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Teh S, Bowland K, Halper-Stromberg E, Kotwal A, Bennett A, Skaist A, Tang J, Cai F, Macoretta A, Liang H, Kamiyama H, Wheelan S, Lin MT, Hruban R, Hung CF, Goldstein M, Scharpf R, Roberts N, Eshleman J. CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers. NAR Cancer 2024; 6:zcae028. [PMID: 38915758 PMCID: PMC11195629 DOI: 10.1093/narcan/zcae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within noncoding regions. We have adapted the CRISPR-Cas9 gene editing tool as a novel, cancer-specific killing strategy by targeting the subset of somatic mutations that create protospacer adjacent motifs (PAMs), which have evolutionally allowed bacterial cells to distinguish between self and non-self DNA for Cas9-induced double strand breaks. Whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002) showed an average of 417 somatic PAMs per tumor produced from single base substitutions. Further analyses of 591 paired T-N samples from The International Cancer Genome Consortium found medians of ∼455 somatic PAMs per tumor in pancreatic, ∼2800 in lung, and ∼3200 in esophageal cancer cohorts. Finally, we demonstrated 69-99% selective cell death of three targeted pancreatic cancer cell lines using 4-9 sgRNAs designed using the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs in either the patient's normal cells or an irrelevant cancer using WGS. This study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy, and supports the genetic targeting of adult cancers.
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Affiliation(s)
- Selina Shiqing K Teh
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kirsten Bowland
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eitan Halper-Stromberg
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhil Kotwal
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Bennett
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyza Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacqueline Tang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fidel Cai
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Antonella Macoretta
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Liang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Sarah Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Scientific Review Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Goldstein
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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2
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Puthumana J, Chandrababu A, Sarasan M, Joseph V, Singh ISB. Genetic improvement in edible fish: status, constraints, and prospects on CRISPR-based genome engineering. 3 Biotech 2024; 14:44. [PMID: 38249355 PMCID: PMC10796887 DOI: 10.1007/s13205-023-03891-7] [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: 05/13/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024] Open
Abstract
Conventional selective breeding in aquaculture has been effective in genetically enhancing economic traits like growth and disease resistance. However, its advances are restricted by heritability, the extended period required to produce a strain with desirable traits, and the necessity to target multiple characteristics simultaneously in the breeding programs. Genome editing tools like zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) are promising for faster genetic improvement in fishes. CRISPR/Cas9 technology is the least expensive, most precise, and well compatible with multiplexing of all genome editing approaches, making it a productive and highly targeted approach for developing customized fish strains with specified characteristics. As a result, the use of CRISPR/Cas9 technology in aquaculture is rapidly growing, with the main traits researched being reproduction and development, growth, pigmentation, disease resistance, trans-GFP utilization, and omega-3 metabolism. However, technological obstacles, such as off-target effects, ancestral genome duplication, and mosaicism in founder population, need to be addressed to achieve sustainable fish production. Furthermore, present regulatory and risk assessment frameworks are inadequate to address the technical hurdles of CRISPR/Cas9, even though public and regulatory approval is critical to commercializing novel technology products. In this review, we examine the potential of CRISPR/Cas9 technology for the genetic improvement of edible fish, the technical, ethical, and socio-economic challenges to using it in fish species, and its future scope for sustainable fish production.
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Affiliation(s)
- Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Aswathy Chandrababu
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - I. S. Bright Singh
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
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3
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Zappa F, Intartaglia D, Guarino AM, De Cegli R, Wilson C, Salierno FG, Polishchuk E, Sorrentino NC, Conte I, De Matteis MA. Role of trafficking protein particle complex 2 in medaka development. Traffic 2024; 25:e12924. [PMID: 37963679 DOI: 10.1111/tra.12924] [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: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023]
Abstract
The skeletal dysplasia spondyloepiphyseal dysplasia tarda (SEDT) is caused by mutations in the TRAPPC2 gene, which encodes Sedlin, a component of the trafficking protein particle (TRAPP) complex that we have shown previously to be required for the export of type II collagen (Col2) from the endoplasmic reticulum. No vertebrate model for SEDT has been generated thus far. To address this gap, we generated a Sedlin knockout animal by mutating the orthologous TRAPPC2 gene (olSedl) of Oryzias latipes (medaka) fish. OlSedl deficiency leads to embryonic defects, short size, diminished skeletal ossification and altered Col2 production and secretion, resembling human defects observed in SEDT patients. Moreover, SEDT knock-out animals display photoreceptor degeneration and gut morphogenesis defects, suggesting a key role for Sedlin in the development of these organs. Thus, by studying Sedlin function in vivo, we provide evidence for a mechanistic link between TRAPPC2-mediated membrane trafficking, Col2 export, and developmental disorders.
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Affiliation(s)
- Francesca Zappa
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Daniela Intartaglia
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Andrea M Guarino
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Rossella De Cegli
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Nicolina Cristina Sorrentino
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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4
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Zhang Z, Bao X, Lin CP. Progress and Prospects of Gene Editing in Pluripotent Stem Cells. Biomedicines 2023; 11:2168. [PMID: 37626665 PMCID: PMC10452926 DOI: 10.3390/biomedicines11082168] [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: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
Applying programmable nucleases in gene editing has greatly shaped current research in basic biology and clinical translation. Gene editing in human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), is highly relevant to clinical cell therapy and thus should be examined with particular caution. First, since all mutations in PSCs will be carried to all their progenies, off-target edits of editors will be amplified. Second, due to the hypersensitivity of PSCs to DNA damage, double-strand breaks (DSBs) made by gene editing could lead to low editing efficiency and the enrichment of cell populations with defective genomic safeguards. In this regard, DSB-independent gene editing tools, such as base editors and prime editors, are favored due to their nature to avoid these consequences. With more understanding of the microbial world, new systems, such as Cas-related nucleases, transposons, and recombinases, are also expanding the toolbox for gene editing. In this review, we discuss current applications of programmable nucleases in PSCs for gene editing, the efforts researchers have made to optimize these systems, as well as new tools that can be potentially employed for differentiation modeling and therapeutic applications.
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Affiliation(s)
| | | | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (Z.Z.); (X.B.)
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5
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Zhang J, Zhang Y, Khanal S, Cao D, Zhao J, Dang X, Nguyen LNT, Schank M, Wu XY, Jiang Y, Ning S, Wang L, El Gazzar M, Moorman JP, Guo H, Yao ZQ. Synthetic gRNA/Cas9 ribonucleoprotein targeting HBV DNA inhibits viral replication. J Med Virol 2023; 95:e28952. [PMID: 37455550 PMCID: PMC10977344 DOI: 10.1002/jmv.28952] [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: 06/07/2022] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
The presence of hepatitis B virus (HBV) covalently closed circular (ccc) DNA (cccDNA), which serves as a template for viral replication and integration of HBV DNA into the host cell genome, sustains liver pathogenesis and constitutes an intractable barrier to the eradication of chronic HBV infection. The current antiviral therapy for HBV infection, using nucleos(t)ide analogues (NAs), can suppress HBV replication but cannot eliminate integrated HBV DNA and episomal cccDNA. Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 is a powerful genetic tool that can edit integrated HBV DNA and minichromosomal cccDNA for gene therapy, but its expression and delivery require a viral vector, which poses safety concerns for therapeutic applications in humans. In the present study, we used synthetic guide RNA (gRNA)/Cas9-ribonucleoprotein (RNP) as a nonviral formulation to develop a novel CRISPR/Cas9-mediated gene therapy for eradicating HBV infection. We designed a series of gRNAs targeting multiple specific HBV genes and tested their antiviral efficacy and cytotoxicity in different HBV cellular models. Transfection of stably HBV-infected human hepatoma cell line HepG2.2.15 with HBV-specific gRNA/Cas9 RNPs resulted in a substantial reduction in HBV transcripts. Specifically, gRNA5 and/or gRNA9 RNPs significantly reduced HBV cccDNA, total HBV DNA, pregenomic RNA, and HBV antigen (HBsAg, HBeAg) levels. T7 endonuclease 1 (T7E1) cleavage assay and DNA sequencing confirmed specific HBV gene cleavage and mutations at or around the gRNA target sites. Notably, this gene-editing system did not alter cellular viability or proliferation in the treated cells. Because of their rapid DNA cleavage capability, low off-target effects, low risk of insertional mutagenesis, and readiness for use in clinical application, these results suggest that synthetic gRNA/Cas9 RNP-based gene-editing can be utilized as a promising therapeutic drug for eradicating chronic HBV infection.
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Affiliation(s)
- Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, Tennessee 37614
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, Tennessee 37614
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6
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Han Y, Yuan Z, Zhong SL, Xu H, Jiang S. Minimizing the off-target frequency of the CRISPR/Cas9 system via zwitterionic polymer conjugation and peptide fusion. Chem Sci 2023; 14:6375-6382. [PMID: 37325144 PMCID: PMC10266473 DOI: 10.1039/d2sc07067g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein 9 (Cas9) system is a powerful genome-editing tool that is widely used in many different applications. However, the high-frequency mutations induced by RNA-guided Cas9 at sites other than the intended on-target sites are a major concern that impedes therapeutic and clinical applications. A deeper analysis shows that most off-target events result from the non-specific mismatch between single guide RNA (sgRNA) and target DNA. Therefore, minimizing the non-specific RNA-DNA interaction can be an effective solution to this issue. Here we provide two novel methods at the protein and mRNA levels to minimize this mismatch issue by chemically conjugating Cas9 with zwitterionic pCB polymers or genetically fusing Cas9 with zwitterionic (EK)n peptides. The zwitterlated or EKylated CRISPR/Cas9 ribonucleoproteins (RNPs) show reduced off-target DNA editing while maintaining a similar level of on-target gene editing activity. Results show that the off-target efficiency of zwitterlated CRISPR/Cas9 is reduced on average by 70% and can be as high as 90% when compared with naive CRISPR/Cas9 editing. These approaches provide a simple and effective way to streamline the development of genome editing with the potential to accelerate a wide array of biological and therapeutic applications based on CRISPR/Cas9 technology.
