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Ghaemi A, Abnous K, Taghdisi SM, Vakili-Azghandi M, Ramezani M, Alibolandi M. Robust aptamer-targeted CRISPR/Cas9 delivery using mesenchymal stem cell membrane -liposome hybrid: BIRC5 gene knockout against melanoma. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 62:102778. [PMID: 39127174 DOI: 10.1016/j.nano.2024.102778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/10/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
In this study, a platform was fabricated by combining a cationic lipid, 1,2-Dioleoyl-3-trimethylammonium-propane (DOTAP) with mesenchymal stem cell membrane (MSCM) to produce a positively charged hybrid vesicle. The prepared hybrid vesicle was used to condense BIRC5 CRISPR/Cas9 plasmid for survivin (BIRC5) gene editing. The Sgc8-c aptamer (against protein tyrosine kinase 7) was then attached to the surface of the prepared NPs through electrostatic interactions. In this regard, melanoma cancer cells (B16F0 cell line) overexpressing PTK7 receptor could be targeted. Investigations were conducted on this system to evaluate its transfection efficiency, cellular toxicity, and therapeutic performance in preclinical stage using B16F0 tumor bearing C57BL/6 J mice. The results verified the superiority of the Hybrid/ BIRC5 compared to Liposome/ BIRC5 in terms of cellular toxicity and transfection efficiency. The cells exposure to Hybrid/BIRC5 significantly enhanced cytotoxicity. Moreover, cells treated with Apt-Hybrid/BIRC5 showed higher anti-proliferation activity toward PTK7-positive B16F0 cancer cells than that of the PKT7-negative CHO cell line. The active tumor targeting nanoparticles increased the cytotoxicity through down-regulation of BIRC5 expression as confirmed by Western blot analysis. In preclinical stage, Apt-Hybrid/BIRC5 showed remarkable tumor growth suppression toward B16F0 tumorized mice. Thus, our study suggested that genome editing for BIRC5 through the CRISPR/Cas9 system could provide a potentially safe approach for melanoma cancer therapy and has great potential for clinical translation.
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Affiliation(s)
- Asma Ghaemi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoumeh Vakili-Azghandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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3
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He J, Zeng C, Li M. Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300203. [PMID: 38465224 PMCID: PMC10919289 DOI: 10.1002/ggn2.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Indexed: 03/12/2024]
Abstract
Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.
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Affiliation(s)
- Jianjie He
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Can Zeng
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
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4
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [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: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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5
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Nuttle X, Burt ND, Currall B, Moysés-Oliveira M, Mohajeri K, Bhavsar R, Lucente D, Yadav R, Tai DJC, Gusella JF, Talkowski ME. Parallelized engineering of mutational models using piggyBac transposon delivery of CRISPR libraries. CELL REPORTS METHODS 2024; 4:100672. [PMID: 38091988 PMCID: PMC10831954 DOI: 10.1016/j.crmeth.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/14/2023] [Accepted: 11/21/2023] [Indexed: 01/25/2024]
Abstract
New technologies and large-cohort studies have enabled novel variant discovery and association at unprecedented scale, yet functional characterization of these variants remains paramount to deciphering disease mechanisms. Approaches that facilitate parallelized genome editing of cells of interest or induced pluripotent stem cells (iPSCs) have become critical tools toward this goal. Here, we developed an approach that incorporates libraries of CRISPR-Cas9 guide RNAs (gRNAs) together with inducible Cas9 into a piggyBac (PB) transposon system to engineer dozens to hundreds of genomic variants in parallel against isogenic cellular backgrounds. This method empowers loss-of-function (LoF) studies through the introduction of insertions or deletions (indels) and copy-number variants (CNVs), though generating specific nucleotide changes is possible with prime editing. The ability to rapidly establish high-quality mutational models at scale will facilitate the development of isogenic cellular collections and catalyze comparative functional genomic studies investigating the roles of hundreds of genes and mutations in development and disease.
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Affiliation(s)
- Xander Nuttle
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Nicholas D Burt
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin Currall
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Mariana Moysés-Oliveira
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Kiana Mohajeri
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; PhD program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Derek J C Tai
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - James F Gusella
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Michael E Talkowski
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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6
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Tong C, Liang Y, Zhang Z, Wang S, Zheng X, Liu Q, Song B. Review of knockout technology approaches in bacterial drug resistance research. PeerJ 2023; 11:e15790. [PMID: 37605748 PMCID: PMC10440060 DOI: 10.7717/peerj.15790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023] Open
Abstract
Gene knockout is a widely used method in biology for investigating gene function. Several technologies are available for gene knockout, including zinc-finger nuclease technology (ZFN), suicide plasmid vector systems, transcription activator-like effector protein nuclease technology (TALEN), Red homologous recombination technology, CRISPR/Cas, and others. Of these, Red homologous recombination technology, CRISPR/Cas9 technology, and suicide plasmid vector systems have been the most extensively used for knocking out bacterial drug resistance genes. These three technologies have been shown to yield significant results in researching bacterial gene functions in numerous studies. This study provides an overview of current gene knockout methods that are effective for genetic drug resistance testing in bacteria. The study aims to serve as a reference for selecting appropriate techniques.
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Affiliation(s)
- Chunyu Tong
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yimin Liang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Zhelin Zhang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Sen Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Xiaohui Zheng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Qi Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Bocui Song
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
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7
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Song N, Chu Y, Tang J, Yang D. Lipid-, Inorganic-, Polymer-, and DNA-Based Nanocarriers for Delivery of the CRISPR/Cas9 system. Chembiochem 2023; 24:e202300180. [PMID: 37183575 DOI: 10.1002/cbic.202300180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/16/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (CRISPR/Cas9) system has been widely explored for the precise manipulation of target DNA and has enabled efficient genomic editing in cells. Recently, CRISPR/Cas9 has shown promising potential in biomedical applications, including disease treatment, transcriptional regulation and genome-wide screening. Despite these exciting achievements, efficient and controlled delivery of the CRISPR/Cas9 system has remained a critical obstacle to its further application. Herein, we elaborate on the three delivery forms of the CRISPR/Cas9 system, and discuss the composition, advantages and limitations of these forms. Then we provide a comprehensive overview of the carriers of the system, and focus on the nonviral nanocarriers in chemical methods that facilitate efficient and controlled delivery of the CRISPR/Cas9 system. Finally, we discuss the challenges and prospects of the delivery methods of the CRISPR/Cas9 system in depth, and propose strategies to address the intracellular and extracellular barriers to delivery in clinical applications.
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Affiliation(s)
- Nachuan Song
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Yiwen Chu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Jianpu Tang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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8
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Kim C, Cnaani A, Kültz D. Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system. Sci Rep 2023; 13:12086. [PMID: 37495710 PMCID: PMC10371998 DOI: 10.1038/s41598-023-37928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia (Oreochromis mossambicus) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line and an optimized vector-based CRISPR/Cas9 system to functionally disrupt MYC in the tilapia genome and to establish causal links between MYC and cell functions, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal myca (a gene encoding MYC) knockout (ko) cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2%). Subsequent isolation and dilution of cells from these pools produced a myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.
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Affiliation(s)
- Chanhee Kim
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, 7528809, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA.
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9
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Arif T, Farooq A, Ahmad FJ, Akhtar M, Choudhery MS. Prime editing: A potential treatment option for β-thalassemia. Cell Biol Int 2023; 47:699-713. [PMID: 36480796 DOI: 10.1002/cbin.11972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022]
Abstract
The potential to therapeutically alter the genome is one of the remarkable scientific developments in recent years. Genome editing technologies have provided an opportunity to precisely alter genomic sequence(s) in eukaryotic cells as a treatment option for various genetic disorders. These technologies allow the correction of harmful mutations in patients by precise nucleotide editing. Genome editing technologies such as CRISPR (clustered regularly interspaced short palindromic repeat) and base editors have greatly contributed to the practical applications of gene editing. However, these technologies have certain limitations, including imperfect editing, undesirable mutations, off-target effects, and lack of potential to simultaneously edit multiple loci. Recently, prime editing (PE) has emerged as a new gene editing technology with the potential to overcome the above-mentioned limitations. Interestingly, PE not only has higher specificity but also does not require double-strand breaks. In addition, a minimum possibility of potential off-target mutant sites makes PE a preferred choice for therapeutic gene editing. Furthermore, PE has the potential to introduce insertion and deletions of all 12 single-base mutations at target sequences. Considering its potential, PE has been applied as a treatment option for genetic diseases including hemoglobinopathies. β-Thalassemia, for example, one of the most significant blood disorders characterized by reduced levels of functional hemoglobin, could potentially be treated using PE. Therapeutic reactivation of the γ-globin gene in adult β-thalassemia patients through PE technology is considered a promising therapeutic strategy. The current review aims to briefly discuss the genome editing strategies and potential applications of PE for the treatment of β-thalassemia. In addition, the review will also focus on challenges associated with the use of PE.
