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Long TF, Zhou SY, Huang ZL, Li G, Zhong Q, Zhang XJ, Li YY, Chen CP, Xia LJ, Wei R, Wan L, Gao A, Ren H, Liao XP, Liu YH, Chen L, Sun J. Innovative Delivery System Combining CRISPR-Cas12f for Combatting Antimicrobial Resistance in Gram-Negative Bacteria. ACS Synth Biol 2024; 13:1831-1841. [PMID: 38863339 DOI: 10.1021/acssynbio.4c00112] [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: 06/13/2024]
Abstract
Antimicrobial resistance poses a significant global challenge, demanding innovative approaches, such as the CRISPR-Cas-mediated resistance plasmid or gene-curing system, to effectively combat this urgent crisis. To enable successful curing of antimicrobial genes or plasmids through CRISPR-Cas technology, the development of an efficient broad-host-range delivery system is paramount. In this study, we have successfully designed and constructed a novel functional gene delivery plasmid, pQ-mini, utilizing the backbone of a broad-host-range Inc.Q plasmid. Moreover, we have integrated the CRISPR-Cas12f system into the pQ-mini plasmid to enable gene-curing in broad-host of bacteria. Our findings demonstrate that pQ-mini facilitates the highly efficient transfer of genetic elements to diverse bacteria, particularly in various species in the order of Enterobacterales, exhibiting a broader host range and superior conjugation efficiency compared to the commonly used pMB1-like plasmid. Notably, pQ-mini effectively delivers the CRISPR-Cas12f system to antimicrobial-resistant strains, resulting in remarkable curing efficiencies for plasmid-borne mcr-1 or blaKPC genes that are comparable to those achieved by the previously reported pCasCure system. In conclusion, our study successfully establishes and optimizes pQ-mini as a broad-host-range functional gene delivery vector. Furthermore, in combination with the CRISPR-Cas system, pQ-mini demonstrates its potential for broad-host delivery, highlighting its promising role as a novel antimicrobial tool against the growing threat of antimicrobial resistance.
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Affiliation(s)
- Teng-Fei Long
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Shi-Ying Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Zi-Lei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Gong Li
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qin Zhong
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Xiao-Jing Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Yuan-Yuan Li
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Cai-Ping Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Li-Juan Xia
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ran Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Lei Wan
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ang Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Hao Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Xiao-Ping Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ya-Hong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14214, United States
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
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2
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Yang G, Wang H, Jiang G, Zhao L, Qu F. Aptamer inhibitor selection of SpyCas9 through CE-SELEX. Talanta 2024; 273:125837. [PMID: 38479030 DOI: 10.1016/j.talanta.2024.125837] [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: 10/20/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 04/09/2024]
Abstract
CRISPR/Cas9 is a natural immune system of archaea and bacteria, which has been widely used in gene editing. In order to better control and improve the accuracy and safety of the system, inhibitors for SpyCas9 as "switches" have been selected for several years. The available inhibitors currently are all natural polypeptides inhibitors derived from phages, except one small molecule inhibitor. These natural inhibitors are challenging to obtain and are available in limited quantities, and the small molecule inhibitor is cytotoxic. Herein, we discover aptamers against the SpyCas9 protein, by coupling CE-SELEX within one-round pressure controllable selection strategy. One of the identified aptamers, Apt2, shows high affinity at the nanomolar level and leads for effective SpyCas9 enzymatic inhibition in vitro. It is predicted that Apt2 interacts with the HNH and RuvC domains of SpyCas9, competitively inhibiting the binding of substrate DNA to SpyCas9. The proposed aptamer inhibitor is the oligonucleotide inhibitor of SpyCas9, which has the potential in construction of the universal, simple and precise CRISPR-Cas9 system activity control strategy. Meanwhile, these aptamers could also be valuable tools for study of the functions of CRISPR/Cas9 and the related functional mechanisms.
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Affiliation(s)
- Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China; CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Huimin Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Guangyu Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Liping Zhao
- Institute of Quality Standard and Testing Technology of BAAFS, Agricultural Product Quality and Safety Risk Assessment Laboratory of the Department of Agriculture, Beijing, 100097, China.
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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3
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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4
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Li X, Chen Z, Ye W, Yu J, Zhang X, Li Y, Niu Y, Ran S, Wang S, Luo Z, Zhao J, Hao Y, Zong J, Xia C, Xia J, Wu J. High-throughput CRISPR technology: a novel horizon for solid organ transplantation. Front Immunol 2024; 14:1295523. [PMID: 38239344 PMCID: PMC10794540 DOI: 10.3389/fimmu.2023.1295523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.
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Affiliation(s)
- Xiaohan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weicong Ye
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhang Yu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Niu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuan Ran
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Song Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilong Luo
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiulu Zhao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanglin Hao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjie Zong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengkun Xia
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Jie Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
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5
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Sharrar A, Arake de Tacca L, Collingwood T, Meacham Z, Rabuka D, Staples-Ager J, Schelle M. Discovery and Characterization of Novel Type V Cas12f Nucleases with Diverse Protospacer Adjacent Motif Preferences. CRISPR J 2023; 6:350-358. [PMID: 37267210 DOI: 10.1089/crispr.2023.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Small Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) effectors are key to developing gene editing therapies due to the packaging constraints of viral vectors. While Cas9 and Cas12a CRISPR-Cas effectors have advanced into select clinical applications, their size is prohibitive for efficient delivery of both nuclease and guide RNA in a single viral vector. Type V Cas12f effectors present a solution given their small size. In this study, we describe a novel set of miniature (<490AA) Cas12f nucleases that cleave double-stranded DNA in human cells. We determined their optimal trans-activating RNA empirically through rational modifications, which resulted in an optimal single guide RNA. We show that these nucleases have broad protospacer adjacent motif (PAM) preferences, allowing for expanded genome targeting. The unique characteristics of these novel nucleases add to the diversity of the miniature CRISPR-Cas toolbox while the expanded PAM allows for the editing of genomic locations that could not be accessed with existing Cas12f nucleases.
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Affiliation(s)
| | | | | | | | - David Rabuka
- Acrigen Biosciences, Inc., Alameda, California, USA
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6
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Mayorga-Ramos A, Zúñiga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance. ACS Infect Dis 2023; 9:1283-1302. [PMID: 37347230 PMCID: PMC10353011 DOI: 10.1021/acsinfecdis.2c00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 06/23/2023]
Abstract
The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.
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Affiliation(s)
- Arianna Mayorga-Ramos
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Johana Zúñiga-Miranda
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Saskya E. Carrera-Pacheco
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Carlos Barba-Ostria
- Escuela
de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170902, Ecuador
| | - Linda P. Guamán
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
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7
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Nevola R, Beccia D, Rosato V, Ruocco R, Mastrocinque D, Villani A, Perillo P, Imbriani S, Delle Femine A, Criscuolo L, Alfano M, La Montagna M, Russo A, Marfella R, Cozzolino D, Sasso FC, Rinaldi L, Marrone A, Adinolfi LE, Claar E. HBV Infection and Host Interactions: The Role in Viral Persistence and Oncogenesis. Int J Mol Sci 2023; 24:ijms24087651. [PMID: 37108816 PMCID: PMC10145402 DOI: 10.3390/ijms24087651] [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: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Hepatitis B virus (HBV) is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Despite the advent of vaccines and potent antiviral agents able to suppress viral replication, recovery from chronic HBV infection is still an extremely difficult goal to achieve. Complex interactions between virus and host are responsible for HBV persistence and the risk of oncogenesis. Through multiple pathways, HBV is able to silence both innate and adaptive immunological responses and become out of control. Furthermore, the integration of the viral genome into that of the host and the production of covalently closed circular DNA (cccDNA) represent reservoirs of viral persistence and account for the difficult eradication of the infection. An adequate knowledge of the virus-host interaction mechanisms responsible for viral persistence and the risk of hepatocarcinogenesis is necessary for the development of functional cures for chronic HBV infection. The purpose of this review is, therefore, to analyze how interactions between HBV and host concur in the mechanisms of infection, persistence, and oncogenesis and what are the implications and the therapeutic perspectives that follow.