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Affiliation(s)
- Yanjiao Han
- Molecular Engineering and Science Institute, University of Washington WA 98195 USA
| | - Zhefan Yuan
- Meinig School of Biomedical Engineering, Cornell University Ithaca NY 14853 USA
| | - Sijin Luo Zhong
- Meinig School of Biomedical Engineering, Cornell University Ithaca NY 14853 USA
| | - Haoxian Xu
- Department of Material Science and Engineering, University of Washington Seattle WA 98195 USA
| | - Shaoyi Jiang
- Meinig School of Biomedical Engineering, Cornell University Ithaca NY 14853 USA
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7
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Shan S, Li Q, Criswell T, Atala A, Zhang Y. Stem cell therapy combined with controlled release of growth factors for the treatment of sphincter dysfunction. Cell Biosci 2023; 13:56. [PMID: 36927578 PMCID: PMC10018873 DOI: 10.1186/s13578-023-01009-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Sphincter dysfunction often occurs at the end of tubule organs such as the urethra, anus, or gastroesophageal sphincters. It is the primary consequence of neuromuscular impairment caused by trauma, inflammation, and aging. Despite intensive efforts to recover sphincter function, pharmacological treatments have not achieved significant improvement. Cell- or growth factor-based therapy is a promising approach for neuromuscular regeneration and the recovery of sphincter function. However, a decrease in cell retention and viability, or the short half-life and rapid degradation of growth factors after implantation, remain obstacles to the translation of these therapies to the clinic. Natural biomaterials provide unique tools for controlled growth factor delivery, which leads to better outcomes for sphincter function recovery in vivo when stem cells and growth factors are co-administrated, in comparison to the delivery of single therapies. In this review, we discuss the role of stem cells combined with the controlled release of growth factors, the methods used for delivery, their potential therapeutic role in neuromuscular repair, and the outcomes of preclinical studies using combination therapy, with the hope of providing new therapeutic strategies to treat incontinence or sphincter dysfunction of the urethra, anus, or gastroesophageal tissues, respectively.
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Affiliation(s)
- Shengzhou Shan
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Qingfeng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
| | - Tracy Criswell
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
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8
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Xu CL, Ruan MZ, Ragi SD, Tsang SH. CRISPR Off-Target Analysis Platforms. Methods Mol Biol 2022; 2560:279-285. [PMID: 36481904 DOI: 10.1007/978-1-0716-2651-1_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Caspase9 (Cas9) system provides a programmable technology that may be used to edit the eukaryotic genome and epigenome. CRISPR/Cas9 includes a guide RNA targeted to a gene of interest which hybridizes to a nucleotide sequence next to a protospacer-adjacent motif (PAM) which guides the Cas9 endonucleases to the target site for cleavage via double-strand breaks. A caveat of the CRISPR/Cas9 system is the creation of off-target double-strand breaks (DSBs) which may result in anomalous insertions, deletions, and translocations. Thus, assays for the sensitive detection and analysis of off-target editing are critical. Here, we describe currently available CRISPR technologies, CRISPR applications, and current analysis platforms to detect off-target effects including genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-Seq), high-throughput genomic translocation sequencing (HTGTS), breaks labeling, enrichments on streptavidin and next-generation sequencing (BLESS), and in vitro nuclease-digested genome sequencing (Digenome-seq).
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Affiliation(s)
- Christine L Xu
- Stanford University School of Medicine, Stanford, CA, USA
| | - Merry Zhechao Ruan
- Department of Ophthalmology, New York-Presbyterian Hospital, New York, NY, USA
| | - Sara D Ragi
- Warren Alpert Medical School at Brown University, Providence, RI, USA
| | - Stephen H Tsang
- Departments of Ophthalmology, Pathology & Cell Biology, Graduate Programs in Nutritional & Metabolic Biology and Neurobiology & Behavior, Columbia Stem Cell Initiative, New York, NY, USA.
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9
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Harmatz P, Prada CE, Burton BK, Lau H, Kessler CM, Cao L, Falaleeva M, Villegas AG, Zeitler J, Meyer K, Miller W, Wong Po Foo C, Vaidya S, Swenson W, Shiue LH, Rouy D, Muenzer J. First-in-human in vivo genome editing via AAV-zinc-finger nucleases for mucopolysaccharidosis I/II and hemophilia B. Mol Ther 2022; 30:3587-3600. [PMID: 36299240 PMCID: PMC9734078 DOI: 10.1016/j.ymthe.2022.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/26/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022] Open
Abstract
Zinc-finger nuclease (ZFN)-based in vivo genome editing is a novel treatment that can potentially provide lifelong protein replacement with single intravenous administration. Three first-in-human open-label ascending single-dose phase 1/2 studies were performed in parallel (starting November 2017) primarily to assess safety and tolerability of ZFN in vivo editing therapy in mucopolysaccharidosis I (MPS I) (n = 3), MPS II (n = 9), and hemophilia B (n = 1). Treatment was well tolerated with no serious treatment-related adverse events. At the 1e13 vg/kg dose, evidence of genome editing was detected through albumin-transgene fusion transcripts in liver for MPS II (n = 2) and MPS I (n = 1) subjects. The MPS I subject also had a transient increase in leukocyte iduronidase activity to the lower normal range. At the 5e13 vg/kg dose, one MPS II subject had a transient increase in plasma iduronate-2-sulfatase approaching normal levels and one MPS I subject approached mid-normal levels of leukocyte iduronidase activity with no evidence of genome editing. The hemophilia B subject was not able to decrease use of factor IX concentrate; genome editing could not be assessed. Overall, ZFN in vivo editing therapy had a favorable safety profile with evidence of targeted genome editing in liver, but no long-term enzyme expression in blood.
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Affiliation(s)
- Paul Harmatz
- UCSF Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA,Corresponding author
| | - Carlos E. Prada
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA,Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, IL, USA,Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Barbara K. Burton
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA,Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, IL, USA
| | - Heather Lau
- Department of Neurology, NYU School of Medicine, New York, NY, USA
| | | | - Liching Cao
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | | | | | | | | | | | | | | | | | - Didier Rouy
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | - Joseph Muenzer
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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10
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Wang Y, Zafar N, Ali Q, Manghwar H, Wang G, Yu L, Ding X, Ding F, Hong N, Wang G, Jin S. CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:3928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
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Affiliation(s)
- Yaxin Wang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Naeem Zafar
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qurban Ali
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hakim Manghwar
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao Ding
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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11
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In Vivo Hematopoietic Stem Cell Genome Editing: Perspectives and Limitations. Genes (Basel) 2022; 13:genes13122222. [PMID: 36553489 PMCID: PMC9778055 DOI: 10.3390/genes13122222] [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: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The tremendous evolution of genome-editing tools in the last two decades has provided innovative and effective approaches for gene therapy of congenital and acquired diseases. Zinc-finger nucleases (ZFNs), transcription activator- like effector nucleases (TALENs) and CRISPR-Cas9 have been already applied by ex vivo hematopoietic stem cell (HSC) gene therapy in genetic diseases (i.e., Hemoglobinopathies, Fanconi anemia and hereditary Immunodeficiencies) as well as infectious diseases (i.e., HIV), and the recent development of CRISPR-Cas9-based systems using base and prime editors as well as epigenome editors has provided safer tools for gene therapy. The ex vivo approach for gene addition or editing of HSCs, however, is complex, invasive, technically challenging, costly and not free of toxicity. In vivo gene addition or editing promise to transform gene therapy from a highly sophisticated strategy to a "user-friendly' approach to eventually become a broadly available, highly accessible and potentially affordable treatment modality. In the present review article, based on the lessons gained by more than 3 decades of ex vivo HSC gene therapy, we discuss the concept, the tools, the progress made and the challenges to clinical translation of in vivo HSC gene editing.
