverse transcription reaction. Furthermore, we optimized MAIDEN into a one-step reaction that can detect SARS-CoV-2 RNA at the nanomolar concentration at a constant temperature of 42°C within 60 min. Therefore, MAIDEN shows advantageous portability and easy-to-implement operation, avoiding the possibility of open-lid contamination. Our study was the first attempt to demonstrate that mesophilic Agos can be harnessed as diagnostic tools, and MAIDEN was easily extended to detect other pathogens in a rapid and efficient manner.
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Affiliation(s)
- Xiao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huarong Dong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyi Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nuolan Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tianbao Yao
- Department of Cardiology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Qian Liu
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Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
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Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
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40
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Wei J, Brophy B, Cole SA, Moormann J, Boch J, Laible G. Cytoplasmic Injection of Zygotes to Genome Edit Naturally Occurring Sequence Variants Into Bovine Embryos. Front Genet 2022; 13:925913. [PMID: 35899192 PMCID: PMC9310181 DOI: 10.3389/fgene.2022.925913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022] Open
Abstract
Genome editing provides opportunities to improve current cattle breeding strategies through targeted introduction of natural sequence variants, accelerating genetic gain. This can be achieved by harnessing homology-directed repair mechanisms following editor-induced cleavage of the genome in the presence of a repair template. Introducing the genome editors into zygotes and editing in embryos has the advantage of uncompromised development into live animals and alignment with contemporary embryo-based improvement practices. In our study, we investigated the potential to introduce sequence variants, known from the pre-melanosomal protein 17 (PMEL) and prolactin receptor (PRLR) genes, and produce non-mosaic, edited embryos, completely converted into the precision genotype. Injection of gRNA/Cas9 editors into bovine zygotes to introduce a 3 bp deletion variant into the PMEL gene produced up to 11% fully converted embryos. The conversion rate was increased to up to 48% with the use of TALEN but only when delivered by plasmid. Testing three gRNA/Cas9 editors in the context of several known PRLR sequence variants, different repair template designs and delivery as DNA, RNA or ribonucleoprotein achieved full conversion rates up to 8%. Furthermore, we developed a biopsy-based screening strategy for non-mosaic embryos which has the potential for exclusively producing non-mosaic animals with intended precision edits.
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Affiliation(s)
- Jingwei Wei
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Brigid Brophy
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Sally-Ann Cole
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Jannis Moormann
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Gӧtz Laible
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
- *Correspondence: Gӧtz Laible,
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41
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Tasca F, Brescia M, Wang Q, Liu J, Janssen JM, Szuhai K, Gonçalves MAFV. Large-scale genome editing based on high-capacity adenovectors and CRISPR-Cas9 nucleases rescues full-length dystrophin synthesis in DMD muscle cells. Nucleic Acids Res 2022; 50:7761-7782. [PMID: 35776127 PMCID: PMC9303392 DOI: 10.1093/nar/gkac567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/20/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
Targeted chromosomal insertion of large genetic payloads in human cells leverages and broadens synthetic biology and genetic therapy efforts. Yet, obtaining large-scale gene knock-ins remains particularly challenging especially in hard-to-transfect stem and progenitor cells. Here, fully viral gene-deleted adenovector particles (AdVPs) are investigated as sources of optimized high-specificity CRISPR-Cas9 nucleases and donor DNA constructs tailored for targeted insertion of full-length dystrophin expression units (up to 14.8-kb) through homologous recombination (HR) or homology-mediated end joining (HMEJ). In muscle progenitor cells, donors prone to HMEJ yielded higher CRISPR-Cas9-dependent genome editing frequencies than HR donors, with values ranging between 6% and 34%. In contrast, AdVP transduction of HR and HMEJ substrates in induced pluripotent stem cells (iPSCs) resulted in similar CRISPR-Cas9-dependent genome editing levels. Notably, when compared to regular iPSCs, in p53 knockdown iPSCs, CRISPR-Cas9-dependent genome editing frequencies increased up to 6.7-fold specifically when transducing HMEJ donor constructs. Finally, single DNA molecule analysis by molecular combing confirmed that AdVP-based genome editing achieves long-term complementation of DMD-causing mutations through the site-specific insertion of full-length dystrophin expression units. In conclusion, AdVPs are a robust and flexible platform for installing large genomic edits in human cells and p53 inhibition fosters HMEJ-based genome editing in iPSCs.