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Affiliation(s)
- Riccardo Nevola
- Liver Unit, Ospedale Evangelico Betania, 80147 Naples, Italy
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Domenico Beccia
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Valerio Rosato
- Liver Unit, Ospedale Evangelico Betania, 80147 Naples, Italy
| | - Rachele Ruocco
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | | | - Angela Villani
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | | | - Simona Imbriani
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Augusto Delle Femine
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Livio Criscuolo
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Maria Alfano
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Marco La Montagna
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Antonio Russo
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Raffaele Marfella
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Domenico Cozzolino
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Ferdinando Carlo Sasso
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Luca Rinaldi
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Aldo Marrone
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Luigi Elio Adinolfi
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Ernesto Claar
- Liver Unit, Ospedale Evangelico Betania, 80147 Naples, Italy
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8
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Hussain MS, Anand V, Kumar M. Functional PAM sequence for DNA interference by CRISPR-Cas I-B system of Leptospira interrogans and the role of LinCas11b encoded within lincas8b. Int J Biol Macromol 2023; 237:124086. [PMID: 36940764 DOI: 10.1016/j.ijbiomac.2023.124086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Pathogenic species of Leptospira are recalcitrant for genetic manipulation using conventional tools, and therefore there is a need to explore techniques of higher efficiency. Application of endogenous CRISPR-Cas tool is emerging and efficient; nevertheless, it is limited by a poor understanding of interference machinery in the bacterial genome and its associated protospacer adjacent motif (PAM). In this study, interference machinery of CRISPR-Cas subtype I-B (Lin_I-B) from L. interrogans was experimentally validated in E. coli using the various identified PAM (TGA, ATG, ATA). The overexpression of the Lin_I-B interference machinery in E. coli demonstrated that LinCas5, LinCas6, LinCas7, and LinCas8b can self-assemble on cognate CRISPR RNA to form an interference complex (LinCascade). Moreover, a robust interference of target plasmids containing a protospacer with a PAM suggested a functional LinCascade. We also recognized a small open reading frame within lincas8b that independently co-translates LinCas11b. A mutant variant of LinCascade-Cas11b that lacks LinCas11b co-expression erred to mount target plasmid interference. At the same time, LinCas11b complementation in LinCascade-Cas11b rescued target plasmid interference. Thus, the present study establishes Leptospira subtype I-B interference machinery to be functional and, soon, may pave the way for scientists to harness it as a programmable endogenous genetic manipulation tool.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Vineet Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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9
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Zhang Q, Xia K, Jiang M, Li Q, Chen W, Han M, Li W, Ke R, Wang F, Zhao Y, Liu Y, Fan C, Gu H. Catalytic DNA-Assisted Mass Production of Arbitrary Single-Stranded DNA. Angew Chem Int Ed Engl 2023; 62:e202212011. [PMID: 36347780 DOI: 10.1002/anie.202212011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Synthetic single-stranded (ss) DNA is a cornerstone for life and materials science, yet the purity, quantity, length, and customizability of synthetic DNA are still limiting in various applications. Here, we present PECAN, paired-end cutting assisted by DNAzymes (DNA enzymes or deoxyribozymes), which enables mass production of ssDNA of arbitrary sequence (up to 7000 nucleotides, or nt) with single-base precision. At the core of PECAN technique are two newly identified classes of DNAzymes, each robustly self-hydrolyzing with minimal sequence requirement up- or down-stream of its cleavage site. Flanking the target ssDNA with a pair of such DNAzymes generates a precursor ssDNA amplifiable by pseudogene-recombinant bacteriophage, which subsequently releases the target ssDNA in large quantities after efficient auto-processing. PECAN produces ssDNA of virtually any terminal bases and compositions with >98.5 % purity at the milligram-to-gram scale. We demonstrate the feasibility of using PECAN ssDNA for RNA in situ detection, homology-directed genome editing, and DNA-based data storage.
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Affiliation(s)
- Qiao Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Kai Xia
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China.,Shanghai Frontier Innovation Research Institute, Shanghai, 201108, China
| | - Meng Jiang
- School of Medicine and School of Biomedical Science, Huaqiao University, Fujian, 362021, China
| | - Qingting Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Weigang Chen
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Mingzhe Han
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Rongqin Ke
- School of Medicine and School of Biomedical Science, Huaqiao University, Fujian, 362021, China
| | - Fei Wang
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Yongxing Zhao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, and Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan, 450001, China
| | - Yuehua Liu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Chunhai Fan
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
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10
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Contiliani DF, Moraes VN, Passos GA, Pereira TC. What Is the CRISPR System and How It Is Used? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:1-11. [PMID: 37486513 DOI: 10.1007/978-3-031-33325-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
CRISPR is a revolutionary gene editing technology that has enabled scientists worldwide to explore the cell's genetic blueprint in an unprecedented easy way. In this chapter, we will briefly present the history behind the development of this innovative tool, how it emerged from a natural bacterial mechanism for antiviral defense, its key components (Cas9 endonuclease and single guide RNA), mode of action (DNA cleavage and repair via NHEJ or HDR), and versatility (acting on single- or double-stranded DNA or RNA) for diverse purposes beyond gene editing such as stochastic marking, digital encoding, high-fidelity SNP genotyping, programmed chromosome fission/fusion, gene mapping, nucleic acid detection, regulation of gene expression, DNA/RNA labeling or tracking, and more.
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Affiliation(s)
- Danyel F Contiliani
- Centro de Cana, Instituto Agronômico de Campinas, Ribeirão Preto, SP, Brazil
- Graduate Program in Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Vitor N Moraes
- Graduate Program in Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, USP, Ribeirão Preto, SP, Brazil
| | - Geraldo A Passos
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto Campus, SP, Brazil
- Laboratory of Genetics and Molecular Biology, Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto Campus, SP, Brazil
| | - Tiago Campos Pereira
- Graduate Program in Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil.
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, USP, Ribeirão Preto, SP, Brazil.
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11
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Mitra S, Anand U, Ghorai M, Kant N, Kumar M, Radha, Jha NK, Swamy MK, Proćków J, de la Lastra JMP, Dey A. Genome editing technologies, mechanisms and improved production of therapeutic phytochemicals: Opportunities and prospects. Biotechnol Bioeng 2023; 120:82-94. [PMID: 36224758 PMCID: PMC10091730 DOI: 10.1002/bit.28260] [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: 05/18/2022] [Revised: 09/10/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2022]
Abstract
Plants produce a large number of secondary metabolites, known as phytometabolites that may be employed as medicines, dyes, poisons, and insecticides in the field of medicine, agriculture, and industrial use, respectively. The rise of genome management approaches has promised a factual revolution in genetic engineering. Targeted genome editing in living entities permits the understanding of the biological systems very clearly, and also sanctions to address a wide-ranging objective in the direction of improving features of plant and their yields. The last few years have introduced a number of unique genome editing systems, including transcription activator-like effector nucleases, zinc finger nucleases, and miRNA-regulated clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). Genome editing systems have helped in the transformation of metabolic engineering, allowing researchers to modify biosynthetic pathways of different secondary metabolites. Given the growing relevance of editing genomes in plant research, the exciting novel methods are briefly reviewed in this chapter. Also, this chapter highlights recent discoveries on the CRISPR-based modification of natural products in different medicinal plants.