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Affiliation(s)
- Taqdees Arif
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
| | - Aroosa Farooq
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
| | - Fridoon Jawad Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of Punjab Lahore, Lahore, Punjab, Pakistan
| | - Mahmood S Choudhery
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
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10
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Engineering CRISPR/Cas-based nanosystems for therapeutics, diagnosis and bioimaging. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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11
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Bashor CJ, Hilton IB, Bandukwala H, Smith DM, Veiseh O. Engineering the next generation of cell-based therapeutics. Nat Rev Drug Discov 2022; 21:655-675. [PMID: 35637318 PMCID: PMC9149674 DOI: 10.1038/s41573-022-00476-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 12/19/2022]
Abstract
Cell-based therapeutics are an emerging modality with the potential to treat many currently intractable diseases through uniquely powerful modes of action. Despite notable recent clinical and commercial successes, cell-based therapies continue to face numerous challenges that limit their widespread translation and commercialization, including identification of the appropriate cell source, generation of a sufficiently viable, potent and safe product that meets patient- and disease-specific needs, and the development of scalable manufacturing processes. These hurdles are being addressed through the use of cutting-edge basic research driven by next-generation engineering approaches, including genome and epigenome editing, synthetic biology and the use of biomaterials.
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Affiliation(s)
- Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Department of Biosciences, Rice University, Houston, TX, USA.
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Department of Biosciences, Rice University, Houston, TX, USA.
| | - Hozefa Bandukwala
- Sigilon Therapeutics, Cambridge, MA, USA
- Flagship Pioneering, Cambridge, MA, USA
| | - Devyn M Smith
- Sigilon Therapeutics, Cambridge, MA, USA
- Arbor Biotechnologies, Cambridge, MA, USA
| | - Omid Veiseh
- Department of Bioengineering, Rice University, Houston, TX, USA.
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12
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Wei X, Pu A, Liu Q, Hou Q, Zhang Y, An X, Long Y, Jiang Y, Dong Z, Wu S, Wan X. The Bibliometric Landscape of Gene Editing Innovation and Regulation in the Worldwide. Cells 2022; 11:cells11172682. [PMID: 36078090 PMCID: PMC9454589 DOI: 10.3390/cells11172682] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Gene editing (GE) has become one of the mainstream bioengineering technologies over the past two decades, mainly fueled by the rapid development of the CRISPR/Cas system since 2012. To date, plenty of articles related to the progress and applications of GE have been published globally, but the objective, quantitative and comprehensive investigations of them are relatively few. Here, 13,980 research articles and reviews published since 1999 were collected by using GE-related queries in the Web of Science. We used bibliometric analysis to investigate the competitiveness and cooperation of leading countries, influential affiliations, and prolific authors. Text clustering methods were used to assess technical trends and research hotspots dynamically. The global application status and regulatory framework were also summarized. This analysis illustrates the bottleneck of the GE innovation and provides insights into the future trajectory of development and application of the technology in various fields, which will be helpful for the popularization of gene editing technology.
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Affiliation(s)
- Xun Wei
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
| | - Aqing Pu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Qianqian Liu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yong Zhang
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Xueli An
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yan Long
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yilin Jiang
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Zhenying Dong
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
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13
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Wang K, Escobar M, Li J, Mahata B, Goell J, Shah S, Cluck M, Hilton I. Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions. Nucleic Acids Res 2022; 50:7842-7855. [PMID: 35849129 PMCID: PMC9371918 DOI: 10.1093/nar/gkac582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 12/29/2022] Open
Abstract
Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer-promoter pairs. Here, we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as an activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer-promoter pairs. We find that these platforms display variable relative expression levels in different human cell types and that their transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs) and that this eRNA induction is positively correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to demonstrate that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that enhancer-mediated tracking and engagement of a downstream promoter can be synthetically driven by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.
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Affiliation(s)
- Kaiyuan Wang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Jing Li
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Spencer Shah
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Madeleine Cluck
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
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14
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Stanciu GD, Ababei DC, Rusu RN, Bild V, Tamba BI. Exploring the Involvement of the Amyloid Precursor Protein A673T Mutation against Amyloid Pathology and Alzheimer's Disease in Relation to Therapeutic Editing Tools. Pharmaceutics 2022; 14:1270. [PMID: 35745842 PMCID: PMC9228826 DOI: 10.3390/pharmaceutics14061270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Alzheimer's disease (AD) is biologically defined as a complex neurodegenerative condition with a multilayered nature that leads to a progressive decline in cognitive function and irreversible neuronal loss. It is one of the primary diseases among elderly individuals. With an increasing incidence and a high failure rate for pharmaceutical options that are merely symptom-targeting and supportive with many side effects, there is an urgent need for alternative strategies. Despite extensive knowledge on the molecular basis of AD, progress concerning effective disease-modifying therapies has proven to be a challenge. The ability of the CRISPR-Cas9 gene editing system to help identify target molecules or to generate new preclinical disease models could shed light on the pathogenesis of AD and provide promising therapeutic possibilities. Here, we sought to highlight the current understanding of the involvement of the A673T mutation in amyloid pathology, focusing on its roles in protective mechanisms against AD, in relation to the recent status of available therapeutic editing tools.
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Affiliation(s)
- Gabriela Dumitrita Stanciu
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (G.D.S.); (B.-I.T.)
| | - Daniela Carmen Ababei
- Pharmacodynamics and Clinical Pharmacy Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (R.N.R.); (V.B.)
| | - Razvan Nicolae Rusu
- Pharmacodynamics and Clinical Pharmacy Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (R.N.R.); (V.B.)
| | - Veronica Bild
- Pharmacodynamics and Clinical Pharmacy Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (R.N.R.); (V.B.)
| | - Bogdan-Ionel Tamba
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (G.D.S.); (B.-I.T.)
- Department of Pharmacology, Clinical Pharmacology and Algesiology, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
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15
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Nayeri S, Baghban Kohnehrouz B, Ahmadikhah A, Mahna N. CRISPR/Cas9-mediated P-CR domain-specific engineering of CESA4 heterodimerization capacity alters cell wall architecture and improves saccharification efficiency in poplar. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1197-1212. [PMID: 35266285 PMCID: PMC9129088 DOI: 10.1111/pbi.13803] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 05/21/2023]
Abstract
Cellulose is the most abundant unique biopolymer in nature with widespread applications in bioenergy and high-value bioproducts. The large transmembrane-localized cellulose synthase (CESA) complexes (CSCs) play a pivotal role in the biosynthesis and orientation of the para-crystalline cellulose microfibrils during secondary cell wall (SCW) deposition. However, the hub CESA subunit with high potential homo/heterodimerization capacity and its functional effects on cell wall architecture, cellulose crystallinity, and saccharification efficiency remains unclear. Here, we reported the highly potent binding site containing four residues of Pro435, Trp436, Pro437, and Gly438 in the plant-conserved region (P-CR) of PalCESA4 subunit, which are involved in the CESA4-CESA8 heterodimerization. The CRISPR/Cas9-knockout mutagenesis in the predicted binding site results in physiological abnormalities, stunt growth, and deficient roots. The homozygous double substitution of W436Q and P437S and heterozygous double deletions of W436 and P437 residues potentially reduced CESA4-binding affinity resulting in normal roots, 1.5-2-fold higher plant growth and cell wall regeneration rates, 1.7-fold thinner cell wall, high hemicellulose content, 37%-67% decrease in cellulose content, high cellulose DP, 25%-37% decrease in cellulose crystallinity, and 50% increase in saccharification efficiency. The heterozygous deletion of W436 increases about 2-fold CESA4 homo/heterodimerization capacity led to the 50% decrease in plant growth and increase in cell walls thickness, cellulose content (33%), cellulose DP (20%), and CrI (8%). Our findings provide a strategy for introducing commercial CRISPR/Cas9-mediated bioengineered poplars with promising cellulose applications. We anticipate our results could create an engineering revolution in bioenergy and cellulose-based nanomaterial technologies.