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12
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Madhi ZS, Shallan MA, Almaamuri AM, Alhussainy AA, AL- Salih SSS, Raheem AK, Alwan HJ, Jalil AT. Lipids and lipid derivatives for delivery of the CRISPR/Cas9 system. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Kumari D, Prasad BD, Dwivedi P, Hidangmayum A, Sahni S. CRISPR/Cas9 mediated genome editing tools and their possible role in disease resistance mechanism. Mol Biol Rep 2022; 49:11587-11600. [DOI: 10.1007/s11033-022-07851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/14/2022] [Accepted: 08/08/2022] [Indexed: 10/14/2022]
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14
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Liang W, He J, Mao C, Yu C, Meng Q, Xue J, Wu X, Li S, Wang Y, Yi H. Gene editing monkeys: Retrospect and outlook. Front Cell Dev Biol 2022; 10:913996. [PMID: 36158194 PMCID: PMC9493099 DOI: 10.3389/fcell.2022.913996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Animal models play a key role in life science research, especially in the study of human disease pathogenesis and drug screening. Because of the closer proximity to humans in terms of genetic evolution, physiology, immunology, biochemistry, and pathology, nonhuman primates (NHPs) have outstanding advantages in model construction for disease mechanism study and drug development. In terms of animal model construction, gene editing technology has been widely applied to this area in recent years. This review summarizes the current progress in the establishment of NHPs using gene editing technology, which mainly focuses on rhesus and cynomolgus monkeys. In addition, we discuss the limiting factors in the applications of genetically modified NHP models as well as the possible solutions and improvements. Furthermore, we highlight the prospects and challenges of the gene-edited NHP models.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
| | - Junli He
- Department of Pediatrics, Shenzhen University General Hospital, Shenzhen, China
| | - Chenyu Mao
- University of Pennsylvania, Philadelphia, PA, United States
| | - Chengwei Yu
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Qingxue Meng
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Xueliang Wu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Shanliang Li
- Department of Pharmacology, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
| | - Yukai Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- National Stem Cell Resource Center, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
| | - Hongyang Yi
- National Clinical Research Centre for Infectious Diseases, The Third People’s Hospital of Shenzhen and The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
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15
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Khanal S, Cao D, Zhang J, Zhang Y, Schank M, Dang X, Nguyen LNT, Wu XY, Jiang Y, Ning S, Zhao J, Wang L, Gazzar ME, Moorman JP, Yao ZQ. Synthetic gRNA/Cas9 Ribonucleoprotein Inhibits HIV Reactivation and Replication. Viruses 2022; 14:1902. [PMID: 36146709 PMCID: PMC9500661 DOI: 10.3390/v14091902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
The current antiretroviral therapy (ART) for human immunodeficiency virus (HIV) can halt viral replication but cannot eradicate HIV infection because proviral DNA integrated into the host genome remains genetically silent in reservoir cells and is replication-competent upon interruption or cessation of ART. CRISPR/Cas9-based technology is widely used to edit target genes via mutagenesis (i.e., nucleotide insertion/deletion and/or substitution) and thus can inactivate integrated proviral DNA. However, CRISPR/Cas9 delivery systems often require viral vectors, which pose safety concerns for therapeutic applications in humans. In this study, we used synthetic guide RNA (gRNA)/Cas9-ribonucleoprotein (RNP) as a non-viral formulation to develop a novel HIV gene therapy. We designed a series of gRNAs targeting different HIV genes crucial for HIV replication and tested their antiviral efficacy and cellular cytotoxicity in lymphoid and monocytic latent HIV cell lines. Compared with the scramble gRNA control, HIV-gRNA/Cas9 RNP-treated cells exhibited efficient viral suppression with no apparent cytotoxicity, as evidenced by the significant inhibition of latent HIV DNA reactivation and RNA replication. Moreover, HIV-gRNA/Cas9 RNP inhibited p24 antigen expression, suppressed infectious viral particle production, and generated specific DNA cleavages in the targeted HIV genes that are confirmed by DNA sequencing. Because of its rapid DNA cleavage, low off-target effects, low risk of insertional mutagenesis, easy production, and readiness for use in clinical application, this study provides a proof-of-concept that synthetic gRNA/Cas9 RNP drugs can be utilized as a novel therapeutic approach for HIV eradication.
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Affiliation(s)
- Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
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16
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Pant S, Ritika, Nag P, Ghati A, Chakraborty D, Maximiano MR, Franco OL, Mandal AK, Kuila A. Employment of the CRISPR/Cas9 system to improve cellulase production in Trichoderma reesei. Biotechnol Adv 2022; 60:108022. [PMID: 35870723 DOI: 10.1016/j.biotechadv.2022.108022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 12/27/2022]
Abstract
Trichoderma reesei has been explored intensively in the laboratory and on an industrial scale for its highly potent cellulase secretion machinery since its characterization over 70 years ago. Emergence of new genetic tools over the past decade has strengthened the understanding of mechanism involved in transcription of cellulase genes in fungi and provided a boost to edit them at molecular level. Since several transcriptional factors work synergistically for cellulase expression in fungi; engineering of cellulase secretome for enhanced cellulase titer require combined manipulation of these factors. In the same context, CRISPR/Cas9 has emerged as a powerful, versatile genetic engineering tool for multiplex gene editing in fungi. It is true that considerable efforts with CRISPR technologies have largely developed fungal genetic engineering, but its application in fungi is still challenging and limited. The present review illustrates the precision, strengths and challenges of using CRISPR/Cas9 technology for cellulase engineering in T. reesei, highlighting key strategies that could be employed for strain improvement.
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Affiliation(s)
- Shailja Pant
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan 304022, India
| | - Ritika
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan 304022, India
| | - Piyali Nag
- Department of Microbiology, Barrackpore Rastraguru Surendranath College, Barrackpore, Kolkata 700120, India
| | - Amit Ghati
- Department of Microbiology, Barrackpore Rastraguru Surendranath College, Barrackpore, Kolkata 700120, India.
| | - Dipjyoti Chakraborty
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan 304022, India
| | - Mariana Rocha Maximiano
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Amit Kumar Mandal
- Centre for Nanotechnology Sciences & Chemical Biology Laboratory, Department of Sericulture, Raiganj University, Raiganj, 733134, India
| | - Arindam Kuila
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan 304022, India.
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17
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Huang X, Yang D, Zhang J, Xu J, Chen YE. Recent Advances in Improving Gene-Editing Specificity through CRISPR-Cas9 Nuclease Engineering. Cells 2022; 11:2186. [PMID: 35883629 PMCID: PMC9319960 DOI: 10.3390/cells11142186] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
CRISPR-Cas9 is the state-of-the-art programmable genome-editing tool widely used in many areas. For safe therapeutic applications in clinical medicine, its off-target effect must be dramatically minimized. In recent years, extensive studies have been conducted to improve the gene-editing specificity of the most popular CRISPR-Cas9 nucleases using different strategies. In this review, we summarize and discuss these strategies and achievements, with a major focus on improving the gene-editing specificity through Cas9 protein engineering.
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Affiliation(s)
- Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA; (D.Y.); (J.Z.); (J.X.)
| | | | | | | | - Y. Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA; (D.Y.); (J.Z.); (J.X.)
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18
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Awan MJA, Pervaiz K, Rasheed A, Amin I, Saeed NA, Dhugga KS, Mansoor S. Genome edited wheat- current advances for the second green revolution. Biotechnol Adv 2022; 60:108006. [PMID: 35732256 DOI: 10.1016/j.biotechadv.2022.108006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/21/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022]
Abstract
Common wheat is a major source of nutrition around the globe, but unlike maize and rice hybrids, no breakthrough has been made to enhance wheat yield since Green Revolution. With the availability of reference genome sequence of wheat and advancement of allied genomics technologies, understanding of genes involved in grain yield components and disease resistance/susceptibility has opened new avenues for crop improvement. Wheat has a huge hexaploidy genome of approximately 17 GB with 85% repetition, and it is a daunting task to induce any mutation across three homeologues that can be helpful for the enhancement of agronomic traits. The CRISPR-Cas9 system provides a promising platform for genome editing in a site-specific manner. In wheat, CRISPR-Cas9 is being used in the improvement of yield, grain quality, biofortification, resistance against diseases, and tolerance against abiotic factors. The promising outcomes of the CRISPR-based multiplexing approach circumvent the constraint of targeting merely one gene at a time. Deployment of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) 9 endonuclease (CRISPR-Cas9) and Cas9 variant systems such as cytidine base editing, adenosine base editing, and prime editing in wheat has been used to induce point mutations more precisely. Scientists have acquired major events such as induction of male sterility, fertility restoration, and alteration of seed dormancy through Cas9 in wheat that can facilitate breeding programs for elite variety development. Furthermore, a recent discovery in tissue culturing enables scientists to significantly enhance regeneration efficiency in wheat by transforming the GRF4-GIF1 cassette. Rapid generation advancement by speed breeding technology provides the opportunity for the generation advancement of the desired plants to segregate out unwanted transgenes and allows rapid integration of gene-edited wheat into the breeding pipeline. The combination of these novel technologies addresses some of the most important limiting factors for sustainable and climate-smart wheat that should lead to the second "Green Revolution" for global food security.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Komal Pervaiz
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguanccun South Street, Beijing 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Kanwarpal S Dhugga
- Corteva Agriscience, Johnston, IA, USA; International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
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19
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Rahman MU, Bilal M, Shah JA, Kaushik A, Teissedre PL, Kujawska M. CRISPR-Cas9-Based Technology and Its Relevance to Gene Editing in Parkinson's Disease. Pharmaceutics 2022; 14:1252. [PMID: 35745824 PMCID: PMC9229276 DOI: 10.3390/pharmaceutics14061252] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) and other chronic and debilitating neurodegenerative diseases (NDs) impose a substantial medical, emotional, and financial burden on individuals and society. The origin of PD is unknown due to a complex combination of hereditary and environmental risk factors. However, over the last several decades, a significant amount of available data from clinical and experimental studies has implicated neuroinflammation, oxidative stress, dysregulated protein degradation, and mitochondrial dysfunction as the primary causes of PD neurodegeneration. The new gene-editing techniques hold great promise for research and therapy of NDs, such as PD, for which there are currently no effective disease-modifying treatments. As a result, gene therapy may offer new treatment options, transforming our ability to treat this disease. We present a detailed overview of novel gene-editing delivery vehicles, which is essential for their successful implementation in both cutting-edge research and prospective therapeutics. Moreover, we review the most recent advancements in CRISPR-based applications and gene therapies for a better understanding of treating PD. We explore the benefits and drawbacks of using them for a range of gene-editing applications in the brain, emphasizing some fascinating possibilities.