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Affiliation(s)
- Sicon Mitra
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | | | - Mimosa Ghorai
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Nishi Kant
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Delhi, New Delhi, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Niraj K Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, India.,Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, Punjab, India.,Department of Biotechnology, School of Applied & Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Mallappa K Swamy
- Department of Biotechnology, East West First Grade College of Science, Bengaluru, Karnataka, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - José M Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Department of Life and Earth Sciences, Instituto de Productos Naturales y Agrobiología-Consejo Superior de Investigaciones Científicas, (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Spain
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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12
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New Therapeutics for Extracellular Vesicles: Delivering CRISPR for Cancer Treatment. Int J Mol Sci 2022; 23:ijms232415758. [PMID: 36555398 PMCID: PMC9779094 DOI: 10.3390/ijms232415758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Cancers are defined by genetic defects, which underlines the prospect of using gene therapy in patient care. During the past decade, CRISPR technology has rapidly evolved into a powerful gene editing tool with high fidelity and precision. However, one of the impediments slowing down the clinical translation of CRISPR-based gene therapy concerns the lack of ideal delivery vectors. Extracellular vesicles (EVs) are nano-sized membrane sacs naturally released from nearly all types of cells. Although EVs are secreted for bio-information conveyance among cells or tissues, they have been recognized as superior vectors for drug or gene delivery. Recently, emerging evidence has spotlighted EVs in CRISPR delivery towards cancer treatment. In this review, we briefly introduce the biology and function of the CRISPR system and follow this with a summary of current delivery methods for CRISPR applications. We emphasize the recent progress in EV-mediated CRISPR editing for various cancer types and target genes. The reported strategies for constructing EV-CRISPR vectors, as well as their limitations, are discussed in detail. The review aims to throw light on the clinical potential of engineered EVs and encourage the expansion of our available toolkit to defeat cancer.
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13
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Ma E, Chen K, Shi H, Stahl EC, Adler B, Trinidad M, Liu J, Zhou K, Ye J, Doudna J. Improved genome editing by an engineered CRISPR-Cas12a. Nucleic Acids Res 2022; 50:12689-12701. [PMID: 36537251 PMCID: PMC9825149 DOI: 10.1093/nar/gkac1192] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2-18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.
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Affiliation(s)
- Enbo Ma
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kai Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Ben Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Junjie Liu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kaihong Zhou
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jinjuan Ye
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94114, USA
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14
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Almeida RS, Wisnieski F, Takao Real Karia B, Smith MAC. CRISPR/Cas9 Genome-Editing Technology and Potential Clinical Application in Gastric Cancer. Genes (Basel) 2022; 13:2029. [PMID: 36360266 PMCID: PMC9690943 DOI: 10.3390/genes13112029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 10/09/2023] Open
Abstract
Gastric cancer is the subject of clinical and basic studies due to its high incidence and mortality rates worldwide. Due to the diagnosis occurring in advanced stages and the classic treatment methodologies such as gastrectomy and chemotherapy, they are extremely aggressive and limit the quality of life of these patients. CRISPR/Cas9 is a tool that allows gene editing and has been used to explore the functions of genes related to gastric cancer, in addition to being used in the treatment of this neoplasm, greatly increasing our understanding of cancer genomics. In this mini-review, we seek the current status of the CRISPR/Cas9 gene-editing technology in gastric cancer research and clinical research.
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Affiliation(s)
- Renata Sanches Almeida
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
| | - Fernanda Wisnieski
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
- Discipline of Gastroenterology, Department of Medicine, Federal University of São Paulo, Rua Loefgreen, 1726, São Paulo 04040002, Brazil
| | - Bruno Takao Real Karia
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
| | - Marilia Arruda Cardoso Smith
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
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15
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Genomic Features of Pseudomonas putida PCL1760: A Biocontrol Agent Acting via Competition for Nutrient and Niche. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Pseudomonasputida strain PCL1760 is a biocontrol agent protecting plants from pathogens via the mechanism of competition for nutrients and niches (CNN). To confirm this mechanism as well as to adapt the strain for biotechnological applications, full genome analysis was compared with the known biotechnological model, P. putida S12, and other related species, which were analyzed on different genomic databases. Moreover, the antibacterial activity of PCL1760 was tested against Staphylococcus aureus, Pseudomonas aeruginosa, and Pseudomonas syringae. No genetic systems involved in antibiosis were revealed among the secondary metabolite clusters of the strain of PCL1760. The only antagonistic effect was observed against P. syringae, which might be because of siderophore (yellow-greenish fluorescence), although less than 19% pyoverdin biosynthesis clusters were predicted using the AntiSMASH server. P. putida PCL1760 in comparison with the Pseudomonas simiae strain PCL1751, another biocontrol agent acting solely via CNN, which lost its ‘luxury’ genes necessary for antibiosis or parasitism/predation mechanisms, but carries genetic systems providing motility. Interestingly, immunity genes (CRISPR/Cas and prophages) showed PCL1760 to be robust in comparison with S12, while annotation on OrthoVenn2 showed PCL1760 to be amenable for genetic manipulations. It is tempting to state that rhizobacteria using the mechanism of CNN are distinguishable from biocontrol agents acting via antibiosis or parasitism/predation at the genomic level. This confirms the CNN of PCL1760 as the sole mechanism for biocontrol and we suggest the strain as a new model for genetic engineering.
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16
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Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A. Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Nat Commun 2022; 13:4624. [PMID: 35941106 PMCID: PMC9360449 DOI: 10.1038/s41467-022-32079-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 12/26/2022] Open
Abstract
Argonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes and prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos that uniquely use DNA guides to process RNA targets. The biochemical and structural analysis of Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization of the guide binding pocket that does not rely on divalent cations and the canonical set of contacts for 5'-end interactions. Unconventional interactions of PliAgo with the 5'-phosphate of guide DNA define its new position within pAgo and shift the site of target RNA cleavage in comparison with known Argonautes. The specificity for RNA over DNA is defined by ribonucleotide residues at the cleavage site. The analysed pAgos sense mismatches and modifications in the RNA target. The results broaden our understanding of prokaryotic defense systems and extend the spectrum of programmable nucleases with potential use in RNA technology.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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17
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Gonzalez-Salinas F, Martinez-Amador C, Trevino V. Characterizing genes associated with cancer using the CRISPR/Cas9 system: A systematic review of genes and methodological approaches. Gene 2022; 833:146595. [PMID: 35598687 DOI: 10.1016/j.gene.2022.146595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022]
Abstract
The CRISPR/Cas9 system enables a versatile set of genomes editing and genetic-based disease modeling tools due to its high specificity, efficiency, and accessible design and implementation. In cancer, the CRISPR/Cas9 system has been used to characterize genes and explore different mechanisms implicated in tumorigenesis. Different experimental strategies have been proposed in recent years, showing dependency on various intrinsic factors such as cancer type, gene function, mutation type, and technical approaches such as cell line, Cas9 expression, and transfection options. However, the successful methodological approaches, genes, and other experimental factors have not been analyzed. We, therefore, initially considered more than 1,300 research articles related to CRISPR/Cas9 in cancer to finally examine more than 400 full-text research publications. We summarize findings regarding target genes, RNA guide designs, cloning, Cas9 delivery systems, cell enrichment, and experimental validations. This analysis provides valuable information and guidance for future cancer gene validation experiments.
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Affiliation(s)
- Fernando Gonzalez-Salinas
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Claudia Martinez-Amador
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico; Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada avenue 2501, Monterrey, Nuevo Leon 64849, México.
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18
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La-Rostami F, Wax N, Druschka M, Adams E, Albert C, Fischer M. In Vitro CRISPR-Cpf1 Assay for Differentiation of Fine and Bulk Cocoa ( Theobroma cacao L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8819-8826. [PMID: 35786882 DOI: 10.1021/acs.jafc.2c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cocoa cultivation is dominated by the clone "Colleción Castro Naranjal 51" (CCN-51). In contrast, CCN-51 is the expensive and aromatic fine cocoa "Arriba Nacional" from Ecuador. The differences in the overall quality of the beans and in the prices show that it is necessary to develop a rapid and accurate method to distinguish these varieties and prevent food fraud. To this end, we used a CRISPR-Cpf1 assay suitable for AT-rich targets such as the chloroplast genome (cpGenome). SNPs in cocoa plastid genomes were selected to replace the canonical PAM sequence of Cpf1 (5'-TTTV-3'). We developed two assay systems to digest both Arriba and CCN-51. The results were tested qualitatively by agarose gel electrophoresis and quantitatively by capillary gel electrophoresis. Using the assay described here, we were able to reliably detect admixtures of 5% CCN-51 (P < 0.01) and 10% Arriba (P < 0.05). The application to processed cocoa products was also successful.