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Affiliation(s)
- Shahnoush Nayeri
- Department of Plant Sciences and BiotechnologyFaculty of Life Sciences and BiotechnologyShahid Beheshti UniversityTehranIran
| | | | - Asadollah Ahmadikhah
- Department of Plant Sciences and BiotechnologyFaculty of Life Sciences and BiotechnologyShahid Beheshti UniversityTehranIran
| | - Nasser Mahna
- Department of Horticultural SciencesFaculty of AgricultureUniversity of TabrizTabrizIran
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16
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Wei C, Liu H, Wang W, Luo P, Chen Q, Li R, Wang C, Botella JR, Zhang H. Expanding the Editing Window of Cytidine Base Editors With the Rad51 DNA-Binding Domain in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:865848. [PMID: 35548314 PMCID: PMC9083192 DOI: 10.3389/fpls.2022.865848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
Recently developed base editors provide a powerful tool for plant research and crop improvement. Although a number of different deaminases and Cas proteins have been used to improve base editors the editing efficiency, and editing window are still not optimal. Fusion of a non-sequence-specific single-stranded DNA-binding domain (DBD) from the human Rad51 protein between Cas9 nickase and the deaminase has been reported to dramatically increase the editing efficiency and expand the editing window of base editors in the mammalian cell lines and mouse embryos. We report the use of this strategy in rice, by fusing a rice codon-optimized human Rad51 DBD to the cytidine base editors AncBE4max, AncBE4max-NG, and evoFERNY. Our results show that the addition of Rad51 DBD did not increase editing efficiency in the major editing window but the editing range was expanded in all the three systems. Replacing the human Rad51 DBD with the rice Rad51 DBD homolog also expanded the editing window effectively.
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Affiliation(s)
- Chunjie Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hao Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenwen Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Pengyu Luo
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qiuling Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Rou Li
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chong Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - José Ramón Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Hui Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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Luo J, Junaid M, Hamid N, Duan JJ, Yang X, Pei DS. Current understanding of gliomagenesis: from model to mechanism. Int J Med Sci 2022; 19:2071-2079. [PMID: 36483593 PMCID: PMC9724244 DOI: 10.7150/ijms.77287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Glioma, a kind of central nervous system (CNS) tumor, is hard to cure and accounts for 32% of all CNS tumors. Establishing a stable glioma model is critically important to investigate the underlying molecular mechanisms involved in tumorigenesis and tumor progression. Various core signaling pathways have been identified in gliomagenesis, such as RTK/RAS/PI3K, TP53, and RB1. Traditional methods of establishing glioma animal models have included chemical induction, xenotransplantation, and genetic modifications (RCAS/t-va system, Cre-loxP, and TALENs). Recently, CRISPR/Cas9 has emerged as an efficient gene editing tool with high germline transmission and has extended the scope of stable and efficient glioma models that can be generated. Therefore, this review will highlight the documented evidence about the molecular characteristics, critical genetic markers, and signaling pathways responsible for gliomagenesis and progression. Moreover, methods of establishing glioma models using gene editing techniques and therapeutic aspects will be discussed. Finally, the prospect of applying gene editing in glioma by using CRISPR/Cas9 strategy and future research directions to establish a stable glioma model are also included in this review. In-depth knowledge of glioma signaling pathways and use of CRISPR/Cas9 can greatly assist in the development of a stable, efficient, and spontaneous glioma model, which can ultimately improve the effectiveness of therapeutic responses and cure glioma patients.
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Affiliation(s)
- Juanjuan Luo
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Muhammad Junaid
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naima Hamid
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Jing Duan
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
| | - Xiaojun Yang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
- ✉ Corresponding authors: De-Sheng Pei, E-mail: ; Xiaojun Yang, E-mail:
| | - De-Sheng Pei
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
- ✉ Corresponding authors: De-Sheng Pei, E-mail: ; Xiaojun Yang, E-mail:
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18
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Desjardins J, Cowan M, Yamanaka Y. Designing Genetically Engineered Mouse Models (GEMMs) Using CRISPR Mediated Genome Editing. Methods Mol Biol 2022; 2429:515-531. [PMID: 35507186 DOI: 10.1007/978-1-0716-1979-7_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genetically engineered mouse models (GEMMs) are very powerful tools to study lineage hierarchy and cellular dynamics of stem cells in vivo. Stem cell behavior in various contexts such as development, normal homeostasis and diseases have been investigated using GEMMs. The strategies to generate GEMMs have drastically changed in the last decade with the development of the CRISPR/Cas9 system for manipulation of the mammalian genome. The advantages of the CRISPR/Cas9 are its simplicity and efficiency. The bioinformatics tools available now allow us to quickly identify appropriate guide RNAs and design experimental conditions to generate the targeted mutation. In addition, the genome can be manipulated directly in the zygote which reduces the time to modify target genes compared to other technologies such as Embryonic Stem (ES) cells. Equally important is that we can manipulate the genome of any mouse background with the CRISPR/Cas9 system which omits time-consuming backcrossing processes, accelerates research and increases flexibility. Here, we will summarize basic allelic types and our standard strategies of how to generate them.
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Affiliation(s)
- Jade Desjardins
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada.
| | - Yojiro Yamanaka
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
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19
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Lai CY, Yeh KY, Liu BF, Chang TM, Chang CH, Liao YF, Liu YW, Her GM. MicroRNA-21 Plays Multiple Oncometabolic Roles in Colitis-Associated Carcinoma and Colorectal Cancer via the PI3K/AKT, STAT3, and PDCD4/TNF-α Signaling Pathways in Zebrafish. Cancers (Basel) 2021; 13:5565. [PMID: 34771727 PMCID: PMC8583575 DOI: 10.3390/cancers13215565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Patients with inflammatory bowel disease (IBD) have a high risk of developing CRC. Inflammatory cytokines are regulated by complex gene networks and regulatory RNAs, especially microRNAs. MicroRNA-21 (miR-21) is amongst the most frequently upregulated microRNAs in inflammatory responses and cancer development. miR-21 has become a target for genetic and pharmacological regulation in various diseases. However, the association between inflammation and tumorigenesis in the gut is largely unknown. Hence, in this study, we generated a zebrafish model (ImiR-21) with inducible overexpression of miR-21 in the intestine. The results demonstrate that miR-21 can induce CRC or colitis-associated cancer (CAC) in ImiR-21 through the PI3K/AKT, PDCD4/TNF-α, and IL-6/STAT3 signaling network. miR-21 activated the PI3K/AKT and NF-κB signaling pathways, leading to initial inflammation; thereafter, miR-21 and TNF-α repressed PDCD4 and its tumor suppression activity. Eventually, active STAT3 stimulated a strong inflammatory response and activated the invasion/metastasis process of tumor cells. Hence, our findings indicate that miR-21 is critical for the development of CRC/CAC via the PI3K/AKT, STAT3, and PDCD4/TNF-α signaling networks.
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Affiliation(s)
- Chi-Yu Lai
- Institute of Biopharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-Y.L.); (B.-F.L.); (Y.-W.L.)
| | - Kun-Yun Yeh
- Division of Hemato-Oncology, Department of Internal Medicine, Chang-Chung Memorial Hospital, Keelung 204, Taiwan;
| | - Bi-Feng Liu
- Institute of Biopharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-Y.L.); (B.-F.L.); (Y.-W.L.)
| | - Tzu-Ming Chang
- Division of Surgical Oncology, Department of Surgery, Cheng Hsin General Hospital, Taipei 112, Taiwan; (T.-M.C.); (C.-H.C.)
| | - Chuan-Hsun Chang
- Division of Surgical Oncology, Department of Surgery, Cheng Hsin General Hospital, Taipei 112, Taiwan; (T.-M.C.); (C.-H.C.)
- Division of General Surgery, Cheng Hsin General Hospital, Taipei 112, Taiwan
| | - Yung-Feng Liao
- Laboratory of Molecular Neurobiology, Institute of Cellular and Organismic Biology, Academia Sinica, ICOB 238, 128 Sec. 2 Academia Rd., Taipei 11529, Taiwan;
| | - Yi-Wen Liu
- Institute of Biopharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-Y.L.); (B.-F.L.); (Y.-W.L.)
| | - Guor Mour Her
- Institute of Biopharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-Y.L.); (B.-F.L.); (Y.-W.L.)
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20
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Rees HA, Minella AC, Burnett CA, Komor AC, Gaudelli NM. CRISPR-derived genome editing therapies: Progress from bench to bedside. Mol Ther 2021; 29:3125-3139. [PMID: 34619370 PMCID: PMC8572140 DOI: 10.1016/j.ymthe.2021.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
The development of CRISPR-derived genome editing technologies has enabled the precise manipulation of DNA sequences within the human genome. In this review, we discuss the initial development and cellular mechanism of action of CRISPR nucleases and DNA base editors. We then describe factors that must be taken into consideration when developing these tools into therapeutic agents, including the potential for unintended and off-target edits when using these genome editing tools, and methods to characterize these types of edits. We finish by considering specific challenges associated with bringing a CRISPR-based therapy to the clinic, including manufacturing, regulatory oversight, and considerations for clinical trials that involve genome editing agents.