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Affiliation(s)
- Mujeeb ur Rahman
- Department of Toxicology, Faculty of Pharmacy, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznan, Poland;
| | - Muhammad Bilal
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China;
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
- Fergana Medical Institute of Public Health Uzbekistan, Fergana 150110, Uzbekistan
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Health System Engineering, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, FL 33805, USA;
- School of Engineering, University of Petroleum and Energy Studies (UPES), Dehradun 248007, Uttarakhand, India
| | - Pierre-Louis Teissedre
- Institut des Sciences de la Vigne et du Vin, Université de Bordeaux, EA 4577, Œnologie, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France;
- Institut des Sciences de la Vigne et du Vin, INRA, USC 1366 INRA, IPB, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France
| | - Małgorzata Kujawska
- Department of Toxicology, Faculty of Pharmacy, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznan, Poland;
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20
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Ni D, Lin J, Zhang N, Li S, Xue Y, Wang Z, Liu Q, Liu K, Zhang H, Zhao Y, Chen C, Liu Y. Combinational application of metal-organic frameworks-based nanozyme and nucleic acid delivery in cancer therapy. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1773. [PMID: 35014211 DOI: 10.1002/wnan.1773] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
The rapid development of nanotechnology has generated numerous ideas for cancer treatment, and a wide variety of relevant nanoparticle platforms have been reported. Metal-organic frameworks (MOFs) have been widely investigated as an anti-cancer drug delivery vehicle owing to their unique porous hybrid structure, biocompatibility, structural tunability, and multi-functionality. MOF materials with catalytic activity, known as nanozymes, have applications in photodynamic and chemodynamic therapy. Nucleic acids have also attracted increasing research attention owing to their programmability, ease of synthesis, and versatility. A variety of functional DNAs and RNAs have been applied both therapeutically (gene-targeting drugs for cancer treatment) and nontherapeutically (used as modified materials to enhance the therapeutic effects of other nanomedicines). The combined use of MOFs and functional nucleic acids have been extensively investigated and has been associated with excellent tumor-suppressor activity in various treatment methods. In this review, we summarize the progress in the research and development of tumor therapy based on MOFs and nucleic acid delivery over recent years, focusing on the combinational use of different delivery and design strategies for MOF/therapeutic nucleic acid platforms. We further summarize the strategies for combining MOFs (universal carrier, functional carrier) and nucleic acids (therapeutic nucleic acids, nontherapeutic nucleic acids) and discuss the corresponding therapeutic effects in cancer treatment. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Dongqi Ni
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinhui Lin
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Nuozi Zhang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Shilin Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueguang Xue
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziyao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qianglin Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Hongjie Zhang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- GBA National Institute for Nanotechnology Innovation, Guangdong, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- GBA National Institute for Nanotechnology Innovation, Guangdong, China
| | - Ying Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- GBA National Institute for Nanotechnology Innovation, Guangdong, China
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21
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Phage peptides mediate precision base editing with focused targeting window. Nat Commun 2022; 13:1662. [PMID: 35351888 PMCID: PMC8964698 DOI: 10.1038/s41467-022-29365-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/11/2022] [Indexed: 11/22/2022] Open
Abstract
Base editors (BEs) are genome engineering tools that can generate nucleotide substitutions without introducing double-stranded breaks (DSBs). A variety of strategies have been developed to improve the targeting scope and window of BEs. In a previous study, we found that a bacteriophage-derived peptide, referred to as G8PPD, could improve the specificity of Cas9 nuclease. Herein, we investigate the applicability of G8PPD as molecular modulators of BEs. We show that G8PPD can improve cytidine base editor (CBEs) and adenine base editor (ABE) to more focused targeting windows. Notably, in a cell-based disease model, G8PPD increases the percentage of perfectly edited gene alleles by BEs from less than 4% to more than 38% of the whole population. In addition, G8PPD can improve the targeting scope of BE in mouse embryos. In summary, our study presents the peptidyl modulators that can improve BEs for precision base editing. Base editors are genome engineering tools that can generate nucleotide substitutions without introducing double-stranded breaks. Here the authors show that a phage-derived peptidyl CRISPR inhibitor can be employed to modulate the activity and targeting scope of CRISPR base editor for precision base editing applications.
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22
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Seah I, Goh D, Chan HW, Su X. Developing Non-Human Primate Models of Inherited Retinal Diseases. Genes (Basel) 2022; 13:344. [PMID: 35205388 PMCID: PMC8872446 DOI: 10.3390/genes13020344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/31/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a genetically and clinically heterogenous group of diseases that can eventually lead to blindness. Advances in sequencing technologies have resulted in better molecular characterization and genotype-phenotype correlation of IRDs. This has fueled research into therapeutic development over the recent years. Animal models are required for pre-clinical efficacy assessment. Non-human primates (NHP) are ideal due to the anatomical and genetic similarities shared with humans. However, developing NHP disease to recapitulate the disease phenotype for specific IRDs may be challenging from both technical and cost perspectives. This review discusses the currently available NHP IRD models and the methods used for development, with a particular focus on gene-editing technologies.
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Affiliation(s)
- Ivan Seah
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 7, Singapore 119 228, Singapore; (I.S.); (H.W.C.)
| | - Debbie Goh
- Department of Ophthalmology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block Level 7, Singapore 119 228, Singapore;
| | - Hwei Wuen Chan
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 7, Singapore 119 228, Singapore; (I.S.); (H.W.C.)
- Department of Ophthalmology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block Level 7, Singapore 119 228, Singapore;
| | - Xinyi Su
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 7, Singapore 119 228, Singapore; (I.S.); (H.W.C.)
- Department of Ophthalmology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block Level 7, Singapore 119 228, Singapore;
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138 673, Singapore
- Singapore Eye Research Institute (SERI), The Academia, 20 College Road, Level 6 Discovery Tower, Singapore 169 856, Singapore
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Atkins A, Chung CH, Allen AG, Dampier W, Gurrola TE, Sariyer IK, Nonnemacher MR, Wigdahl B. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy. Front Genome Ed 2021; 3:673022. [PMID: 34713260 PMCID: PMC8525399 DOI: 10.3389/fgeed.2021.673022] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022] Open
Abstract
As genome-editing nucleases move toward broader clinical applications, the need to define the limits of their specificity and efficiency increases. A variety of approaches for nuclease cleavage detection have been developed, allowing a full-genome survey of the targeting landscape and the detection of a variety of repair outcomes for nuclease-induced double-strand breaks. Each approach has advantages and disadvantages relating to the means of target-site capture, target enrichment mechanism, cellular environment, false discovery, and validation of bona fide off-target cleavage sites in cells. This review examines the strengths, limitations, and origins of the different classes of off-target cleavage detection systems including anchored primer enrichment (GUIDE-seq), in situ detection (BLISS), in vitro selection libraries (CIRCLE-seq), chromatin immunoprecipitation (ChIP) (DISCOVER-Seq), translocation sequencing (LAM PCR HTGTS), and in vitro genomic DNA digestion (Digenome-seq and SITE-Seq). Emphasis is placed on the specific modifications that give rise to the enhanced performance of contemporary techniques over their predecessors and the comparative performance of techniques for different applications. The clinical relevance of these techniques is discussed in the context of assessing the safety of novel CRISPR/Cas9 HIV-1 curative strategies. With the recent success of HIV-1 and SIV-1 viral suppression in humanized mice and non-human primates, respectively, using CRISPR/Cas9, rigorous exploration of potential off-target effects is of critical importance. Such analyses would benefit from the application of the techniques discussed in this review.
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Affiliation(s)
- Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States,*Correspondence: Brian Wigdahl
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24
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Gugustea R, Jia Z. Genetic manipulations of AMPA glutamate receptors in hippocampal synaptic plasticity. Neuropharmacology 2021; 194:108630. [PMID: 34089730 DOI: 10.1016/j.neuropharm.2021.108630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/06/2021] [Accepted: 05/18/2021] [Indexed: 01/17/2023]
Abstract
Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are the principal mediators of fast excitatory synaptic transmission and they are required for various forms of synaptic plasticity, including long-term potentiation (LTP) and depression (LTD), which are key mechanisms of learning and memory. AMPARs are tetrameric complexes assembled from four subunits (GluA1-4), however, the lack of subunit-specific pharmacological tools has made the assessment of individual subunits difficult. The application of genetic techniques, particularly gene targeting, allows for precise manipulation and dissection of each subunit in the regulation of neuronal function and behaviour. In this review, we summarize studies using various mouse models with genetically altered AMPARs and focus on their roles in basal synaptic transmission, LTP, and LTD at the hippocampal CA1 synapse. These studies provide strong evidence that there are multiple forms of LTP and LTD at this synapse which can be induced by various induction protocols, and they are differentially regulated by different AMPAR subunits and domains. We conclude that it is necessary to delineate the mechanism of each of these forms of plasticity and their contribution to memory and brain disorders.