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Affiliation(s)
- Farshad La-Rostami
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nils Wax
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Michael Druschka
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Elena Adams
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Chenyang Albert
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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19
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Ferreira P, Choupina AB. CRISPR/Cas9 a simple, inexpensive and effective technique for gene editing. Mol Biol Rep 2022; 49:7079-7086. [PMID: 35716290 PMCID: PMC9206401 DOI: 10.1007/s11033-022-07442-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 04/01/2022] [Indexed: 11/27/2022]
Abstract
In recent years, the number of tools and techniques that enable genetic material to be added, removed or altered at specific locations in the genome has increased significantly. The objective is to know the structure of genomes, the function of genes and improve gene therapy.In this work we intend to explain the functioning of the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) and the advantages that this technique may have compared to previously developed techniques, such as RNA interference (RNAi), Zinc Finger Nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) in gene and genome editing.We will start with the story of the discovery, then its biological function in the adaptive immune system of bacteria against bacteriophage attack, and ending with a description of the mechanism of action and its use in gene editing. We will also discuss other Cas enzymes with great potential for use in genome editing as an alternative to Cas9.CRISPR/Cas9 is a simple, inexpensive, and effective technique for gene editing with multiple applications from the development of functional genomics and epigenetics. This technique will, in the near future, have great applications in the development of cell models for use in medical and pharmaceutical processes, in targeted therapy, and improvement of agricultural and environmental species.
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Affiliation(s)
- Patrick Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Altino Branco Choupina
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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Review of CRISPR-Cas Systems in Listeria Species: Current Knowledge and Perspectives. Int J Microbiol 2022; 2022:9829770. [PMID: 35502187 PMCID: PMC9056214 DOI: 10.1155/2022/9829770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/03/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Listeria spp. are pathogens widely distributed in the environment and Listeria monocytogenes is associated with food-borne illness in humans. Food facilities represent an adverse environment for this bacterium, mainly due to the disinfection and cleaning processes included in good hygiene practices, and its virulence is related to stress responses. One of the recently described stress-response systems is CRISPR-Cas. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes have been found in several bacteria. CRISPR-Cas has revolutionized biotechnology since it acts as an adaptive immune system of bacteria, which also helps in the evasion of the host immune response. There are three CRISPR systems described on Listeria species. Type II is present in many pathogenic bacteria and characterized by the presence of cas9 that becomes the main target of some anti-CRISPR proteins, such as AcrIIA1, encoded on Listeria phages. The presence of Cas9, either alone or in combination with anti-CRISPR proteins, suggests having a main role on the virulence of bacteria. In this review, we describe the most recent information on CRISPR-Cas systems in Listeria spp., particularly in L. monocytogenes, and their relationship with the virulence and pathogenicity of those bacteria. Besides, some applications of CRISPR systems and future challenges in the food processing industry, bacterial vaccination, antimicrobial resistance, pathogens biocontrol by phage therapy, and regulation of gene expression have been explored.
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21
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Hussain MS, Kumar M. Assembly of Cas7 subunits of Leptospira on the mature crRNA of CRISPR-Cas I-B is modulated by divalent ions. Gene X 2022; 818:146244. [PMID: 35074418 DOI: 10.1016/j.gene.2022.146244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/02/2023] Open
Abstract
The spirochete Leptospira interrogans serovar Copenhageni harbors the genetic elements of the CRISPR-Cas type I-B system in its genome. CRISPR-Cas is a CRISPR RNA (crRNA) mediated adaptive immune system in most prokaryotes against mobile genetic elements (MGEs). To eliminate the intruding MGEs, CRISPR-Cas type I systems utilize a Cascade (CRISPR-associated complex for antiviral defense) complex composed of Cas5, Cas6, Cas7, and Cas8 bound with a crRNA. The Cas7 is essentially known to constitute the major component of the Cascade complex. The present study reports the biochemical characterization of the Cas7 (LinCas7) from the CRISPR-Cas type I-B system of L. interrogans serovar Copenhageni. The pure recombinant LinCas7 (rLinCas7) exists as a monomer in the solution by size exclusion chromatography. The rLinCas7 demonstrates an endoDNase activity dependent upon divalent Mg2+ ions, monovalent ions, pH, temperature, and substrate size. Analysis of ribonucleoprotein composite (rLinCas7-crRNA) by electron microscopy and native-PAGE demonstrated that rLinCas7 could oligomerize on the mature CRISPR RNA (crRNA) framework in the presence of Mg2+ ions. The ribonucleoprotein composite attains a helical shape similar to the backbone of the Cascade complex. However, in the absence of Mg2+ ions, rLinCas7 acts as an RNase. The fluorescence spectroscopy disclosed a weak interaction (Kd = 26.81 mM) between rLinCas7 and Mg2+ ions, leading to an overall conformational change in rLinCas7 that modulates the rLinCas7's activity on DNA and RNA substrates. The nuclease activity of LinCas7 characterized in this study aids to the functional divergences among proteins of the Cas7 family from different CRISPR-Cas systems in various organisms.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India.
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22
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Happi Mbakam C, Lamothe G, Tremblay G, Tremblay JP. CRISPR-Cas9 Gene Therapy for Duchenne Muscular Dystrophy. Neurotherapeutics 2022; 19:931-941. [PMID: 35165856 PMCID: PMC9294086 DOI: 10.1007/s13311-022-01197-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/26/2022] Open
Abstract
Discovery of the CRISPR-Cas (clustered regularly interspaced short palindromic repeat, CRISPR-associated) system a decade ago has opened new possibilities in the field of precision medicine. CRISPR-Cas was initially identified in bacteria and archaea to play a protective role against foreign genetic elements during viral infections. The application of this technique for the correction of different mutations found in the Duchenne muscular dystrophy (DMD) gene led to the development of several potential therapeutic approaches for DMD patients. The mutations responsible for Duchenne muscular dystrophy mainly include exon deletions (70% of patients) and point mutations (about 30% of patients). The CRISPR-Cas 9 technology is becoming increasingly precise and is acquiring diverse functions through novel innovations such as base editing and prime editing. However, questions remain about its translation to the clinic. Current research addressing off-target editing, efficient muscle-specific delivery, immune response to nucleases, and vector challenges may eventually lead to the clinical use of the CRISPR-Cas9 technology. In this review, we present recent CRISPR-Cas9 strategies to restore dystrophin expression in vitro and in animal models of DMD.
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Affiliation(s)
- Cedric Happi Mbakam
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Gabriel Lamothe
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Guillaume Tremblay
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Jacques P Tremblay
- CHU de Québec Research Center - Laval University, Québec, Canada.
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada.
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23
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dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nat Cell Biol 2022; 24:268-278. [PMID: 35145221 PMCID: PMC8843813 DOI: 10.1038/s41556-021-00836-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022]
Abstract
Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering. Wang, Qu et al. developed a genome-editing system, utilizing catalytically inactive Cas9 fused to microbial single-strand annealing proteins, for kilobase-scale insertion in human cells without introducing DNA nicks or breaks.
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24
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Wang Y, Sang S, Zhang X, Tao H, Guan Q, Liu C. Efficient Genome Editing by a Miniature CRISPR-AsCas12f1 Nuclease in Bacillus anthracis. Front Bioeng Biotechnol 2022; 9:825493. [PMID: 35096801 PMCID: PMC8795892 DOI: 10.3389/fbioe.2021.825493] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/27/2021] [Indexed: 01/19/2023] Open
Abstract
A miniature CRISPR-Cas12f has been demonstrated to serve as an effective genome editing tool in gram negative bacteria as well as human cells. Here, we developed an alternative method to edit the genome of Bacillus anthracis based on the AsCas12f1 nuclease from Acidibacillus sulfuroxidans. When the htrA gene on the chromosome and the lef gene on the plasmid pXO1 were selected as targets, the CRISPR-AsCas12f1 system showed very high efficiency (100%). At the same time, a high efficiency was observed for large-fragment deletion. Our results also indicated that the length of the homologous arms of the donor DNA had a close relationship with the editing efficiency. Furthermore, a two-plasmid CRISPR-AsCas12f1 system was also constructed and combined with the endonuclease I-SceI for potential multi-gene modification. This represents a novel tool for mutant strain construction and gene function analyses in B. anthracis and other Bacillus cereus group bacteria.