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21
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Abkallo HM, Svitek N, Oduor B, Awino E, Henson SP, Oyola SO, Mwalimu S, Assad-Garcia N, Fuchs W, Vashee S, Steinaa L. Rapid CRISPR/Cas9 Editing of Genotype IX African Swine Fever Virus Circulating in Eastern and Central Africa. Front Genet 2021; 12:733674. [PMID: 34527025 PMCID: PMC8435729 DOI: 10.3389/fgene.2021.733674] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
African swine fever virus (ASFV) is the etiological agent of a contagious and fatal disease of domestic pigs that has significant economic consequences for the global swine industry. Due to the lack of effective treatment and vaccines against African swine fever, there is an urgent need to leverage cutting-edge technologies and cost-effective approaches for generating and purifying recombinant virus to fast-track the development of live-attenuated ASFV vaccines. Here, we describe the use of the CRISPR/Cas9 gene editing and a cost-effective cloning system to produce recombinant ASFVs. Combining these approaches, we developed a recombinant virus lacking the non-essential gene A238L (5EL) in the highly virulent genotype IX ASFV (ASFV-Kenya-IX-1033) genome in less than 2 months as opposed to the standard homologous recombination with conventional purification techniques which takes up to 6 months on average. Our approach could therefore be a method of choice for less resourced laboratories in developing nations.
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Affiliation(s)
- Hussein M Abkallo
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Nicholas Svitek
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Bernard Oduor
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Elias Awino
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Sonal P Henson
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Samuel O Oyola
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Stephen Mwalimu
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Nacrya Assad-Garcia
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, United States
| | - Walter Fuchs
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Sanjay Vashee
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, United States
| | - Lucilla Steinaa
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
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22
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Torabi Dalivandan S, Plummer J, Gayther SA. Risks and Function of Breast Cancer Susceptibility Alleles. Cancers (Basel) 2021; 13:3953. [PMID: 34439109 PMCID: PMC8393346 DOI: 10.3390/cancers13163953] [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: 07/07/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/22/2022] Open
Abstract
Family history remains one of the strongest risk factors for breast cancer. It is well established that women with a first-degree relative affected by breast cancer are twice as likely to develop the disease themselves. Twins studies indicate that this is most likely due to shared genetics rather than shared epidemiological/lifestyle risk factors. Linkage and targeted sequencing studies have shown that rare high- and moderate-penetrance germline variants in genes involved in the DNA damage response (DDR) including BRCA1, BRCA2, PALB2, ATM, and TP53 are responsible for a proportion of breast cancer cases. However, breast cancer is a heterogeneous disease, and there is now strong evidence that different risk alleles can predispose to different subtypes of breast cancer. Here, we review the associations between the different genes and subtype-specificity of breast cancer based on the most comprehensive genetic studies published. Genome-wide association studies (GWAS) have also been used to identify an additional hereditary component of breast cancer, and have identified hundreds of common, low-penetrance susceptibility alleles. The combination of these low penetrance risk variants, summed as a polygenic risk score (PRS), can identify individuals across the spectrum of disease risk. However, there remains a substantial bottleneck between the discovery of GWAS-risk variants and their contribution to tumorigenesis mainly because the majority of these variants map to the non-protein coding genome. A range of functional genomic approaches are needed to identify the causal risk variants and target susceptibility genes and establish their underlying role in disease biology. We discuss how the application of these multidisciplinary approaches to understand genetic risk for breast cancer can be used to identify individuals in the population that may benefit from clinical interventions including screening for early detection and prevention, and treatment strategies to reduce breast cancer-related mortalities.
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Affiliation(s)
| | | | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA; (S.T.D.); (J.P.)
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23
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Cheng M, Cheng Z, Yu Y, Liu W, Li R, Guo Z, Qin J, Zeng Z, Di L, Mo Y, Pan C, Liang Y, Li J, Tong Y, Yan Y, Zhan Y, Ning K. An engineered genetic circuit for lactose intolerance alleviation. BMC Biol 2021; 19:137. [PMID: 34225711 PMCID: PMC8259030 DOI: 10.1186/s12915-021-01070-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lactose malabsorption occurs in around 68% of the world's population, causing lactose intolerance (LI) symptoms, such as abdominal pain, bloating, and diarrhea. To alleviate LI, previous studies have mainly focused on strengthening intestinal β-galactosidase activity while neglecting the inconspicuous drop in the colon pH caused by the fermentation of non-hydrolyzed lactose by the gut microbes. A drop in colon pH will reduce the intestinal β-galactosidase activity and influence intestinal homeostasis. RESULTS Here, we synthesized a tri-stable-switch circuit equipped with high β-galactosidase activity and pH rescue ability. This circuit can switch in functionality between the expression of β-galactosidase and expression of L-lactate dehydrogenase in response to an intestinal lactose signal and intestinal pH signal, respectively. We confirmed that the circuit functionality was efficient in bacterial cultures at a range of pH levels, and in preventing a drop in pH and β-galactosidase activity after lactose administration to mice. An impact of the circuit on gut microbiota composition was also indicated. CONCLUSIONS Due to its ability to flexibly adapt to environmental variation, in particular to stabilize colon pH and maintain β-galactosidase activity after lactose influx, the tri-stable-switch circuit can serve as a promising prototype for the relief of lactose intolerance.
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Affiliation(s)
- Mingyue Cheng
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Zhangyu Cheng
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Yiyan Yu
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Wangjie Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Ruihao Li
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Zhenyi Guo
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Jiyue Qin
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Zhi Zeng
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Lin Di
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Yufeng Mo
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Chunxiu Pan
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Yuanhao Liang
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China
| | - Jinman Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, Beijing, People's Republic of China
| | - Yunjun Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China. .,Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.
| | - Yi Zhan
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China. .,Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China. .,Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.
| | - Kang Ning
- College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China. .,Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.
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24
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Abhimanyu, Ontiveros CO, Guerra-Resendez RS, Nishiguchi T, Ladki M, Hilton IB, Schlesinger LS, DiNardo AR. Reversing Post-Infectious Epigenetic-Mediated Immune Suppression. Front Immunol 2021; 12:688132. [PMID: 34163486 PMCID: PMC8215363 DOI: 10.3389/fimmu.2021.688132] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
The immune response must balance the pro-inflammatory, cell-mediated cytotoxicity with the anti-inflammatory and wound repair response. Epigenetic mechanisms mediate this balance and limit host immunity from inducing exuberant collateral damage to host tissue after severe and chronic infections. However, following treatment for these infections, including sepsis, pneumonia, hepatitis B, hepatitis C, HIV, tuberculosis (TB) or schistosomiasis, detrimental epigenetic scars persist, and result in long-lasting immune suppression. This is hypothesized to be one of the contributing mechanisms explaining why survivors of infection have increased all-cause mortality and increased rates of unrelated secondary infections. The mechanisms that induce epigenetic-mediated immune suppression have been demonstrated in-vitro and in animal models. Modulation of the AMP-activated protein kinase (AMPK)-mammalian target of rapamycin (mTOR), nuclear factor of activated T cells (NFAT) or nuclear receptor (NR4A) pathways is able to block or reverse the development of detrimental epigenetic scars. Similarly, drugs that directly modify epigenetic enzymes, such as those that inhibit histone deacetylases (HDAC) inhibitors, DNA hypomethylating agents or modifiers of the Nucleosome Remodeling and DNA methylation (NuRD) complex or Polycomb Repressive Complex (PRC) have demonstrated capacity to restore host immunity in the setting of cancer-, LCMV- or murine sepsis-induced epigenetic-mediated immune suppression. A third clinically feasible strategy for reversing detrimental epigenetic scars includes bioengineering approaches to either directly reverse the detrimental epigenetic marks or to modify the epigenetic enzymes or transcription factors that induce detrimental epigenetic scars. Each of these approaches, alone or in combination, have ablated or reversed detrimental epigenetic marks in in-vitro or in animal models; translational studies are now required to evaluate clinical applicability.