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Affiliation(s)
- Radu Gugustea
- The Hospital for Sick Children, Neurosciences and Mental Health Program, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada; Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zhengping Jia
- The Hospital for Sick Children, Neurosciences and Mental Health Program, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada; Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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25
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Barazesh M, Mohammadi S, Bahrami Y, Mokarram P, Morowvat MH, Saidijam M, Karimipoor M, Kavousipour S, Vosoughi AR, Khanaki K. CRISPR/Cas9 Technology as a Modern Genetic Manipulation Tool for Recapitulating of Neurodegenerative Disorders in Large Animal Models. Curr Gene Ther 2021; 21:130-148. [PMID: 33319680 DOI: 10.2174/1566523220666201214115024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/12/2020] [Accepted: 11/23/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neurodegenerative diseases are often the consequence of alterations in structures and functions of the Central Nervous System (CNS) in patients. Despite obtaining massive genomic information concerning the molecular basis of these diseases and since the neurological disorders are multifactorial, causal connections between pathological pathways at the molecular level and CNS disorders development have remained obscure and need to be elucidated to a great extent. OBJECTIVE Animal models serve as accessible and valuable tools for understanding and discovering the roles of causative factors in the development of neurodegenerative disorders and finding appropriate treatments. Contrary to rodents and other small animals, large animals, especially non-human primates (NHPs), are remarkably similar to humans; hence, they establish suitable models for recapitulating the main human's neuropathological manifestations that may not be seen in rodent models. In addition, they serve as useful models to discover effective therapeutic targets for neurodegenerative disorders due to their similarity to humans in terms of physiology, evolutionary distance, anatomy, and behavior. METHODS In this review, we recommend different strategies based on the CRISPR-Cas9 system for generating animal models of human neurodegenerative disorders and explaining in vivo CRISPR-Cas9 delivery procedures that are applied to disease models for therapeutic purposes. RESULTS With the emergence of CRISPR/Cas9 as a modern specific gene-editing technology in the field of genetic engineering, genetic modification procedures such as gene knock-in and knock-out have become increasingly easier compared to traditional gene targeting techniques. Unlike the old techniques, this versatile technology can efficiently generate transgenic large animal models without the need to complicate lab instruments. Hence, these animals can accurately replicate the signs of neurodegenerative disorders. CONCLUSION Preclinical applications of CRISPR/Cas9 gene-editing technology supply a unique opportunity to establish animal models of neurodegenerative disorders with high accuracy and facilitate perspectives for breakthroughs in the research on the nervous system disease therapy and drug discovery. Furthermore, the useful outcomes of CRISPR applications in various clinical phases are hopeful for their translation to the clinic in a short time.
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Affiliation(s)
- Mahdi Barazesh
- School of Paramedical, Gerash University of Medical Sciences, Gerash, Iran
| | - Shiva Mohammadi
- Department of Medical Biotechnology, School of Medicine, Lorestan University of Medical Sciences, Khoram Abad, Iran
| | - Yadollah Bahrami
- Molecular Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pooneh Mokarram
- Autophagy Research center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Massoud Saidijam
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amir Reza Vosoughi
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Korosh Khanaki
- Medical Biotechnology Research Center, Paramedicine Faculty, Guilan University of Medical Sciences, Rasht, Iran
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26
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CRISPR-Cas systems for genome editing of mammalian cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:15-30. [PMID: 34127192 DOI: 10.1016/bs.pmbts.2021.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the past decade, ZFNs and TALENs have been used for targeted genome engineering and have gained scientific attention. It has demonstrated huge potential for gene knockout, knock-in, and indels in desired locations of genomes to understand molecular mechanism of diseases and also discover therapy. However, both the genome engineering techniques are still suffering from design, screening and validation in cell and higher organisms. CRISPR-Cas9 is a rapid, simple, specific, and versatile technology and it has been applied in many organisms including mammalian cells. CRISPR-Cas9 has been used for animal models to modify animal cells for understanding human disease for novel drug discovery and therapy. Additionally, base editing has also been discussed herewith for conversion of C/G-to-T/A or A/T-to-G/C without DNA cleavage or donor DNA templates for correcting mutations or altering gene functions. In this chapter, we highlight CRISPR-Cas9 and base editing for desired genome editing in mammalian cells for a better understanding of molecular mechanisms, and biotechnological and therapeutic applications.
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27
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Kim D, Kang BC, Kim JS. Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq. Nat Protoc 2021; 16:1170-1192. [PMID: 33462439 DOI: 10.1038/s41596-020-00453-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/22/2020] [Indexed: 01/29/2023]
Abstract
Digested genome sequencing (Digenome-seq) is a highly sensitive, easy-to-carry-out, cell-free method for experimentally identifying genome-wide off-target sites of programmable nucleases and deaminases (also known as base editors). Genomic DNA is digested in vitro using clustered regularly interspaced short palindromic repeats ribonucleoproteins (RNPs; plus DNA-modifying enzymes to cleave both strands of DNA at sites containing deaminated base products, in the case of base editors) and subjected to whole-genome sequencing (WGS) with a typical sequencing depth of 30×. A web-based program is available to map in vitro cleavage sites corresponding to on- and off-target sites. Chromatin DNA, in parallel with histone-free genomic DNA, can also be used to account for the effects of chromatin structure on off-target nuclease activity. Digenome-seq is more sensitive and comprehensive than cell-based methods for identifying off-target sites. Unlike other cell-free methods, Digenome-seq does not involve enrichment of DNA ends through PCR amplification. The entire process other than WGS, which takes ~1-2 weeks, including purification and preparation of RNPs, digestion of genomic DNA and bioinformatic analysis after WGS, takes about several weeks.
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Affiliation(s)
- Daesik Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Beum-Chang Kang
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
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28
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Klaver-Flores S, Zittersteijn HA, Canté-Barrett K, Lankester A, Hoeben RC, Gonçalves MAFV, Pike-Overzet K, Staal FJT. Genomic Engineering in Human Hematopoietic Stem Cells: Hype or Hope? Front Genome Ed 2021; 2:615619. [PMID: 34713237 PMCID: PMC8525357 DOI: 10.3389/fgeed.2020.615619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Many gene editing techniques are developed and tested, yet, most of these are optimized for transformed cell lines, which differ from their primary cell counterparts in terms of transfectability, cell death propensity, differentiation capability, and chromatin accessibility to gene editing tools. Researchers are working to overcome the challenges associated with gene editing of primary cells, namely, at the level of improving the gene editing tool components, e.g., the use of modified single guide RNAs, more efficient delivery of Cas9 and RNA in the ribonucleoprotein of these cells. Despite these efforts, the low efficiency of proper gene editing in true primary cells is an obstacle that needs to be overcome in order to generate sufficiently high numbers of corrected cells for therapeutic use. In addition, many of the therapeutic candidate genes for gene editing are expressed in more mature blood cell lineages but not in the hematopoietic stem cells (HSCs), where they are tightly packed in heterochromatin, making them less accessible to gene editing enzymes. Bringing HSCs in proliferation is sometimes seen as a solution to overcome lack of chromatin access, but the induction of proliferation in HSCs often is associated with loss of stemness. The documented occurrences of off-target effects and, importantly, on-target side effects also raise important safety issues. In conclusion, many obstacles still remain to be overcome before gene editing in HSCs for gene correction purposes can be applied clinically. In this review, in a perspective way, we will discuss the challenges of researching and developing a novel genetic engineering therapy for monogenic blood and immune system disorders.
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Affiliation(s)
| | - Hidde A. Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan Lankester
- Department of Pediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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29
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Abstract
CRISPR-associated nuclease (Cas) has been widely applied to modify the genomes of various cell types. As RNA-guided endonucleases, Cas enzymes can target different genomic sequences simply by changing the guide sequence of the CRISPR RNA (crRNA) or single guide RNA (sgRNA). Recent studies have demonstrated that DNA-RNA chimeric crRNA or sgRNA can efficiently guide the Cas9 protein for genome editing with reduced off-target effects. This chapter aims to describe a procedure for using chimeric RNA to modify the genomes of mammalian cells.
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Affiliation(s)
- Shuhan Lu
- Department of Pathology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ying Zhang
- Medical Research Institute, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Hao Yin
- Department of Pathology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
- Department of Urology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
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30
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Blattner G, Cavazza A, Thrasher AJ, Turchiano G. Gene Editing and Genotoxicity: Targeting the Off-Targets. Front Genome Ed 2020; 2:613252. [PMID: 34713236 PMCID: PMC8525370 DOI: 10.3389/fgeed.2020.613252] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/20/2020] [Indexed: 12/26/2022] Open
Abstract
Gene editing technologies show great promise for application to human disease as a result of rapid developments in targeting tools notably based on ZFN, TALEN, and CRISPR-Cas systems. Precise modification of a DNA sequence is now possible in mature human somatic cells including stem and progenitor cells with increasing degrees of efficiency. At the same time new technologies are required to evaluate their safety and genotoxicity before widespread clinical application can be confidently implemented. A number of methodologies have now been developed in an attempt to predict expected and unexpected modifications occurring during gene editing. This review surveys the techniques currently available as state of the art, highlighting benefits and limitations, and discusses approaches that may achieve sufficient accuracy and predictability for application in clinical settings.
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Affiliation(s)
| | | | | | - Giandomenico Turchiano
- Infection, Immunity and Inflammation Research and Teaching Department, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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31
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Kumar P, Malik YS, Ganesh B, Rahangdale S, Saurabh S, Natesan S, Srivastava A, Sharun K, Yatoo MI, Tiwari R, Singh RK, Dhama K. CRISPR-Cas System: An Approach With Potentials for COVID-19 Diagnosis and Therapeutics. Front Cell Infect Microbiol 2020; 10:576875. [PMID: 33251158 PMCID: PMC7673385 DOI: 10.3389/fcimb.2020.576875] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
COVID-19, the human coronavirus disease caused by SARS-CoV-2, was reported for the first time in Wuhan, China in late 2019. COVID-19 has no preventive vaccine or proven standard pharmacological treatment, and consequently, the outbreak swiftly became a pandemic affecting more than 215 countries around the world. For the diagnosis of COVID-19, the only reliable diagnostics is a qPCR assay. Among other diagnostic tools, the CRISPR-Cas system is being investigated for rapid and specific diagnosis of COVID-19. The CRISPR-Cas-based methods diagnose the SARS-CoV-2 infections within an hour. Apart from its diagnostic ability, CRISPR-Cas system is also being assessed for antiviral therapy development; however, till date, no CRISPR-based therapy has been approved for human use. The Prophylactic Antiviral CRISPR in huMAN cells (PAC-MAN), which is Cas 13 based strategy, has been developed against coronavirus. Although this strategy has the potential to be developed as a therapeutic modality, it may face significant challenges for approval in human clinical trials. This review is focused on describing potential use and challenges of CRISPR-Cas based approaches for the development of rapid and accurate diagnostic technique and/or a possible therapeutic alternative for combating COVID-19. The assessment of potential risks associated with use of CRISPR will be important for future clinical advancements.