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Affiliation(s)
| | | | | | | | | | - Chunjie Liu
- *Correspondence: Yanchun Wang, ; Chunjie Liu,
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25
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Chavez-Granados PA, Manisekaran R, Acosta-Torres LS, Garcia-Contreras R. CRISPR/Cas gene-editing technology and its advances in dentistry. Biochimie 2021; 194:96-107. [PMID: 34974144 DOI: 10.1016/j.biochi.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022]
Abstract
A recent discovery of revolutionary Clustered regularly interspaced palindromic repeats (CRISPR) is a gene-editing tool that provides a type of adaptive immunity in prokaryotic organisms, which is currently used as a revolutionizing tool in biomedical research. It has a mechanism of correcting genome errors, turning on/off genes in cells and organisms. Most importantly playing a crucial function in bacterial defence by identifying and destroying Deoxyribonucleic acid (DNA) segments during bacteriophage invasions since the CRISPR-associated protein 9 (Cas9) enzyme recognizes and cleaves invasive DNA sequences complementary to CRISPR. Therefore, researchers employ this biological device to manipulate the genes to develop new therapies to combat systemic diseases. Currently, the most significant advance at the laboratory level is the generation of cell and animal models, functional genomic screens, live images of the cell genome, and defective DNA repairs to find the cure for genetic disorders. Even though this technology has enormous biomedical applications in various sectors, this review will summarize CRISPR/Cas emphasizing both the therapeutic and diagnostic mechanisms developed in the field of dentistry and the promising attempts to transfer this technology to clinical application. Finally, future developments are also described, which proposes to use CRISPR/Cas systems for prospective clinical dentistry applications.
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Affiliation(s)
- Patricia Alejandra Chavez-Granados
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) León Unit, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684, León, Mexico
| | - Ravichandran Manisekaran
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) León Unit, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684, León, Mexico
| | - Laura Susana Acosta-Torres
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) León Unit, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684, León, Mexico
| | - Rene Garcia-Contreras
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) León Unit, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37684, León, Mexico.
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26
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Askoura M, Almalki AJ, Lila ASA, Almansour K, Alshammari F, Khafagy ES, Ibrahim TS, Hegazy WAH. Alteration of Salmonella enterica Virulence and Host Pathogenesis through Targeting sdiA by Using the CRISPR-Cas9 System. Microorganisms 2021; 9:microorganisms9122564. [PMID: 34946165 PMCID: PMC8707642 DOI: 10.3390/microorganisms9122564] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 01/31/2023] Open
Abstract
Salmonella enterica is a common cause of many enteric infections worldwide and is successfully engineered to deliver heterologous antigens to be used as vaccines. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) RNA-guided Cas9 endonuclease is a promising genome editing tool. In the current study, a CRISPR-Cas9 system was used to target S.enterica sdiA that encodes signal molecule receptor SdiA and responds to the quorum sensing (QS) signaling compounds N-acylhomoserine lactones (AHLs). For this purpose, sdiA was targeted in both S.enterica wild type (WT) and the ΔssaV mutant strain, where SsaV has been reported to be an essential component of SPI2-T3SS. The impact of sdiA mutation on S. enterica virulence was evaluated at both early invasion and later intracellular replication in both the presence and absence of AHL. Additionally, the influence of sdiA mutation on the pathogenesis S. enterica WT and mutants was investigated in vivo, using mice infection model. Finally, the minimum inhibitory concentrations (MICs) of various antibiotics against S. enterica strains were determined. Present findings show that mutation in sdiA significantly affects S.enterica biofilm formation, cell adhesion and invasion. However, sdiA mutation did not affect bacterial intracellular survival. Moreover, in vivo bacterial pathogenesis was markedly lowered in S.enterica ΔsdiA in comparison with the wild-type strain. Significantly, double-mutant sdiA and ssaV attenuated the S. enterica virulence and in vivo pathogenesis. Moreover, mutations in selected genes increased Salmonella susceptibility to tested antibiotics, as revealed by determining the MICs and MBICs of these antibiotics. Altogether, current results clearly highlight the importance of the CRISPR-Cas9 system as a bacterial genome editing tool and the valuable role of SdiA in S.enterica virulence. The present findings extend the understanding of virulence regulation and host pathogenesis of Salmonellaenterica.
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Affiliation(s)
- Momen Askoura
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Correspondence: (M.A.); (W.A.H.H.); Tel.: +20-1125226642 (M.A.); +20-1101188800 (W.A.H.H.)
| | - Ahmad J. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.J.A.); (T.S.I.)
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amr S. Abu Lila
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt;
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; (K.A.); (F.A.)
| | - Khaled Almansour
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; (K.A.); (F.A.)
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; (K.A.); (F.A.)
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia;
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia 41552, Egypt
| | - Tarek S. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.J.A.); (T.S.I.)
| | - Wael A. H. Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Correspondence: (M.A.); (W.A.H.H.); Tel.: +20-1125226642 (M.A.); +20-1101188800 (W.A.H.H.)
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27
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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28
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Verma AK, Mandal S, Tiwari A, Monachesi C, Catassi GN, Srivastava A, Gatti S, Lionetti E, Catassi C. Current Status and Perspectives on the Application of CRISPR/Cas9 Gene-Editing System to Develop a Low-Gluten, Non-Transgenic Wheat Variety. Foods 2021; 10:foods10102351. [PMID: 34681400 PMCID: PMC8534962 DOI: 10.3390/foods10102351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
Wheat gluten contains epitopes that trigger celiac disease (CD). A life-long strict gluten-free diet is the only treatment accepted for CD. However, very low-gluten wheat may provide an alternative treatment to CD. Conventional plant breeding methods have not been sufficient to produce celiac-safe wheat. RNA interference technology, to some extent, has succeeded in the development of safer wheat varieties. However, these varieties have multiple challenges in terms of their implementation. Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease 9 (CRISPR/Cas9) is a versatile gene-editing tool that has the ability to edit immunogenic gluten genes. So far, only a few studies have applied CRISPR/Cas9 to modify the wheat genome. In this article, we reviewed the published literature that applied CRISPR/Cas9 in wheat genome editing to investigate the current status of the CRISPR/Cas9 system to produce a low-immunogenic wheat variety. We found that in recent years, the CRISPR/Cas9 system has been continuously improved to edit the complex hexaploid wheat genome. Although some reduced immunogenic wheat varieties have been reported, CRISPR/Cas9 has still not been fully explored in terms of editing the wheat genome. We conclude that further studies are required to apply the CRISPR/Cas9 gene-editing system efficiently for the development of a celiac-safe wheat variety and to establish it as a "tool to celiac safe wheat".