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Affiliation(s)
- Abhimanyu
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
| | - Carlos O Ontiveros
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, United States.,UT Health San Antonio, San Antonio, TX, United States
| | - Rosa S Guerra-Resendez
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
| | - Malik Ladki
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
| | - Isaac B Hilton
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States.,Department of Bioengineering, Rice University, Houston, TX, United States.,Department of BioSciences, Rice University, Houston, TX, United States
| | - Larry S Schlesinger
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andrew R DiNardo
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
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25
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Lyu Y, Yang C, Lyu X, Pu K. Active Delivery of CRISPR System Using Targetable or Controllable Nanocarriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005222. [PMID: 33759340 DOI: 10.1002/smll.202005222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/30/2020] [Indexed: 05/17/2023]
Abstract
Among programmable nuclease-based genome editing tools, the clustered regularly interspaced short palindromic repeats (CRISPR) system with accuracy and the convenient operation is most promising to be applied in gene therapy. The development of effective delivery carriers for the CRISPR system is the major premise to achieve practical applications. Although many nanocarrier-mediated deliveries have been reported to be safer and cheaper over the physical and viral delivery, the accumulation at disease sites or controllability with the spatial or temporal resolution are still desired on nanocarriers to reduce side effects and off-target from the CRISPR system. Therefore, the targetable and controllable nanocarriers to actively deliver the CRISPR system are summarized. The cell or even organ selective nanocarriers are introduced first, followed by the discussion of nanocarriers controlled by biochemical or physical signals. At last, the potential challenges faced by existing nanocarriers are discussed.
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Affiliation(s)
- Yan Lyu
- Cosmetic Innovation Center, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Synthetic and Biological Colloids Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Cheng Yang
- Cosmetic Innovation Center, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Synthetic and Biological Colloids Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637457, Singapore
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26
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Liu Y, Chang J, Yang C, Zhang T, Chen X, Shi R, Liang Y, Xia Q, Ma S. Genome-wide CRISPR-Cas9 screening in Bombyx mori reveals the toxicological mechanisms of environmental pollutants, fluoride and cadmium. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124666. [PMID: 33279320 DOI: 10.1016/j.jhazmat.2020.124666] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Fluoride and cadmium, two typical environmental pollutants, have been extensively existed in the ecosystem and severely injured various organisms including humans. To explore the toxicological properties and the toxicological mechanism of fluoride and cadmium in silkworm, we perform a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) -based functional genomic screen, which can directly measure the genetic requirement of genes in response to the pollutants. Our screen identifies 751 NaF-resistance genes, 753 NaF-sensitive genes, 757 CdCl2-resistance genes, and 725 CdCl2-sensitive genes. The top-ranked resistant genes are experimentally verified and the results show that their loss conferred resistance to fluoride or cadmium. Functional analysis of the resistant- and sensitive-genes demonstrates enrichment of multiple signaling pathways, among which the MAPK signaling pathway and DNA damage and repair are both required for fluoride- or cadmium-induced cell death, whereas the Toll and Imd signaling pathway and Autophagy are fluoride- or cadmium-specific. Moreover, we confirm that these pathways are truly involved in the toxicological mechanism in both cultured cells and individual tissues. Our results supply potential targets for rescuing the biohazards of fluoride and cadmium in silkworm, and reveal the feasible toxicological mechanism, which highlights the role of functional genomic screens in elucidating the toxicity mechanisms of environmental pollutants.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Jiasong Chang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Chengfei Yang
- Department of Urology, The Second Affiliated Hospital, Army Medical University, Chongqing 400037, China
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Xiaoxu Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Run Shi
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Yan Liang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
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27
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Recent Advances in Genome Editing Tools in Medical Mycology Research. J Fungi (Basel) 2021; 7:jof7040257. [PMID: 33808382 PMCID: PMC8067129 DOI: 10.3390/jof7040257] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Manipulating fungal genomes is an important tool to understand the function of target genes, pathobiology of fungal infections, virulence potential, and pathogenicity of medically important fungi, and to develop novel diagnostics and therapeutic targets. Here, we provide an overview of recent advances in genetic manipulation techniques used in the field of medical mycology. Fungi use several strategies to cope with stress and adapt themselves against environmental effectors. For instance, mutations in the 14 alpha-demethylase gene may result in azole resistance in Aspergillusfumigatus strains and shield them against fungicide's effects. Over the past few decades, several genome editing methods have been introduced for genetic manipulations in pathogenic fungi. Application of restriction enzymes to target and cut a double-stranded DNA in a pre-defined sequence was the first technique used for cloning in Aspergillus and Candida. Genome editing technologies, including zinc-finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), have been also used to engineer a double-stranded DNA molecule. As a result, TALENs were considered more practical to identify single nucleotide polymorphisms. Recently, Class 2 type II Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 technology has emerged as a more useful tool for genome manipulation in fungal research.
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28
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Rautela I, Uniyal P, Thapliyal P, Chauhan N, Bhushan Sinha V, Dev Sharma M. An extensive review to facilitate understanding of CRISPR technology as a gene editing possibility for enhanced therapeutic applications. Gene 2021; 785:145615. [PMID: 33775851 DOI: 10.1016/j.gene.2021.145615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023]
Abstract
CRISPR are the sequences in bacterial and archaeal genome which provide resistance against viral infections. They might be the natural part of bacterial genomes for providing protection against viruses like bacteriophages but science has successfully achieved their use in the benefit of man-kind by using them for the treatment of deadly diseases like cancer, AIDS or genetic disorders like sickle cell disease and Leber congenital amaurosis. CRISPR system is majorly divided into two classes i.e class I and class II, of which the class II CRISPR/Cas9 system performs site specific cleavage of DNA with a guide RNA Cas12 (Cpf1). With the new emerging discoveries it is being found that CRISPR not only works on double stranded DNA but can also be useful to induce any sort of site specific cleavage in RNA too by Cas13 earlier known as C2c2, which is a protein found in CRISPR system and has ability to cure viral infections in plants. CRISPR is being used in the field of gene manipulation and various animals models are available to serve this purpose with short lifespan, rapid reproducibility and lower maintenance cost. Many successful studies and experiments performed using CRISPR, reveals their potency and utility to bring revolution in the areas which were previously believed to be out of scope of science and medicine.
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Affiliation(s)
- Indra Rautela
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun 248001, Uttarakhand, India
| | - Pooja Uniyal
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun 248001, Uttarakhand, India
| | - Priya Thapliyal
- Department of Biochemistry, H.N.B. Garhwal (A Central) University, Srinagar 246174, Uttarakhand, India
| | - Neha Chauhan
- Department of Medical Microbiology, College of Paramedical Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun 248001, Uttarakhand, India
| | | | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun 248001, Uttarakhand, India.
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30
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Heigwer F, Boutros M. Cloud-Based Design of Short Guide RNA (sgRNA) Libraries for CRISPR Experiments. Methods Mol Biol 2021; 2162:3-22. [PMID: 32926374 DOI: 10.1007/978-1-0716-0687-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CRISPR/Cas-based genome editing in any biological application requires the evaluation of suitable genomic target sites to design efficient reagents. Considerations for the design of short guide (sg) RNAs include the assessment of possible off-target activities, the prediction of on-target efficacies and mutational outcome. Manual design of sgRNAs taking into account these parameters, however, remains a difficult task. Thus, computational tools to design sgRNA reagents from small scale to genome-wide libraries have been developed that assist during all steps of the design process. Here, we will describe practical guidance for the sgRNA design process using the web-based tool E-CRISP used in the design of individual sgRNAs. E-CRISP ( www.e-crisp.org ) has been the first web-based sgRNA design tool and uniquely features simple, yet efficient, scoring schemes in combination with fast evaluation and simple usage. We will also discuss the installation of a dockerized version of CRISPR Library Designer (CLD) that can be deployed locally or in the cloud to support the end-to-end design of sgRNA libraries for more than 50 different organisms. CLD was built upon E-CRISP to further increase the scope of sgRNA design to more experimental modalities (CRISPRa/i, Cas12a, all possible protospacer adjacency motifs) offering the same flexibility as E-CRISP, plus the scalability through local and cloud installation. Together, these tools facilities the design of small and large-scale CRISPR/Cas experiments.
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Affiliation(s)
- Florian Heigwer
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
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31
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Jin Y, Marquardt S. Dual sgRNA-based Targeted Deletion of Large Genomic Regions and Isolation of Heritable Cas9-free Mutants in Arabidopsis. Bio Protoc 2020; 10:e3796. [PMID: 33659450 PMCID: PMC7842341 DOI: 10.21769/bioprotoc.3796] [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: 05/28/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 11/02/2022] Open
Abstract
CRISPR/Cas9 system directed by a gene-specific single guide RNA (sgRNA) is an effective tool for genome editing such as deletions of few bases in coding genes. However, targeted deletion of larger regions generate loss-of-function alleles that offer a straightforward starting point for functional dissections of genomic loci. We present an easy-to-use strategy including a fast cloning dual-sgRNA vector linked to efficient isolation of heritable Cas9-free genomic deletions to rapidly and cost-effectively generate a targeted heritable genome deletion. This step-by-step protocol includes gRNA design, cloning strategy and mutation detection for Arabidopsis and may be adapted for other plant species.