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Affiliation(s)
- Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, India
| | - Balasubramanian Ganesh
- Laboratory Division, Indian Council of Medical Research—National Institute of Epidemiology, Ministry of Health & Family Welfare, Chennai, India
| | - Somnath Rahangdale
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, India
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Sharad Saurabh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Mohd. Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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Watanabe K, Nakamura T, Onodera S, Saito A, Shibahara T, Azuma T. A novel GNAS-mutated human induced pluripotent stem cell model for understanding GNAS-mutated tumors. Tumour Biol 2020; 42:1010428320962588. [PMID: 32996421 DOI: 10.1177/1010428320962588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A missense mutation of the guanine nucleotide binding protein alpha stimulating activity polypeptide 1 (GNAS) gene, typically Arg201Cys or Arg201His (R201H/R201C), leads to constitutive activation of the Gsα-cyclic AMP (cAMP) signaling pathway that causes several diseases. However, no germline mutations of GNAS have been identified to date, likely due to their lethality, and no robust human cell models have been generated. Therefore, the aim of this study was to generate GNAS-mutated disease-specific induced pluripotent stem cells as a model for these diseases. We then analyzed the functionality of this induced pluripotent stem cell model and differentiated epithelial cells. We generated disease-specific induced pluripotent stem cells by introducing a mutation in GNAS with the clustered regularly interspaced short palindromic repeats (CRISPR) nickase method, which has lower off-target effects than the conventional CRISPR/Cas9 method. We designed the target vector to contain the R201H mutation in GNAS, which was transfected into human control induced pluripotent stem cells (Nips-B2) by electroporation. We confirmed the establishment of GNASR201H-mutated (GNASR201H/+) induced pluripotent stem cells that exhibited a pluripotent stem cell phenotype. We analyzed the effect of the mutation on cAMP production, and further generated teratomas for immunohistochemical analysis of the luminal epithelial structure. GNAS-mutated induced pluripotent stem cells showed significantly higher levels of intracellular cAMP, which remained elevated state for a long time upon hormonal stimulation with parathyroid hormone or adrenocorticotropic hormone. Immunohistochemical analysis revealed that several mucins, including MUC1, 2, and MUC5AC, are expressed in cytokeratin 18 (CK18)-positive epithelial cells. However, we found few CK18-positive cells in mutated induced pluripotent stem cell-derived teratoma tissues, and reduced MUCINs expression in mutated epithelial cells. There was no difference in CDX2 expression; however, mutated epithelial cells were positive for CEA and CA19-9 expression. GNASR201H-mutated induced pluripotent stem cells and GNASR201H-mutated epithelial cells have distinct phenotypic and differentiation characteristics. We successfully established GNASR201H-mutated human induced pluripotent stem cells with increased cAMP production. Considering the differentiation potential of induced pluripotent stem cells, these cells will be useful as a model for elucidating the pathological mechanisms of GNAS-mutated diseases.
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Affiliation(s)
- Katsuhito Watanabe
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo, Japan
| | | | - Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, Tokyo, Japan
| | - Akiko Saito
- Department of Biochemistry, Tokyo Dental College, Tokyo, Japan
| | - Takahiko Shibahara
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, Tokyo, Japan.,Department of Oral Health Science Center, Tokyo Dental College, Tokyo, Japan
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33
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Ye C, Low BE, Wiles MV, Brusko TM, Serreze DV, Driver JP. CD70 Inversely Regulates Regulatory T Cells and Invariant NKT Cells and Modulates Type 1 Diabetes in NOD Mice. THE JOURNAL OF IMMUNOLOGY 2020; 205:1763-1777. [PMID: 32868408 DOI: 10.4049/jimmunol.2000148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/31/2020] [Indexed: 11/19/2022]
Abstract
The CD27-CD70 costimulatory pathway is essential for the full activation of T cells, but some studies show that blocking this pathway exacerbates certain autoimmune disorders. In this study, we report on the impact of CD27-CD70 signaling on disease progression in the NOD mouse model of type 1 diabetes (T1D). Specifically, our data demonstrate that CD70 ablation alters thymocyte selection and increases circulating T cell levels. CD27 signaling was particularly important for the thymic development and peripheral homeostasis of Foxp3+Helios+ regulatory T cells, which likely accounts for our finding that CD70-deficient NOD mice develop more-aggressive T1D onset. Interestingly, we found that CD27 signaling suppresses the thymic development and effector functions of T1D-protective invariant NKT cells. Thus, rather than providing costimulatory signals, the CD27-CD70 axis may represent a coinhibitory pathway for this immunoregulatory T cell population. Moreover, we showed that a CD27 agonist Ab reversed the effects of CD70 ablation, indicating that the phenotypes observed in CD70-deficient mice were likely due to a lack of CD27 signaling. Collectively, our results demonstrate that the CD27-CD70 costimulatory pathway regulates the differentiation program of multiple T cell subsets involved in T1D development and may be subject to therapeutic targeting.
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Affiliation(s)
- Cheng Ye
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | | | | | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL 32610
| | | | - John P Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611;
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34
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Waldrip ZJ, Jenjaroenpun P, DeYoung O, Nookaew I, Taverna SD, Raney KD, Tackett AJ. Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae. PeerJ 2020; 8:e9442. [PMID: 32821531 PMCID: PMC7395602 DOI: 10.7717/peerj.9442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/08/2020] [Indexed: 12/26/2022] Open
Abstract
The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts.
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Affiliation(s)
- Zachary J Waldrip
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Oktawia DeYoung
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
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35
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Huang D, Miller M, Ashok B, Jain S, Peppas NA. CRISPR/Cas systems to overcome challenges in developing the next generation of T cells for cancer therapy. Adv Drug Deliv Rev 2020; 158:17-35. [PMID: 32707148 DOI: 10.1016/j.addr.2020.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Genetically engineered immune cells with chimeric antigen receptors (CAR) or modified T cell receptors (TCR) have demonstrated their potential as a potent class of new cancer therapeutic strategy. Despite the clinical success of autologous CD19 CAR T cells in hematological malignancies, allogeneic T cells exhibit many advantages over their autologous counterparts and have recently gathered widespread attention due to the emergence of multiplex genome editing techniques, particularly CRISPR/Cas systems. Furthermore, genetically engineered T cells face a host of major challenges in solid tumors that are not as significant for blood cancers such as T cell targeted delivery, target specificity, proliferation, persistence, and the immunosuppressive tumor microenvironment. We take this opportunity to analyze recent strategies to develop allogeneic T cells, specifically in consideration of CRISPR/Cas and its delivery systems for multiplex gene editing. Additionally, we discuss the current methods used to delivery CRISPR/Cas systems for immunotherapeutic applications, and the challenges to continued development of novel delivery systems. We also provide a comprehensive analysis of the major challenges that genetically engineered T cells face in solid tumors along with the most recent strategies to overcome these barriers, with an emphasis on CRISPR-based approaches. We illustrate the synergistic prospects for how the combination of synthetic biology and immune-oncology could pave the way for designing the next generation of precision cancer therapy.
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36
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Nateghi Rostami M. CRISPR/Cas9 gene drive technology to control transmission of vector‐borne parasitic infections. Parasite Immunol 2020; 42:e12762. [DOI: 10.1111/pim.12762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Mahmoud Nateghi Rostami
- Laboratory of Biology of Host‐Parasite Interactions Department of Parasitology Pasteur Institute of Iran Tehran Iran
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37
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Wei H, Wang M, Lv N, Yang H, Zhao M, Huang B, Li R. Increased repetitive self-grooming occurs in Pax2 mutant mice generated using CRISPR/Cas9. Behav Brain Res 2020; 393:112803. [PMID: 32653558 DOI: 10.1016/j.bbr.2020.112803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interaction and communication, and repetitive or restricted interest and behaviors. However, the specific pathogenesis of ASD is still unclear. It has been widely accepted that genetic and environmental risk factors are associated with the pathogenesis of ASD. Paired box2 (Pax2) gene encodes a transcription factor that plays an important role in the development of the central nervous system of humans and mice. In this study, we constructed Pax2 heterozygous gene knockout (Pax2+/-) mice using CRISPR/Cas9 technology and performed several autistic-like behavioral assays, including self-grooming test, sociability approach, the elevated plus maze test and Y maze test. Results showed increased repetitive self-grooming and possible abnormal anxiety-like behavior occur in Pax2+/- mice. Furthermore, no changes were observed in the abilities of sociability and working memory in Pax2+/- mice compared to wild-type C57BL/6 J mice. Finally, we speculated that possible mechanism of abnormal autistic-like behaviors due to the deletion of Pax2 gene.
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Affiliation(s)
- Hongen Wei
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China.
| | - Min Wang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Na Lv
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Hua Yang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Min Zhao
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Bo Huang
- Laboratory Animal Center, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Rongshan Li
- Nephrology Division, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China.