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Affiliation(s)
- Anil K. Verma
- Celiac Disease Research Laboratory, Polytechnic University of Marche, 60123 Ancona, Italy;
- Correspondence: or ; Tel.: +39-0715962834
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, Maharashtra, India;
| | - Aadhya Tiwari
- Department of System Biology, MD Anderson Cancer Center, Houston, TX 77030, USA;
- Laboratory of Cell Biology, Department of Orthopaedic Surgery, University Hospital of Tübingen, Waldhörnlestraße 22, D-72072 Tübingen, Germany
| | - Chiara Monachesi
- Celiac Disease Research Laboratory, Polytechnic University of Marche, 60123 Ancona, Italy;
| | - Giulia N. Catassi
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Akash Srivastava
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02906, USA;
| | - Simona Gatti
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Elena Lionetti
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Carlo Catassi
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA 02114, USA
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29
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Kaligotla VSA, Jasti T, Kandra P. CRISPR/Cas9 in cancer: An attempt to the present trends and future prospects. Biotechnol Appl Biochem 2021; 69:1238-1251. [PMID: 34033692 DOI: 10.1002/bab.2200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/12/2021] [Indexed: 11/08/2022]
Abstract
Cancer is the second leading cause of death globally. Series of sequential, repeated genetic changes and epigenetic modifications are leading to the formation of tumors. These tumors subsequently causing the infected cells to invade and transform their surrounding cells by metastasis are some hallmarks in cancer. Although tremendous efforts have been extended for structurally characterizing the numerous genomic mutations undergoing in cancer cells, there is a lack of information regarding the functions of many mutated genes. Clustered Regularly Interspaced Short Palindromic repeats/CRISPR-associated nuclease 9 (CRISPR/Cas9) has become a robust method for building changes in genome of many organisms. Recent reports have suggested that modification of CRISPR/Cas9 can provide plot form to probe the mechanisms in tumorigenesis and in cancer therapies. This review focuses on the historical perspectives of CRISPR/Cas9. The study highlights the applications and also role in cancer cell genome editing, which is helpful to understand the dynamics. Intense research in progress on mechanism of action of CRISPR/Cas9 has been reviewed and critically discussed. Further, relevant literature on animal models focusing on various approaches has been highlighted to emphasize the therapeutics of CRISPR/Cas9 with current trends and future challenges.
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Affiliation(s)
| | - Tejaswi Jasti
- Department of Biotechnology, GITAM Institute of Technology, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, India
| | - Prameela Kandra
- Department of Biotechnology, GITAM Institute of Technology, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, India
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30
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Wang C, Cheng JKW, Zhang Q, Hughes NW, Xia Q, Winslow MM, Cong L. Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. Nucleic Acids Res 2021; 49:e36. [PMID: 33619540 PMCID: PMC8034634 DOI: 10.1093/nar/gkaa1264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/15/2022] Open
Abstract
Several existing technologies enable short genomic alterations including generating indels and short nucleotide variants, however, engineering more significant genomic changes is more challenging due to reduced efficiency and precision. Here, we developed RecT Editor via Designer-Cas9-Initiated Targeting (REDIT), which leverages phage single-stranded DNA-annealing proteins (SSAP) RecT for mammalian genome engineering. Relative to Cas9-mediated homology-directed repair (HDR), REDIT yielded up to a 5-fold increase of efficiency to insert kilobase-scale exogenous sequences at defined genomic regions. We validated our REDIT approach using different formats and lengths of knock-in templates. We further demonstrated that REDIT tools using Cas9 nickase have efficient gene-editing activities and reduced off-target errors, measured using a combination of targeted sequencing, genome-wide indel, and insertion mapping assays. Our experiments inhibiting repair enzyme activities suggested that REDIT has the potential to overcome limitations of endogenous DNA repair steps. Finally, our REDIT method is applicable across cell types including human stem cells, and is generalizable to different Cas9 enzymes.
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Affiliation(s)
- Chengkun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason K W Cheng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhe Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qiong Xia
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA
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31
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Leong SP, Witz IP, Sagi-Assif O, Izraely S, Sleeman J, Piening B, Fox BA, Bifulco CB, Martini R, Newman L, Davis M, Sanders LM, Haussler D, Vaske OM, Witte M. Cancer microenvironment and genomics: evolution in process. Clin Exp Metastasis 2021; 39:85-99. [PMID: 33970362 DOI: 10.1007/s10585-021-10097-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Cancer heterogeneity is a result of genetic mutations within the cancer cells. Their proliferation is not only driven by autocrine functions but also under the influence of cancer microenvironment, which consists of normal stromal cells such as infiltrating immune cells, cancer-associated fibroblasts, endothelial cells, pericytes, vascular and lymphatic channels. The relationship between cancer cells and cancer microenvironment is a critical one and we are just on the verge to understand it on a molecular level. Cancer microenvironment may serve as a selective force to modulate cancer cells to allow them to evolve into more aggressive clones with ability to invade the lymphatic or vascular channels to spread to regional lymph nodes and distant sites. It is important to understand these steps of cancer evolution within the cancer microenvironment towards invasion so that therapeutic strategies can be developed to control or stop these processes.
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Affiliation(s)
- Stanley P Leong
- California Pacific Medical Center and Research Institute, San Francisco, USA
| | - Isaac P Witz
- The Shmunis School of Biomedicine and Cancer Research, School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Orit Sagi-Assif
- The Shmunis School of Biomedicine and Cancer Research, School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Sivan Izraely
- The Shmunis School of Biomedicine and Cancer Research, School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan Sleeman
- European Center for Angioscience, Medizinische Fakultät Mannheim der Universität Heidelberg, Heidelberg, Germany
| | | | | | | | - Rachel Martini
- Department of Surgery, Weill Cornell Medical College, New York City, NY, USA.,Department of Genetics, University of Georgia, Athens, GA, USA
| | - Lisa Newman
- Department of Surgery, Weill Cornell Medical College, New York City, NY, USA
| | - Melissa Davis
- Department of Surgery, Weill Cornell Medical College, New York City, NY, USA.
| | - Lauren M Sanders
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz and UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, USA.
| | - Olena M Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz and UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | - Marlys Witte
- Department of Surgery, Neurosurgery and Pediatrics, University of Arizona College of Medicine-Tucson, Tucson, AZ, USA
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32
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Jervis AJ, Hanko EK, Dunstan MS, Robinson CJ, Takano E, Scrutton NS. A plasmid toolset for CRISPR-mediated genome editing and CRISPRi gene regulation in Escherichia coli. Microb Biotechnol 2021; 14:1120-1129. [PMID: 33710766 PMCID: PMC8085919 DOI: 10.1111/1751-7915.13780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
CRISPR technologies have become standard laboratory tools for genetic manipulations across all kingdoms of life. Despite their origins in bacteria, the development of CRISPR tools for engineering bacteria has been slower than for eukaryotes; nevertheless, their function and application for genome engineering and gene regulation via CRISPR interference (CRISPRi) has been demonstrated in various bacteria, and adoption has become more widespread. Here, we provide simple plasmid-based systems for genome editing (gene knockouts/knock-ins, and genome integration of large DNA fragments) and CRISPRi in E. coli using a CRISPR-Cas12a system. The described genome engineering protocols allow markerless deletion or genome integration in just seven working days with high efficiency (> 80% and 50%, respectively), and the CRISPRi protocols allow robust transcriptional repression of target genes (> 90%) with a single cloning step. The presented minimized plasmids and their associated design and experimental protocols provide efficient and effective CRISPR-Cas12 genome editing, genome integration and CRISPRi implementation. These simple-to-use systems and protocols will allow the easy adoption of CRISPR technology by any laboratory.
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Affiliation(s)
- Adrian J. Jervis
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Erik K.R. Hanko
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Mark S. Dunstan
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Christopher J. Robinson
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Eriko Takano
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Nigel S. Scrutton
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
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33
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Han P, Gu JQ, Li LS, Wang XY, Wang HT, Wang Y, Chang C, Sun JL. The Association Between Intestinal Bacteria and Allergic Diseases-Cause or Consequence? Front Cell Infect Microbiol 2021; 11:650893. [PMID: 33937097 PMCID: PMC8083053 DOI: 10.3389/fcimb.2021.650893] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
The incidence of allergic disorders has been increasing over the past few decades, especially in industrialized countries. Allergies can affect people of any age. The pathogenesis of allergic diseases is complex and involves genetic, epigenetic, and environmental factors, and the response to medication is very variable. For some patients, avoidance is the sole effective therapy, and only when the triggers are identifiable. In recent years, the intestinal microbiota has emerged as a significant contributor to the development of allergic diseases. However, the precise mechanisms related to the effects of the microbiome on the pathogenesis of allergic diseases are unknown. This review summarizes the recent association between allergic disorders and intestinal bacterial dysbiosis, describes the function of gut microbes in allergic disease development from both preclinical and clinical studies, discusses the factors that influence gut microbial diversity and advanced techniques used in microbial analysis. Ultimately, more studies are required to define the host-microbial relationship relevant to allergic disorders and amenable to new therapeutic interventions.