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Affiliation(s)
- Francesca Tasca
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Marcella Brescia
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.,Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Qian Wang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jin Liu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Josephine M Janssen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Manuel A F V Gonçalves
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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Sathee L, Jagadhesan B, Pandesha PH, Barman D, Adavi B S, Nagar S, Krishna GK, Tripathi S, Jha SK, Chinnusamy V. Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation. Front Genet 2022; 13:900897. [PMID: 35774509 PMCID: PMC9237392 DOI: 10.3389/fgene.2022.900897] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Lekshmy Sathee, ; Viswanathan Chinnusamy,
| | - B. Jagadhesan
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pratheek H. Pandesha
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Dipankar Barman
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sandeep Adavi B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Nagar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. K. Krishna
- Department of Plant Physiology, College of Agriculture, KAU, Thrissur, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Lekshmy Sathee, ; Viswanathan Chinnusamy,
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43
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Negi C, Vasistha NK, Singh D, Vyas P, Dhaliwal HS. Application of CRISPR-Mediated Gene Editing for Crop Improvement. Mol Biotechnol 2022; 64:1198-1217. [PMID: 35672603 DOI: 10.1007/s12033-022-00507-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Plant gene editing has become an important molecular tool to revolutionize modern breeding of crops. Over the past years, remarkable advancement has been made in developing robust and efficient editing methods for plants. Despite a variety of available genome editing methods, the discovery of most recent system of clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) has been one of the biggest advancement in this path, with being the most efficient approach for genome manipulation. Until recently, genetic manipulations were confined to methods, like Agrobacterium-mediated transformations, zinc-finger nucleases, and TAL effector nucleases. However this technology supersedes all other methods for genetic modification. This RNA-guided CRISPR-Cas system is being rapidly developed with enhanced functionalities for better use and greater possibilities in biological research. In this review, we discuss and sum up the application of this simple yet powerful tool of CRISPR-Cas system for crop improvement with recent advancement in this technology.
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Affiliation(s)
- Chandranandani Negi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
| | | | - Pritesh Vyas
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India.
| | - H S Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
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44
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Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
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Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
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45
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Rouatbi N, McGlynn T, Al-Jamal KT. Pre-clinical non-viral vectors exploited for in vivo CRISPR/Cas9 gene editing: an overview. Biomater Sci 2022; 10:3410-3432. [PMID: 35604372 DOI: 10.1039/d1bm01452h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clustered regulatory interspaced short palindromic repeats or CRISPR/Cas9 has emerged as a potent and versatile tool for efficient genome editing. This technology has been exploited for several applications including disease modelling, cell therapy, diagnosis, and treatment of many diseases including cancer. The in vivo application of CRISPR/Cas9 is hindered by poor stability, pharmacokinetic profile, and the limited ability of the CRISPR payloads to cross biological barriers. Although viral vectors have been implemented as delivery tools for efficient in vivo gene editing, their application is associated with high immunogenicity and toxicity, limiting their clinical translation. Hence, there is a need to explore new delivery methods that can guarantee safe and efficient delivery of the CRISPR/Cas9 components to target cells. In this review, we first provide a brief history and principles of nuclease-mediated gene editing, we then focus on the different CRISPR/Cas9 formats outlining their potentials and limitations. Finally, we discuss the alternative non-viral delivery strategies currently adopted for in vivo CRISPR/Cas9 gene editing.