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38
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Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: postnatal malleability and therapeutic prospects. Hum Mol Genet 2020; 28:R254-R264. [PMID: 31595951 DOI: 10.1093/hmg/ddz174] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
The epigenetic machinery in conjunction with the transcriptional machinery is responsible for maintaining genome-wide chromatin states and dynamically regulating gene expression. Mendelian disorders of the epigenetic machinery (MDEMs) are genetic disorders resulting from mutations in components of the epigenetic apparatus. Though individually rare, MDEMs have emerged as a collectively common etiology for intellectual disability (ID) and growth disruption. Studies in model organisms and humans have demonstrated dosage sensitivity of this gene group with haploinsufficiency as a predominant disease mechanism. The epigenetic machinery consists of three enzymatic components (writers, erasers and chromatin remodelers) as well as one non-enzymatic group (readers). A tally of the entire census of such factors revealed that although multiple enzymatic activities never coexist within a single component, individual enzymatic activities often coexist with a reader domain. This group of disorders disrupts both the chromatin and transcription states of target genes downstream of the given component but also DNA methylation on a global scale. Elucidation of these global epigenetic changes may inform our understanding of disease pathogenesis and have diagnostic utility. Moreover, many therapies targeting epigenetic marks already exist, and some have proven successful in treating cancer. This, along with the recent observation that neurological dysfunction in these disorders may in fact be treatable in postnatal life, suggests that the scientific community should prioritize this group as a potentially treatable cause of ID. Here we summarize the recent expansion and major characteristics of MDEMs, as well as the unique therapeutic prospects for this group of disorders.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, 21205.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, 21205.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Landspitali University Hospital, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
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CRISPR-cas9: a powerful tool towards precision medicine in cancer treatment. Acta Pharmacol Sin 2020; 41:583-587. [PMID: 31792341 PMCID: PMC7468325 DOI: 10.1038/s41401-019-0322-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/22/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a highly heterogeneous disease in term of molecular signature even though it is originated from the same tissue type. Cancer heterogeneity may occur during its development or treatment, which is the main cause resulting in drug resistance and recurrence. Precision medicine refers to matching the right medicine to the right patients based on their molecular signatures. Therefore, a thorough understanding of the mechanism of tumorigenesis and drug resistance is essential to precision medicine. CRISPR-cas9 system is a powerful tool for gene editing and CRISPR-based high-throughput screening has been widely applied especially in searching for tumor-driven or synergistic lethal genes aiming to overcome drug resistance. In this review, we describe the progress of CRISPR-cas9-based unbiased screening in precision medicine including identification of new drug targets, biomarkers and elucidation of mechanisms leading to drug resistance. The existing challenges as well as the future directions are also discussed.
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40
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Lee J, Bayarsaikhan D, Bayarsaikhan G, Kim JS, Schwarzbach E, Lee B. Recent advances in genome editing of stem cells for drug discovery and therapeutic application. Pharmacol Ther 2020; 209:107501. [DOI: 10.1016/j.pharmthera.2020.107501] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/10/2020] [Indexed: 12/20/2022]
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41
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Pino-Barrio MJ, Giménez Y, Villanueva M, Hildenbeutel M, Sánchez-Dominguez R, Rodríguez-Perales S, Pujol R, Surrallés J, Río P, Cathomen T, Mussolino C, Bueren JA, Navarro S. TALEN mediated gene editing in a mouse model of Fanconi anemia. Sci Rep 2020; 10:6997. [PMID: 32332829 PMCID: PMC7181878 DOI: 10.1038/s41598-020-63971-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023] Open
Abstract
The promising ability to genetically modify hematopoietic stem and progenitor cells by precise gene editing remains challenging due to their sensitivity to in vitro manipulations and poor efficiencies of homologous recombination. This study represents the first evidence of implementing a gene editing strategy in a murine safe harbor locus site that phenotypically corrects primary cells from a mouse model of Fanconi anemia A. By means of the co-delivery of transcription activator-like effector nucleases and a donor therapeutic FANCA template to the Mbs85 locus, we achieved efficient gene targeting (23%) in mFA-A fibroblasts. This resulted in the phenotypic correction of these cells, as revealed by the reduced sensitivity of these cells to mitomycin C. Moreover, robust evidence of targeted integration was observed in murine wild type and FA-A hematopoietic progenitor cells, reaching mean targeted integration values of 21% and 16% respectively, that were associated with the phenotypic correction of these cells. Overall, our results demonstrate the feasibility of implementing a therapeutic targeted integration strategy into the mMbs85 locus, ortholog to the well-validated hAAVS1, constituting the first study of gene editing in mHSC with TALEN, that sets the basis for the use of a new safe harbor locus in mice.
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Affiliation(s)
- Maria José Pino-Barrio
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Yari Giménez
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariela Villanueva
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcus Hildenbeutel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Rebeca Sánchez-Dominguez
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernandez Almagro, 3, 28029, Madrid, Spain
| | - Roser Pujol
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Jordi Surrallés
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Juan Antonio Bueren
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain.
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
| | - Susana Navarro
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain.
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
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Cui YR, Wang SJ, Chen J, Li J, Chen W, Wang S, Meng B, Zhu W, Zhang Z, Yang B, Jiang B, Yang G, Ma P, Liu J. Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides. Genome Biol 2020; 21:51. [PMID: 32102684 PMCID: PMC7045643 DOI: 10.1186/s13059-020-01956-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells without a temporal control system. Excessive and prolonged expression of CRISPR-Cas9 can lead to elevated off-target cleavage. The need for modulating CRISPR-Cas9 activity over time and dose has created the demand of developing CRISPR-Cas off switches. Protein and small molecule-based CRISPR-Cas inhibitors have been reported in previous studies. RESULTS We report the discovery of Cas9-inhibiting peptides from inoviridae bacteriophages. These peptides, derived from the periplasmic domain of phage major coat protein G8P (G8PPD), can inhibit the in vitro activity of Streptococcus pyogenes Cas9 (SpCas9) proteins in an allosteric manner. Importantly, the inhibitory activity of G8PPD on SpCas9 is dependent on the order of guide RNA addition. Ectopic expression of full-length G8P (G8PFL) or G8PPD in human cells can inactivate the genome-editing activity of SpyCas9 with minimum alterations of the mutation patterns. Furthermore, unlike the anti-CRISPR protein AcrII4A that completely abolishes the cellular activity of CRISPR-Cas9, G8P co-transfection can reduce the off-target activity of co-transfected SpCas9 while retaining its on-target activity. CONCLUSION G8Ps discovered in the current study represent the first anti-CRISPR peptides that can allosterically inactivate CRISPR-Cas9. This finding may provide insights into developing next-generation CRISPR-Cas inhibitors for precision genome engineering.
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Affiliation(s)
- Yan-Ru Cui
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Jie Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Zhuhong Zhang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 264005, Yantai, Shandong, People's Republic of China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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43
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Chen J, Aimanova KG, Gill SS. Aedes cadherin receptor that mediates Bacillus thuringiensis Cry11A toxicity is essential for mosquito development. PLoS Negl Trop Dis 2020; 14:e0007948. [PMID: 32012156 PMCID: PMC7018227 DOI: 10.1371/journal.pntd.0007948] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 02/13/2020] [Accepted: 11/25/2019] [Indexed: 11/20/2022] Open
Abstract
Aedes cadherin (AaeCad, AAEL024535) has been characterized as a receptor for Bacillus thuringiensis subsp. israelensis (Bti) Cry11A toxins. However, its role in development is still unknown. In this study, we modified the cadherin gene using ZFN and TALEN. Even though we obtained heterozygous deletions, no homozygous mutants were viable. Because ZFN and TALEN have lower off-targets than CRISPR/Cas9, we conclude the cadherin gene is essential for Aedes development. In contrast, in lepidopteran insects loss of a homologous cadherin does not appear to be lethal, since homozygous mutants are viable. To analyze the role of AaeCad in vivo, we tagged this protein with EGFP using CRISPR-Cas9-mediated homologous recombination and obtained a homozygous AaeCad-EGFP line. Addition of Aedes Rad51 mRNA enhanced the rate of recombination. We then examined AaeCad protein expression in most tissues and protein dynamics during mosquito development. We observe that AaeCad is expressed in larval and adult midgut-specific manner and its expression pattern changed during the mosquito development. Confocal images showed AaeCad has high expression in larval caecae and posterior midgut, and also in adult midgut. Expression of AaeCad is observed primarily in the apical membranes of epithelial cells, and not in cell-cell junctions. The expression pattern observed suggests AaeCad does not appear to play a role in these junctions. However, we cannot exclude its role beyond cell-cell adhesion in the midgut. We also observed that Cry11A bound to the apical side of larval gastric caecae and posterior midgut cells exactly where AaeCad-EGFP was expressed. Their co-localization suggests that AaeCad is indeed a receptor for the Cry11A toxin. Using this mosquito line we also observed that low doses of Cry11A toxin caused the cells to slough off membranes, which likely represents a defense mechanism, to limit cell damage from Cry11A toxin pores formed in the cell membrane. A number of receptors for Bt Cry toxins, have been identified and characterized, including cadherin proteins. However, the role of these proteins in the insect is unknown and there have been few efforts to elucidate their function. First, in this study we show that in the mosquito, Aedes aegypti, the cadherin protein is essential for development. Secondly, we provide evidence that AaeCad plays a role in the apical membrane and the maintenance of midgut integrity by gene tagging using CRISPR/Cas9, which overcomes the limitation of receptor localization using antibodies in previous studies. These investigations are helpful to further investigate the physiological function of AaeCad. Moreover, this study demonstrated successful tagging of an essential gene with fluorescence protein in a non-model insect. In addition, this study showed that epithelium thinning is possibly a conserved mechanism for host defense against pore-forming toxins, like Cry11A.