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Affiliation(s)
- Pei Han
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Jian-Qing Gu
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Sha Li
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Yan Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong-Tian Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States.,Division of Pediatric Immunology and Allergy, Joe DiMaggio Children's Hospital, Hollywood, FL, United States
| | - Jin-Lyu Sun
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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34
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Dailey KM, Allgood JE, Johnson PR, Ostlie MA, Schaner KC, Brooks BD, Brooks AE. The next frontier of oncotherapy: accomplishing clinical translation of oncolytic bacteria through genetic engineering. Future Microbiol 2021; 16:341-368. [PMID: 33754804 DOI: 10.2217/fmb-2020-0245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of a 'smart' drug capable of distinguishing tumor from host cells has been sought for centuries, but the microenvironment of solid tumors continues to confound therapeutics. Solid tumors present several challenges for current oncotherapeutics, including aberrant vascularization, hypoxia, necrosis, abnormally high pH and local immune suppression. While traditional chemotherapeutics are limited by such an environment, oncolytic microbes are drawn to it - having an innate ability to selectively infect, colonize and eradicate solid tumors. Development of an oncolytic species would represent a shift in the cancer therapeutic paradigm, with ramifications reaching from the medical into the socio-economic. Modern genetic engineering techniques could be implemented to customize 'Frankenstein' bacteria with advantageous characteristics from several species.
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Affiliation(s)
- Kaitlin M Dailey
- Cellular & Molecular Biology Program, North Dakota State University, Fargo, ND 58103, USA.,Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | - JuliAnne E Allgood
- Department of Neuroscience, University of Wyoming, Laramie, WY 82071, USA
| | - Paige R Johnson
- Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | - Mackenzie A Ostlie
- Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | - Kambri C Schaner
- Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | | | - Amanda E Brooks
- Cellular & Molecular Biology Program, North Dakota State University, Fargo, ND 58103, USA.,Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA.,Office of Research & Scholarly Activity. Rocky Vista University, Ivins, UT 84738, USA
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35
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Berkyurek AC, Furlan G, Lampersberger L, Beltran T, Weick E, Nischwitz E, Cunha Navarro I, Braukmann F, Akay A, Price J, Butter F, Sarkies P, Miska EA. The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription. EMBO J 2021; 40:e105565. [PMID: 33533030 PMCID: PMC7917558 DOI: 10.15252/embj.2020105565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 01/03/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate germ cell development and maintain germline integrity in many animals. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. piRNA biogenesis mechanisms are diverse and remain poorly understood. Here, we identify the RNA polymerase II (RNA Pol II) core subunit RPB-9 as required for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We show that rpb-9 initiates heritable piRNA-mediated gene silencing at two DNA transposon families and at a subset of somatic genes in the germline. We provide genetic and biochemical evidence that RPB-9 is required for piRNA biogenesis by recruiting the Integrator complex at piRNA genes, hence promoting transcriptional termination. We conclude that, as a part of its rapid evolution, the piRNA pathway has co-opted an ancient machinery for high-fidelity transcription.
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Affiliation(s)
- Ahmet C Berkyurek
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Giulia Furlan
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Lisa Lampersberger
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Toni Beltran
- MRC London Institute of Medical SciencesLondonUK
- Institute of Clinical SciencesImperial College LondonLondonUK
| | - Eva‐Maria Weick
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Present address:
Structural Biology ProgramSloan Kettering InstituteMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Emily Nischwitz
- Quantitative ProteomicsInstitute of Molecular BiologyMainzGermany
| | - Isabela Cunha Navarro
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Fabian Braukmann
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Alper Akay
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Present address:
School of Biological SciencesUniversity of East AngliaNorwich, NorfolkUK
| | - Jonathan Price
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Falk Butter
- Quantitative ProteomicsInstitute of Molecular BiologyMainzGermany
| | - Peter Sarkies
- MRC London Institute of Medical SciencesLondonUK
- Institute of Clinical SciencesImperial College LondonLondonUK
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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36
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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37
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Bloh K, Kanchana R, Bialk P, Banas K, Zhang Z, Yoo BC, Kmiec EB. Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data. CRISPR J 2021; 4:120-131. [PMID: 33571043 PMCID: PMC7898406 DOI: 10.1089/crispr.2020.0022] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
During CRISPR-directed gene editing, multiple gene repair mechanisms interact to produce a wide and largely unpredictable variety of sequence changes across an edited population of cells. Shortcomings inherent to previously available proposal-based insertion and deletion (indel) analysis software necessitated the development of a more comprehensive tool that could detect a larger range and variety of indels while maintaining the ease of use of tools currently available. To that end, we developed Deconvolution of Complex DNA Repair (DECODR). DECODR can detect indels formed from single or multi-guide CRISPR experiments without a limit on indel size. The software is accurate in determining the identities and positions of inserted and deleted bases in DNA extracts from both clonally expanded and bulk cell populations. The accurate identification and output of any potential indel allows for DECODR analysis to be executed in experiments utilizing potentially any configuration of donor DNA sequences, CRISPR-Cas, and endogenous DNA repair pathways.
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Affiliation(s)
- Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| | - Rohan Kanchana
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Pawel Bialk
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Kelly Banas
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| | - Zugui Zhang
- Value Institute, ChristianaCare, Newark, Delaware, USA
| | - Byung-Chun Yoo
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Eric B. Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
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38
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Cetin R, Quandt E, Kaulich M. Functional Genomics Approaches to Elucidate Vulnerabilities of Intrinsic and Acquired Chemotherapy Resistance. Cells 2021; 10:cells10020260. [PMID: 33525637 PMCID: PMC7912423 DOI: 10.3390/cells10020260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a commonly unavoidable consequence of cancer treatment that results in therapy failure and disease relapse. Intrinsic (pre-existing) or acquired resistance mechanisms can be drug-specific or be applicable to multiple drugs, resulting in multidrug resistance. The presence of drug resistance is, however, tightly coupled to changes in cellular homeostasis, which can lead to resistance-coupled vulnerabilities. Unbiased gene perturbations through RNAi and CRISPR technologies are invaluable tools to establish genotype-to-phenotype relationships at the genome scale. Moreover, their application to cancer cell lines can uncover new vulnerabilities that are associated with resistance mechanisms. Here, we discuss targeted and unbiased RNAi and CRISPR efforts in the discovery of drug resistance mechanisms by focusing on first-in-line chemotherapy and their enforced vulnerabilities, and we present a view forward on which measures should be taken to accelerate their clinical translation.
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Affiliation(s)
- Ronay Cetin
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany;
| | - Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Barcelona, Spain;
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)-69-6301-5450
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39
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Integration of diverse DNA substrates by a casposase can be targeted to R-loops in vitro by its fusion to Cas9. Biosci Rep 2021; 41:227184. [PMID: 33289517 PMCID: PMC7786333 DOI: 10.1042/bsr20203595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/18/2020] [Accepted: 12/03/2020] [Indexed: 12/17/2022] Open
Abstract
CRISPR systems build adaptive immunity against mobile genetic elements by DNA capture and integration catalysed by Cas1–Cas2 protein complexes. Recent studies suggested that CRISPR repeats and adaptation module originated from a novel type of DNA transposons called casposons. Casposons encode a Cas1 homologue called casposase that alone integrates into target molecules single and double-stranded DNA containing terminal inverted repeats (TIRs) from casposons. A recent study showed Methanosarcina mazei casposase is able to integrate random DNA oligonucleotides, followed up in this work using Acidoprofundum boonei casposase, from which we also observe promiscuous substrate integration. Here we first show that the substrate flexibility of Acidoprofundum boonei casposase extends to random integration of DNA without TIRs, including integration of a functional gene. We then used this to investigate targeting of the casposase-catalysed DNA integration reactions to specific DNA sites that would allow insertion of defined DNA payloads. Casposase–Cas9 fusions were engineered that were catalytically proficient in vitro and generated RNA-guided DNA integration products from short synthetic DNA or a gene, with or without TIRs. However, DNA integration could still occur unguided due to the competing background activity of the casposase moiety. Expression of Casposase-dCas9 in Escherichia coli cells effectively targeted chromosomal and plasmid lacZ revealed by reduced β-galactosidase activity but DNA integration was not detected. The promiscuous substrate integration properties of casposases make them potential DNA insertion tools. The Casposase–dCas9 fusion protein may serves as a prototype for development in genetic editing for DNA insertion that is independent of homology-directed DNA repair.