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Affiliation(s)
- Nadia Rouatbi
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - Tasneem McGlynn
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - Khuloud T Al-Jamal
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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46
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Abstract
Inherited retinal dystrophies (IRDs) are a heterogeneous group of diseases that affect more than 2 million people worldwide. Gene therapy (GT) has emerged as an exciting treatment modality with the potential to provide long-term benefit to patients. Today, gene addition is the most straightforward GT for autosomal recessive IRDs. However, there are three scenarios where this approach falls short. First, in autosomal dominant diseases caused by gain-of-function or dominant-negative mutations, the toxic mutated protein needs to be silenced. Second, a number of IRD genes exceed the limited carrying capacity of adeno-associated virus vectors. Third, there are still about 30% of patients with unknown mutations. In the first two contexts, precise editing tools, such as CRISPR-Cas9, base editors, or prime editors, are emerging as potential GT solutions for the treatment of IRDs. Here, we review gene editing tools based on CRISPR-Cas9 technology that have been used in vivo and the recent first-in-human application of CRISPR-Cas9 in an IRD.
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Affiliation(s)
- Juliette Pulman
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Rothschild, Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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47
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Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
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Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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48
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Nganso BT, Pines G, Soroker V. Insights into gene manipulation techniques for Acari functional genomics. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103705. [PMID: 35134533 DOI: 10.1016/j.ibmb.2021.103705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Functional genomics is an essential tool for elucidating the structure and function of genes in any living organism. Here, we review the use of different gene manipulation techniques in functional genomics of Acari (mites and ticks). Some of these Acari species inflict severe economic losses to managed crops and health problems to humans, wild and domestic animals, but many also provide important ecosystem services worldwide. Currently, RNA interference (RNAi) is the leading gene expression manipulation tool followed by gene editing via the bacterial type II Clustered Regularly Interspaced Short Palindromic Repeats and associated protein 9 system (CRISPR-Cas9). Whilst RNAi, via siRNA, does not always lead to expected outcomes, the exploitations of the CRISPR systems in Acari are still in their infancy and are limited only to CRISP/Cas9 to date. In this review, we discuss the advantages and disadvantages of RNAi and CRISPR-Cas9 and the technical challenges associated with their exploitations. We also compare the biochemical machinery of RNAi and CRISPR-Cas9 technologies. We highlight some potential solutions for experimental optimization of each mechanism in gene function studies. The potential benefits of adopting various CRISPR-Cas9 systems for expanding on functional genomics experiments in Acari are also discussed.
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Affiliation(s)
- Beatrice T Nganso
- Department of Entomology, Chemistry and Nematology, Institute of Plant Protection, Agricultural Research Organization, The Volcani Centre, Rishon LeZion, Israel.
| | - Gur Pines
- Department of Entomology, Chemistry and Nematology, Institute of Plant Protection, Agricultural Research Organization, The Volcani Centre, Rishon LeZion, Israel.
| | - Victoria Soroker
- Department of Entomology, Chemistry and Nematology, Institute of Plant Protection, Agricultural Research Organization, The Volcani Centre, Rishon LeZion, Israel.
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49
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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50
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Raven SA, Payne B, Bruce M, Filipovska A, Rackham O. In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold. Nat Chem Biol 2022; 18:403-411. [PMID: 35210620 DOI: 10.1038/s41589-022-00967-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022]
Abstract
Directed evolution emulates the process of natural selection to produce proteins with improved or altered functions. These approaches have proven to be very powerful but are technically challenging and particularly time and resource intensive. To bypass these limitations, we constructed a system to perform the entire process of directed evolution in silico. We employed iterative computational cycles of mutation and evaluation to predict mutations that confer high-affinity binding activities for DNA and RNA to an initial de novo designed protein with no inherent function. Beneficial mutations revealed modes of nucleic acid recognition not previously observed in natural proteins, highlighting the ability of computational directed evolution to access new molecular functions. Furthermore, the process by which new functions were obtained closely resembles natural evolution and can provide insights into the contributions of mutation rate, population size and selective pressure on functionalization of macromolecules in nature.
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Affiliation(s)
- Samuel A Raven
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,University of Western Australia Centre for Medical Research, Nedlands, Western Australia, Australia
| | - Blake Payne
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,University of Western Australia Centre for Medical Research, Nedlands, Western Australia, Australia
| | - Mitchell Bruce
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,University of Western Australia Centre for Medical Research, Nedlands, Western Australia, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia. .,Curtin Medical School, Curtin University, Bentley, Western Australia, Australia. .,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia. .,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia.
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