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Affiliation(s)
- Jianwu Chen
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, United States of America
| | - Karly G. Aimanova
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, United States of America
| | - Sarjeet S. Gill
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, United States of America
- * E-mail:
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CRISPR/Cas9-Mediated TERT Disruption in Cancer Cells. Int J Mol Sci 2020; 21:ijms21020653. [PMID: 31963842 PMCID: PMC7014288 DOI: 10.3390/ijms21020653] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 12/22/2022] Open
Abstract
Mammalian telomere lengths are primarily regulated by telomerase, a ribonucleoprotein consisting of a reverse transcriptase (TERT) and an RNA subunit (TERC). TERC is constitutively expressed in all cells, whereas TERT expression is temporally and spatially regulated, such that in most adult somatic cells, TERT is inactivated and telomerase activity is undetectable. Most tumor cells activate TERT as a mechanism for preventing progressive telomere attrition to achieve proliferative immortality. Therefore, inactivating TERT has been considered to be a promising means of cancer therapy. Here we applied the CRISPR/Cas9 gene editing system to target the TERT gene in cancer cells. We report that disruption of TERT severely compromises cancer cell survival in vitro and in vivo. Haploinsufficiency of TERT in tumor cells is sufficient to result in telomere attrition and growth retardation in vitro. In vivo, TERT haploinsufficient tumor cells failed to form xenograft after transplantation to nude mice. Our work demonstrates that gene editing-mediated TERT knockout is a potential therapeutic option for treating cancer.
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Chung CH, Allen AG, Sullivan NT, Atkins A, Nonnemacher MR, Wigdahl B, Dampier W. Computational Analysis Concerning the Impact of DNA Accessibility on CRISPR-Cas9 Cleavage Efficiency. Mol Ther 2020; 28:19-28. [PMID: 31672284 PMCID: PMC6953893 DOI: 10.1016/j.ymthe.2019.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Defining the variables that impact the specificity of CRISPR/Cas9 has been a major research focus. Whereas sequence complementarity between guide RNA and target DNA substantially dictates cleavage efficiency, DNA accessibility of the targeted loci has also been hypothesized to be an important factor. In this study, functional data from two genome-wide assays, genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq) and circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq), have been computationally analyzed in conjunction with DNA accessibility determined via DNase I-hypersensitive sequencing from the Encyclopedia of DNA Elements (ENCODE) Database and transcriptome from the Sequence Read Archive to determine whether cellular factors influence CRISPR-induced cleavage efficiency. CIRCLE-seq and GUIDE-seq datasets were selected to represent the absence and presence of cellular factors, respectively. Data analysis revealed that correlations between sequence similarity and CRISPR-induced cleavage frequency were altered by the presence of cellular factors that modulated the level of DNA accessibility. The above-mentioned correlation was abolished when cleavage sites were located in less accessible regions. Furthermore, CRISPR-mediated edits were permissive even at regions that were insufficient for most endogenous genes to be expressed. These results provide a strong basis to dissect the contribution of local chromatin modulation markers on CRISPR-induced cleavage efficiency.
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Affiliation(s)
- Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Alexander G Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Neil T Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA 19104, USA.
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Ahmad S, Wei X, Sheng Z, Hu P, Tang S. CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects. Brief Funct Genomics 2020; 19:26-39. [DOI: 10.1093/bfgp/elz041] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Several plant pathogens severely affect crop yield and quality, thereby threatening global food security. In order to cope with this challenge, genetic improvement of plant disease resistance is required for sustainable agricultural production, for which conventional breeding is unlikely to do enough. Luckily, genome editing systems that particularly clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) has revolutionized crop improvement by enabling robust and precise targeted genome modifications. It paves the way towards new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. In this review, the challenges, limitations and prospects for conventional breeding and the applications of CRISPR/Cas9 system for the development of transgene-free disease-resistant crops are discussed.
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Kumar P, Malik YS, Ganesh B, Rahangdale S, Saurabh S, Natesan S, Srivastava A, Sharun K, Yatoo MI, Tiwari R, Singh RK, Dhama K. CRISPR-Cas System: An Approach With Potentials for COVID-19 Diagnosis and Therapeutics. Front Cell Infect Microbiol 2020. [PMID: 33251158 DOI: 10.3389/fcimb] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
COVID-19, the human coronavirus disease caused by SARS-CoV-2, was reported for the first time in Wuhan, China in late 2019. COVID-19 has no preventive vaccine or proven standard pharmacological treatment, and consequently, the outbreak swiftly became a pandemic affecting more than 215 countries around the world. For the diagnosis of COVID-19, the only reliable diagnostics is a qPCR assay. Among other diagnostic tools, the CRISPR-Cas system is being investigated for rapid and specific diagnosis of COVID-19. The CRISPR-Cas-based methods diagnose the SARS-CoV-2 infections within an hour. Apart from its diagnostic ability, CRISPR-Cas system is also being assessed for antiviral therapy development; however, till date, no CRISPR-based therapy has been approved for human use. The Prophylactic Antiviral CRISPR in huMAN cells (PAC-MAN), which is Cas 13 based strategy, has been developed against coronavirus. Although this strategy has the potential to be developed as a therapeutic modality, it may face significant challenges for approval in human clinical trials. This review is focused on describing potential use and challenges of CRISPR-Cas based approaches for the development of rapid and accurate diagnostic technique and/or a possible therapeutic alternative for combating COVID-19. The assessment of potential risks associated with use of CRISPR will be important for future clinical advancements.
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Affiliation(s)
- Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, India
| | - Balasubramanian Ganesh
- Laboratory Division, Indian Council of Medical Research-National Institute of Epidemiology, Ministry of Health & Family Welfare, Chennai, India
| | - Somnath Rahangdale
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, India
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Sharad Saurabh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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48
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Naghizadeh S, Mansoori B, Mohammadi A, Sakhinia E, Baradaran B. Gene Silencing Strategies in Cancer Therapy: An Update for Drug Resistance. Curr Med Chem 2019; 26:6282-6303. [DOI: 10.2174/0929867325666180403141554] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/10/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
RNAi, post-transcriptional gene silencing mechanism, could be considered as one of the
most important breakthroughs and rapidly growing fields in science. Researchers are trying to use this
discovery in the treatment of various diseases and cancer is one of them although there are multiple
treatment procedures for treatment-resistant cancers, eradication of resistance remain as an unsolvable
problem yet. The current review summarizes both transcriptional and post-transcriptional gene silencing
mechanisms, and highlights mechanisms leading to drug-resistance such as, drug efflux, drug inactivation,
drug target alteration, DNA damages repair, and the epithelial-mesenchymal transition, as
well as the role of tumor cell heterogeneity and tumor microenvironment, involving genes in these
processes. It ultimately points out the obstacles of RNAi application for in vivo treatment of diseases
and progressions that have been achieved in this field.
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Affiliation(s)
- Sanaz Naghizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Sakhinia
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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49
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Luo J, Padhi P, Jin H, Anantharam V, Zenitsky G, Wang Q, Willette AA, Kanthasamy A, Kanthasamy AG. Utilization of the CRISPR-Cas9 Gene Editing System to Dissect Neuroinflammatory and Neuropharmacological Mechanisms in Parkinson's Disease. J Neuroimmune Pharmacol 2019; 14:595-607. [PMID: 30879240 PMCID: PMC6746615 DOI: 10.1007/s11481-019-09844-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
Chronic and debilitating neurodegenerative diseases, such as Parkinson's disease (PD), impose an immense medical, emotional, and economic burden on patients and society. Due to a complex interaction between genetic and environmental risk factors, the etiology of PD remains elusive. However, the cumulative evidence emerging from clinical and experimental research over the last several decades has identified mitochondrial dysfunction, oxidative stress, neuroinflammation, and dysregulated protein degradation as the main drivers of PD neurodegeneration. The genome-editing system CRISPR (clustered regularly interspaced short palindromic repeats) has recently transformed the field of biotechnology and biomedical discovery and is poised to accelerate neurodegenerative disease research. It has been leveraged to generate PD animal models, such as Parkin, DJ-1, and PINK1 triple knockout miniature pigs. CRISPR has also allowed the deeper understanding of various PD gene interactions, as well as the identification of novel apoptotic pathways associated with neurodegenerative processes in PD. Furthermore, its application has been used to dissect neuroinflammatory pathways involved in PD pathogenesis, such as the PKCδ signaling pathway, as well as the roles of novel compensatory or protective pathways, such as Prokineticin-2 signaling. This review aims to highlight the historical milestones in the evolution of this technology and attempts to illustrate its transformative potential in unraveling disease mechanisms as well as in the development of innovative treatment strategies for PD. Graphical Abstract.
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Affiliation(s)
- Jie Luo
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Piyush Padhi
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Huajun Jin
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Vellareddy Anantharam
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Gary Zenitsky
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Qian Wang
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, USA
| | - Auriel A Willette
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, USA
| | - Arthi Kanthasamy
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Anumantha G Kanthasamy
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA.
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50
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Li J, Hong S, Chen W, Zuo E, Yang H. Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing. J Genet Genomics 2019; 46:513-521. [PMID: 31911131 DOI: 10.1016/j.jgg.2019.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.
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Affiliation(s)
- Jinjing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Shunyan Hong
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
| | - Erwei Zuo
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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