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Affiliation(s)
- Yu Jin
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 21, 1870 Frederiksberg C, Denmark
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 21, 1870 Frederiksberg C, Denmark
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32
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Tohama T, Sakari M, Tsukahara T. Development of a Single Construct System for Site-Directed RNA Editing Using MS2-ADAR. Int J Mol Sci 2020; 21:E4943. [PMID: 32668759 PMCID: PMC7404196 DOI: 10.3390/ijms21144943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 12/26/2022] Open
Abstract
Site-directed RNA editing (SDRE) technologies have great potential for treating genetic diseases caused by point mutations. Our group and other researchers have developed SDRE methods utilizing adenosine deaminases acting on RNA (ADARs) and guide RNAs recruiting ADARs to target RNAs bearing point mutations. In general, efficient SDRE relies on introducing numerous guide RNAs relative to target genes. However, achieving a large ratio is not possible for gene therapy applications. In order to achieve a realistic ratio, we herein developed a system that can introduce an equal number of genes and guide RNAs into cultured cells using a fusion protein comprising an ADAR fragment and a plasmid vector containing one copy of each gene on a single construct. We transfected the single construct into HEK293T cells and achieved relatively high efficiency (up to 42%). The results demonstrate that efficient SDRE is possible when the copy number is similar for all three factors (target gene, guide RNA, and ADAR enzyme). This method is expected to be capable of highly efficient gene repair in vivo, making it applicable for gene therapy.
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Affiliation(s)
| | | | - Toshifumi Tsukahara
- Area of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan; (T.T.); (M.S.)
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33
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Carlaw TM, Zhang LH, Ross CJD. CRISPR/Cas9 Editing: Sparking Discussion on Safety in Light of the Need for New Therapeutics. Hum Gene Ther 2020; 31:794-807. [PMID: 32586150 DOI: 10.1089/hum.2020.111] [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: 12/26/2022] Open
Abstract
Recent advances in genome sequencing have greatly improved our ability to understand and identify the causes of genetic diseases. However, there remains an urgent need for innovative, safe, and effective treatments for these diseases. CRISPR-based genome editing systems have become important and powerful tools in the laboratory, and efforts are underway to translate these into patient therapies. Therapeutic base editing is one form of genome engineering that has gained much interest because of its simplicity, specificity, and effectiveness. Base editors are a fusion of a partially deactivated Cas9 enzyme with nickase function, together with a base-modifying enzyme. They are capable of precisely targeting and repairing a pathogenic mutation to restore the normal function of a gene, ideally without disturbing the rest of the genome. In the past year, research has identified new safety concerns of base editors and sparked new innovations to improve their safety. In this review, we provide an overview of the recent advances in the safety and effectiveness of therapeutic base editors and prime editing.
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Affiliation(s)
| | - Lin-Hua Zhang
- Faculty of Pharmaceutical Sciences; University of British Columbia, Vancouver, Canada
| | - Colin J D Ross
- Faculty of Pharmaceutical Sciences; University of British Columbia, Vancouver, Canada
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34
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Matsoukas IG. Prime Editing: Genome Editing for Rare Genetic Diseases Without Double-Strand Breaks or Donor DNA. Front Genet 2020; 11:528. [PMID: 32582281 PMCID: PMC7296174 DOI: 10.3389/fgene.2020.00528] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ianis G Matsoukas
- School of Medicine, University of Bolton, Bolton, United Kingdom.,René Descartes College, Athens, Greece
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35
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Lv X, Qiu K, Tu T, He X, Peng Y, Ye J, Fu J, Deng R, Wang Y, Wu J, Liu C, Zhao J, Gu F. Development of a Simple and Quick Method to Assess Base Editing in Human Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:580-588. [PMID: 32335475 PMCID: PMC7184106 DOI: 10.1016/j.omtn.2020.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/10/2020] [Indexed: 11/30/2022]
Abstract
Base editing is a form of genome editing that can directly convert a single base (C or A) to another base (T or G), which is of great potential in biomedical applications. The broad application of base editing is limited by its low activity and specificity, which still needs to be resolved. To address this, a simple and quick method for the determination of its activity/specificity is highly desired. Here, we developed a novel system, which could be harnessed for quick detection of editing activity and specificity of base editors (BEs) in human cells. Specifically, multiple cloning sites (MCS) were inserted into the human genome via lentivirus, and base editing targeting the MCS was performed with BEs. The base editing activities were assessed by specific restriction enzymes. The whole process only includes nucleotide-based targeting the MCS, editing, PCR, and digestion, thus, we named it NOTEPAD. This straightforward approach could be easily accessed by molecular biology laboratories. With this method, we could easily determine the BEs editing efficiency and pattern. The results revealed that BEs triggered more off-target effects in the genome than on plasmids including genomic indels (insertions and deletions). We found that ABEs (adenine base editors) had better fidelity than CBEs (cytosine base editors). Our system could be harnessed as a base editing assessment platform, which would pave the way for the development of next-generation BEs.
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Affiliation(s)
- Xiujuan Lv
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China
| | - Tianxiang Tu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Xiaoxue He
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Yuchen Peng
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Jinbin Ye
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Junhao Fu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Ruzhi Deng
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Yuqin Wang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China
| | - Changbao Liu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Junzhao Zhao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027, China.
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Yuan H, Yu T, Wang L, Yang L, Zhang Y, Liu H, Li M, Tang X, Liu Z, Li Z, Lu C, Chen X, Pang D, Ouyang H. Efficient base editing by RNA-guided cytidine base editors (CBEs) in pigs. Cell Mol Life Sci 2020; 77:719-733. [PMID: 31302752 PMCID: PMC11105001 DOI: 10.1007/s00018-019-03205-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Cytidine base editors (CBEs) have been demonstrated to be useful for precisely inducing C:G-to-T:A base mutations in various organisms. In this study, we showed that the BE4-Gam system induced the targeted C-to-T base conversion in porcine blastocysts at an efficiency of 66.7-71.4% via the injection of a single sgRNA targeting a xeno-antigen-related gene and BE4-Gam mRNA. Furthermore, the efficiency of simultaneous three gene base conversion via the injection of three targeting sgRNAs and BE4-Gam mRNA into porcine parthenogenetic embryos was 18.1%. We also obtained beta-1,4-N-acetyl-galactosaminyl transferase 2, alpha-1,3-galactosyltransferase, and cytidine monophosphate-N-acetylneuraminic acid hydroxylase deficient pig by somatic cell nuclear transfer, which exhibited significantly decreased activity. In addition, a new CBE version (termed AncBE4max) was used to edit genes in blastocysts and porcine fibroblasts (PFFs) for the first time. While this new version demonstrated a three genes base-editing rate of 71.4% at the porcine GGTA1, B4galNT2, and CMAH loci, it increased the frequency of bystander edits, which ranged from 17.8 to 71.4%. In this study, we efficiently and precisely mutated bases in porcine blastocysts and PFFs using CBEs and successfully generated C-to-T and C-to-G mutations in pigs. These results suggest that CBEs provide a more simple and efficient method for improving economic traits, reducing the breeding cycle, and increasing disease tolerance in pigs, thus aiding in the development of human disease models.
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Affiliation(s)
- Hongming Yuan
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Tingting Yu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Lingyu Wang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Lin Yang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Yuanzhu Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Huan Liu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Mengjing Li
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xiaochun Tang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Zhiquan Liu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Zhanjun Li
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Chao Lu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue Chen
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
| | - Hongsheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
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Van Vu T, Sung YW, Kim J, Doan DTH, Tran MT, Kim JY. Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants. RICE (NEW YORK, N.Y.) 2019; 12:95. [PMID: 31858277 PMCID: PMC6923311 DOI: 10.1186/s12284-019-0355-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/04/2019] [Indexed: 05/18/2023]
Abstract
Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging conditions such as climate change and the reduction in arable lands. Monocotyledonous crops are not only responsible for approximately 70% of total global crop production, indicating their important roles in human life, but also the first crops to be challenged with the abovementioned hurdles; hence, monocot crops should be the first to be engineered and/or de novo domesticated/redomesticated. A long time has passed since the first green revolution; the world is again facing the challenge of feeding a predicted 9.7 billion people in 2050, since the decline in world hunger was reversed in 2015. One of the major lessons learned from the first green revolution is the importance of novel and advanced trait-carrying crop varieties that are ideally adapted to new agricultural practices. New plant breeding techniques (NPBTs), such as genome editing, could help us succeed in this mission to create novel and advanced crops. Considering the importance of NPBTs in crop genetic improvement, we attempt to summarize and discuss the latest progress with major approaches, such as site-directed mutagenesis using molecular scissors, base editors and especially homology-directed gene targeting (HGT), a very challenging but potentially highly precise genome modification approach in plants. We therefore suggest potential approaches for the improvement of practical HGT, focusing on monocots, and discuss a potential approach for the regulation of genome-edited products.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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38
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Leukocyte immunoglobulin-like receptor B4 deficiency exacerbates acute lung injury via NF-κB signaling in bone marrow-derived macrophages. Biosci Rep 2019; 39:BSR20181888. [PMID: 31138763 PMCID: PMC6566464 DOI: 10.1042/bsr20181888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 02/08/2023] Open
Abstract
Acute lung injury (ALI) is an acute inflammatory disease. Leukocyte immunoglobulin-like receptor B4 (LILRB4) is an immunoreceptor tyrosine-based inhibitory motif (ITIM)-bearing inhibitory receptor that is implicated in various pathological processes. However, the function of LILRB4 in ALI remains largely unknown. The aim of the present study was to explore the role of LILRB4 in ALI. LILRB4 knockout mice (LILRB4 KO) were used to construct a model of ALI. Bone marrow cell transplantation was used to identify the cell source of the LILRB4 deficiency-aggravated inflammatory response in ALI. The effect on ALI was analyzed by pathological and molecular analyses. Our results indicated that LILRB4 KO exacerbated ALI triggered by LPS. Additionally, LILRB4 deficiency can enhance lung inflammation. According to the results of our bone marrow transplant model, LILRB4 regulates the occurrence and development of ALI by bone marrow-derived macrophages (BMDMs) rather than by stromal cells in the lung. The observed inflammation was mainly due to BMDM-induced NF-κB signaling. In conclusion, our study demonstrates that LILRB4 deficiency plays a detrimental role in ALI-associated BMDM activation by prompting the NF-κB signal pathway.
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39
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Breuls N, Giacomazzi G, Sampaolesi M. (Epi)genetic Modifications in Myogenic Stem Cells: From Novel Insights to Therapeutic Perspectives. Cells 2019; 8:cells8050429. [PMID: 31075875 PMCID: PMC6562881 DOI: 10.3390/cells8050429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
The skeletal muscle is considered to be an ideal target for stem cell therapy as it has an inherent regenerative capacity. Upon injury, the satellite cells, muscle stem cells that reside under the basal lamina of the myofibres, start to differentiate in order to reconstitute the myofibres while maintaining the initial stem cell pool. In recent years, it has become more and more evident that epigenetic mechanisms such as histon modifications, DNA methylations and microRNA modulations play a pivatol role in this differentiation process. By understanding the mechanisms behind myogenesis, researchers are able to use this knowledge to enhance the differentiation and engraftment potential of different muscle stem cells. Besides manipulation on an epigenetic level, recent advances in the field of genome-engineering allow site-specific modifications in the genome of these stem cells. Combining epigenetic control of the stem cell fate with the ability to site-specifically correct mutations or add genes for further cell control, can increase the use of stem cells as treatment of muscular dystrophies drastically. In this review, we will discuss the advances that have been made in genome-engineering and the epigenetic regulation of muscle stem cells and how this knowledge can help to get stem cell therapy to its full potential.
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Affiliation(s)
- Natacha Breuls
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
| | - Giorgia Giacomazzi
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
| | - Maurilio Sampaolesi
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
- Human Anatomy Unit, Department of Public Health, Experimental and Forensic Medicine, and Interuniversity Institute of Myology, University of Pavia, 27100 Pavia, Italy.
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40
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Bhattacharya D, Van Meir EG. A simple genotyping method to detect small CRISPR-Cas9 induced indels by agarose gel electrophoresis. Sci Rep 2019; 9:4437. [PMID: 30872606 PMCID: PMC6418129 DOI: 10.1038/s41598-019-39950-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/25/2019] [Indexed: 01/22/2023] Open
Abstract
CRISPR gene editing creates indels in targeted genes that are detected by genotyping. Separating PCR products generated from wild-type versus mutant alleles with small indels based on size is beyond the resolution capacity of regular agarose gel electrophoresis. To overcome this limitation, we developed a simple genotyping method that exploits the differential electrophoretic mobility of homoduplex versus heteroduplex DNA hybrids in high concentration agarose gels. First, the CRISPR target region is PCR amplified and homo- and hetero-duplexed amplicons formed during the last annealing cycle are separated by 4–6% agarose gel electrophoresis. WT/mutant heteroduplexes migrate more slowly and are distinguished from WT or mutant homoduplexes. Heterozygous alleles are immediately identified as they produce two distinct bands, while homozygous wild-type or mutant alleles yield a single band. To discriminate the latter, equal amounts of PCR products of homozygous samples are mixed with wild-type control samples, subjected to one denaturation/renaturation cycle and products are electrophoresed again. Samples from homozygous mutant alleles now produce two bands, while those from wild-type alleles yield single bands. This method is simple, fast and inexpensive and can identify indels >2 bp. in size in founder pups and genotype offspring in established transgenic mice colonies.
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Affiliation(s)
- Debanjan Bhattacharya
- Laboratory of Molecular Neuro-Oncology, Departments of Neurosurgery and Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Departments of Neurosurgery and Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.
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41
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Sharma D, Sehgal P, Mathew S, Vellarikkal SK, Singh AR, Kapoor S, Jayarajan R, Scaria V, Sivasubbu S. A genome-wide map of circular RNAs in adult zebrafish. Sci Rep 2019; 9:3432. [PMID: 30837568 PMCID: PMC6401160 DOI: 10.1038/s41598-019-39977-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are transcript isoforms generated by back-splicing of exons and circularisation of the transcript. Recent genome-wide maps created for circular RNAs in humans and other model organisms have motivated us to explore the repertoire of circular RNAs in zebrafish, a popular model organism. We generated RNA-seq data for five major zebrafish tissues - Blood, Brain, Heart, Gills and Muscle. The repertoire RNA sequence reads left over after reference mapping to linear transcripts were used to identify unique back-spliced exons utilizing a split-mapping algorithm. Our analysis revealed 3,428 novel circRNAs in zebrafish. Further in-depth analysis suggested that majority of the circRNAs were derived from previously well-annotated protein-coding and long noncoding RNA gene loci. In addition, many of the circular RNAs showed extensive tissue specificity. We independently validated a subset of circRNAs using polymerase chain reaction (PCR) and divergent set of primers. Expression analysis using quantitative real time PCR recapitulate selected tissue specificity in the candidates studied. This study provides a comprehensive genome-wide map of circular RNAs in zebrafish tissues.
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Affiliation(s)
- Disha Sharma
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Paras Sehgal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Samatha Mathew
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Angom Ramcharan Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
| | - Shruti Kapoor
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India. .,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India. .,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India.
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Abstract
CRISPR/Cas9 is an efficient tool to knock down specific genes in various organisms. In this chapter, we describe how to assess knockdown of human rhodopsin (RHO) gene carrying the P23H mutation in vitro, in engineered HeLa cells, and in vivo, in P23H RHO transgenic mice. To this aim, we report two molecular assays: site-specific PCR on P23H RHO cells treated with CRISPR/Cas9 and Western blotting analysis on retinal cells prepared from P23H RHO transgenic mice electroporated with CRISPR/Cas9 and GFP plasmids.
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Affiliation(s)
- Daniela Benati
- Department of Life Sciences, Centre for Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Recchia
- Department of Life Sciences, Centre for Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy.
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Blighe K, DeDionisio L, Christie KA, Chawes B, Shareef S, Kakouli-Duarte T, Chao-Shern C, Harding V, Kelly RS, Castellano L, Stebbing J, Lasky-Su JA, Nesbit MA, Moore CBT. Gene editing in the context of an increasingly complex genome. BMC Genomics 2018; 19:595. [PMID: 30086710 PMCID: PMC6081867 DOI: 10.1186/s12864-018-4963-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catalogued mutations across the primary carcinomas; whilst, for other diseases, we have identified the genetic variants with strongest association. Despite this, we are still awaiting the genetic revolution in healthcare to materialise and translate itself into the health benefits for which we had hoped. A major problem we face relates to our underestimation of the complexity of the genome, and that of biological mechanisms, generally. Fixation on DNA sequence alone and a 'rigid' mode of thinking about the genome has meant that the folding and structure of the DNA molecule -and how these relate to regulation- have been underappreciated. Projects like ENCODE have additionally taught us that regulation at the level of RNA is just as important as that at the spatiotemporal level of chromatin.In this review, we chart the course of the major advances in the biomedical sciences in the era pre- and post the release of the first draft sequence of the human genome, taking a focus on technology and how its development has influenced these. We additionally focus on gene editing via CRISPR/Cas9 as a key technique, in particular its use in the context of complex biological mechanisms. Our aim is to shift the mode of thinking about the genome to that which encompasses a greater appreciation of the folding of the DNA molecule, DNA- RNA/protein interactions, and how these regulate expression and elaborate disease mechanisms.Through the composition of our work, we recognise that technological improvement is conducive to a greater understanding of biological processes and life within the cell. We believe we now have the technology at our disposal that permits a better understanding of disease mechanisms, achievable through integrative data analyses. Finally, only with greater understanding of disease mechanisms can techniques such as gene editing be faithfully conducted.
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Affiliation(s)
- K Blighe
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA.
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK.
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, WC1E 6DD, London, UK.
| | - L DeDionisio
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - K A Christie
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - B Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - S Shareef
- University of Raparin, Ranya, Kurdistan Region, Iraq
| | - T Kakouli-Duarte
- Institute of Technology Carlow, Department of Science and Health, Kilkenny Road, Carlow, Ireland
| | - C Chao-Shern
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - V Harding
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - R S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - L Castellano
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- JMS Building, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - J Stebbing
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - J A Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - M A Nesbit
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - C B T Moore
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK.
- Avellino Laboratories, Menlo Park, CA, 94025, USA.
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44
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Rein LA, Yang H, Chao NJ. Applications of Gene Editing Technologies to Cellular Therapies. Biol Blood Marrow Transplant 2018; 24:1537-1545. [DOI: 10.1016/j.bbmt.2018.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/23/2018] [Indexed: 12/26/2022]
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Moggs J, Terranova R. Chromatin dynamics underlying latent responses to xenobiotics. Toxicol Res (Camb) 2018; 7:606-617. [PMID: 30090610 PMCID: PMC6062062 DOI: 10.1039/c7tx00317j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/26/2018] [Indexed: 11/21/2022] Open
Abstract
Pleiotropic xenobiotics can trigger dynamic alterations in mammalian chromatin structure and function but many of these are likely non-adverse and simply reflect short-term changes in DNA transactions underlying normal homeostatic, adaptive and protective cellular responses. However, it is plausible that a subset of xenobiotic-induced perturbations of somatic tissue or germline epigenomes result in delayed-onset and long-lasting adverse effects, in particular if they occur during critical stages of growth and development. These could include reprogramming, dedifferentiation, uncontrolled growth, and cumulative toxicity effects through molecular memory of prior xenobiotic exposures or altered susceptibility to subsequent xenobiotic exposures. Here we discuss the current evidence for epigenetic mechanisms underlying latent responses to xenobiotics, and the potential for identifying molecular epigenetic changes that are prodromal to overt morphologic or functional toxicity phenotypes.
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Affiliation(s)
- Jonathan Moggs
- Preclinical Safety , Translational Medicine , Novartis Institutes for BioMedical Research , Basel , Switzerland
| | - Rémi Terranova
- Preclinical Safety , Translational Medicine , Novartis Institutes for BioMedical Research , Basel , Switzerland
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Moore CT, Christie KA, Marshall J, Nesbit MA. Personalised genome editing – The future for corneal dystrophies. Prog Retin Eye Res 2018; 65:147-165. [DOI: 10.1016/j.preteyeres.2018.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/21/2022]
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Zhang J, Song F, Sun Y, Yu K, Xiang J. CRISPR/Cas9-mediated deletion of EcMIH shortens metamorphosis time from mysis larva to postlarva of Exopalaemon carinicauda. FISH & SHELLFISH IMMUNOLOGY 2018; 77:244-251. [PMID: 29621632 DOI: 10.1016/j.fsi.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The recently emerged CRISPR/Cas9 technology is the most flexible means to produce targeted mutations at the genomic loci in a variety of organisms. In Crustaceans, molt-inhibiting hormone (MIH) is an important negative-regulatory factor and plays a key role in suppressing the molting process. However, whether precise disruption of MIH in crustacean can be achieved and successfully used to improve the development and growth has not been proved. In this research, the complementary DNA (cDNA) and genomic DNA, including flanking regions of the MIH gene (EcMIH) of ridgetail white prawn Exopalaemon carinicauda, were cloned and sequenced. Sequence analysis revealed that EcMIH was composed of three exons and two introns. Analysis by RT-PCR showed that EcMIH mainly expressed in eyestalks. During different development periods, EcMIH was highest in juvenile stage and extremely low in others but adult prawns eyestalks. In addition, we applied CRISPR/Cas9 technology to generate EcMIH knock-out (KO) prawns and then analyzed the changes in their phenotypes. We efficiently generated 12 EcMIH-KO prawns out of 250 injected one-cell stage embryos and the mutant rate reached 4.8% after embryo injection with one sgRNA targeting the second exon of EcMIH. The EcMIH-KO prawns exhibited increased the body length and shortened the metamorphosis time of larvae from mysis larva to postlarva. Meanwhile, EcMIH-KO did not cause the health problems such as early stage death or deformity. In conclusion, we successfully obtained EcMIH gene and generated EcMIH-KO prawns using CRISPR/Cas9 technology. This study will certainly lead to a wide application prospect of MIH gene in prawns breeding.
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Affiliation(s)
- Jiquan Zhang
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China; CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Fengge Song
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuying Sun
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
| | - Kuijie Yu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
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Lu Y, Jiang Z, Dai H, Miao R, Shu J, Gu H, Liu X, Huang Z, Yang G, Chen AF, Yuan H, Li Y, Cai J. Hepatic leukocyte immunoglobulin-like receptor B4 (LILRB4) attenuates nonalcoholic fatty liver disease via SHP1-TRAF6 pathway. Hepatology 2018; 67:1303-1319. [PMID: 29091299 PMCID: PMC5900726 DOI: 10.1002/hep.29633] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/15/2017] [Accepted: 10/30/2017] [Indexed: 12/27/2022]
Abstract
UNLABELLED Nonalcoholic fatty liver disease (NAFLD) is an increasingly prevalent liver pathology characterized by hepatic steatosis and commonly accompanied by systematic inflammation and metabolic disorder. Despite an accumulating number of studies, no pharmacological strategy is available to treat this condition in the clinic. In this study, we applied extensive gain- and loss-of-function approaches to identify the key immune factor leukocyte immunoglobulin-like receptor B4 (LILRB4) as a negative regulator of NAFLD. The hepatocyte-specific knockout of LILRB4 (LILRB4-HKO) exacerbated high-fat diet-induced insulin resistance, glucose metabolic imbalance, hepatic lipid accumulation, and systematic inflammation in mice, whereas LILRB4 overexpression in hepatocytes showed a completely opposite phenotype relative to that of LILRB4-HKO mice when compared with their corresponding controls. Further investigations of molecular mechanisms demonstrated that LILRB4 recruits SHP1 to inhibit TRAF6 ubiquitination and subsequent inactivation of nuclear factor kappa B and mitogen-activated protein kinase cascades. From a therapeutic perspective, the overexpression of LILRB4 in a genetic model of NAFLD, ob/ob mice, largely reversed the inherent hepatic steatosis, inflammation, and metabolic disorder. CONCLUSION Targeting hepatic LILRB4 to improve its expression or activation represents a promising strategy for the treatment of NAFLD as well as related liver and metabolic diseases. (Hepatology 2018;67:1303-1319).
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Affiliation(s)
- Yao Lu
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina,Department of Clinical PharmacologySt. Thomas' Hospital, KCLLondonUK
| | - Zhou Jiang
- Institute of Model Animal of Wuhan UniversityWuhanChina
| | - Haijiang Dai
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Rujia Miao
- Health Management Center, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Jingxian Shu
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Haotian Gu
- Department of Clinical PharmacologySt. Thomas' Hospital, KCLLondonUK
| | - Xing Liu
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Zhijun Huang
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Guoping Yang
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Alex F. Chen
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Hong Yuan
- Center of Clinical Pharmacology, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Ying Li
- Health Management Center, Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Jingjing Cai
- Department of Cardiology, Third Xiangya HospitalCentral South UniversityChangshaChina
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49
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Matsoukas IG. Commentary: Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage. Front Genet 2018; 9:21. [PMID: 29469899 PMCID: PMC5808320 DOI: 10.3389/fgene.2018.00021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/16/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Ianis G Matsoukas
- Faculty of Health and Human Sciences, School of Sport and Biomedical Sciences. University of Bolton, Bolton, United Kingdom
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Abstract
The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.
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Affiliation(s)
- Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708; , .,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708; , .,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710
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