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40
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Generation of mouse conditional knockout alleles in one step using the i-GONAD method. Genome Res 2020; 31:121-130. [PMID: 33328166 PMCID: PMC7849380 DOI: 10.1101/gr.265439.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
The Cre/loxP system is a powerful tool for gene function study in vivo. Regulated expression of Cre recombinase mediates precise deletion of genetic elements in a spatially– and temporally–controlled manner. Despite the robustness of this system, it requires a great amount of effort to create a conditional knockout model for each individual gene of interest where two loxP sites must be simultaneously inserted in cis. The current undertaking involves labor-intensive embryonic stem (ES) cell–based gene targeting and tedious micromanipulations of mouse embryos. The complexity of this workflow poses formidable technical challenges, thus limiting wider applications of conditional genetics. Here, we report an alternative approach to generate mouse loxP alleles by integrating a unique design of CRISPR donor with the new oviduct electroporation technique i-GONAD. Showing the potential and simplicity of this method, we created floxed alleles for five genes in one attempt with relatively low costs and a minimal equipment setup. In addition to the conditional alleles, constitutive knockout alleles were also obtained as byproducts of these experiments. Therefore, the wider applications of i-GONAD may promote gene function studies using novel murine models.
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41
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Abstract
Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost on a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies, allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here, we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission. Stable associations between insects and bacterial species are widespread in nature. This is the case for many economically important insects, such as tsetse flies. Tsetse flies are the vectors of Trypanosoma brucei, the etiological agent of African trypanosomiasis—a zoonotic disease that incurs a high socioeconomic cost in regions of endemicity. Populations of tsetse flies are often infected with the bacterium Sodalis glossinidius. Following infection, S. glossinidius establishes a chronic, stable association characterized by vertical (maternal) and horizontal (paternal) modes of transmission. Due to the stable nature of this association, S. glossinidius has been long sought as a means for the implementation of anti-Trypanosoma paratransgenesis in tsetse flies. However, the lack of tools for the genetic modification of S. glossinidius has hindered progress in this area. Here, we establish that S. glossinidius is amenable to DNA uptake by conjugation. We show that conjugation can be used as a DNA delivery method to conduct forward and reverse genetic experiments in this bacterium. This study serves as an important step in the development of genetic tools for S. glossinidius. The methods highlighted here should guide the implementation of genetics for the study of the tsetse-Sodalis association and the evaluation of S. glossinidius-based tsetse fly paratransgenesis strategies. IMPORTANCE Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost on a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies, allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here, we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission.
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42
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Fernandez-Garcia L, Pacios O, González-Bardanca M, Blasco L, Bleriot I, Ambroa A, López M, Bou G, Tomás M. Viral Related Tools against SARS-CoV-2. Viruses 2020; 12:E1172. [PMID: 33081350 PMCID: PMC7589879 DOI: 10.3390/v12101172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.
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Affiliation(s)
- Laura Fernandez-Garcia
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Olga Pacios
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Mónica González-Bardanca
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Lucia Blasco
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Inés Bleriot
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Antón Ambroa
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - María López
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - German Bou
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
| | - Maria Tomás
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
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Zhan H, Li A, Cai Z, Huang W, Liu Y. Improving transgene expression and CRISPR-Cas9 efficiency with molecular engineering-based molecules. Clin Transl Med 2020; 10:e194. [PMID: 33135339 PMCID: PMC7533053 DOI: 10.1002/ctm2.194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/08/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
As a novel and robust gene‐editing tool, the Clustered Regularly Interspaced Short Palindromic Repeats CRISPR‐associated protein 9 (CRISPR‐Cas9) system has revolutionized gene therapy. Plasmid vector delivery is the most commonly used method for integrating the CRISPR‐Cas9 system into cells. However, such foreign cytosolic DNAs trigger an innate immune response (IIR) within cells, which can hinder gene editing by inhibiting transgene expression. Although some small molecules have been shown to avoid the action of IIR on plasmids, they only work on a single target and may also affect cell viability. A genetic approach that works at a comprehensive level for manipulating IIR is still lacking. Here, we designed and constructed several artificial nucleic acid molecules (ANAMs), which are combinations of aptamers binding to two key players of IIR (β‐catenin and NF‐κB). ANAMs strongly inhibited the IIR in cells, thus improving transgene expression. We also used ANAMs to improve the gene‐editing efficiency of the CRISPR‐Cas9 system and its derivatives, thus enhancing the apoptosis of cancer cells induced by CRISPR‐Cas9. ANAMs can be valuable tools for improving transgene expression and gene editing in mammalian cells.
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Affiliation(s)
- Hengji Zhan
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Aolin Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhiming Cai
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Weiren Huang
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
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Abstract
Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to this ultimate goal through their ability to deliver a double-strand break (DSB) to a precise target location in various species, obsoleting the preceding editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). The derivative technology, base editing, combines the catalytically inactivated Cas nuclease and nucleotide deaminase and mediates the genetic modifications at single-nucleotide precision without introducing a DSB. Moreover, the cytosine base editors (CBEs) are able to transform multiple codons into stop codons, rapidly inactivating a gene of interest and enabling loss-of-function study in some recombination-deficient species. Here, we present the CRISPR-CBEI tool kit to assist the design of sgRNAs for CBE-mediated gene inactivation. Base editing is a promising technique, allowing precise single-base mutagenesis in genomes without double-strand DNA breaks or donor templates. Cytosine base editors (CBEs) convert cytosine to thymidine. In particular, CBEs can transform four codons, CAA, CAG, CGA, and TGG, into stop codons, providing a new means to rapidly inactivate a gene of interest and enabling loss-of-function study in recombination-deficient species and the construction of gene-inactivation libraries. However, designing single guide RNAs (sgRNAs) for gene inactivation is more complicated and more restricted in applicability than using the lustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (CRISPR/Cas9) system only, especially for researchers who do not specialize in the bioinformatics skills needed to design and evaluate sgRNAs. Here, we present a new user-friendly designing tool kit, namely, CRISPR-CBEI (cytosine base editor-mediated gene inactivation), including a Web tool and a command-line tool. The Web tool is dedicated to the design of sgRNAs for CBE-mediated gene inactivation and integrates various functions, including open reading frame (ORF) identification, CBE customization, sgRNA designing, summarizing, and front-end off-target searching against user-defined unlimited-file-size local genome files without the necessity of uploading to the server. The command-line version serves the same purpose but for a larger number of coding DNA sequences (CDSs), for instance, for designing a CBE-inactivation library in a target species which provides comprehensive evaluations of CBEs and target genomes. We envision that this tool would contribute to CBE-inactivation design. IMPORTANCE Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to this ultimate goal through their ability to deliver a double-strand break (DSB) to a precise target location in various species, obsoleting the preceding editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). The derivative technology, base editing, combines the catalytically inactivated Cas nuclease and nucleotide deaminase and mediates the genetic modifications at single-nucleotide precision without introducing a DSB. Moreover, the cytosine base editors (CBEs) are able to transform multiple codons into stop codons, rapidly inactivating a gene of interest and enabling loss-of-function study in some recombination-deficient species. Here, we present the CRISPR-CBEI tool kit to assist the design of sgRNAs for CBE-mediated gene inactivation.
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Gayet RV, de Puig H, English MA, Soenksen LR, Nguyen PQ, Mao AS, Angenent-Mari NM, Collins JJ. Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release. Nat Protoc 2020; 15:3030-3063. [PMID: 32807909 DOI: 10.1038/s41596-020-0367-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/28/2020] [Indexed: 02/08/2023]
Abstract
Materials that sense and respond to biological signals in their environment have a broad range of potential applications in drug delivery, medical devices and diagnostics. Nucleic acids are important biological cues that encode information about organismal identity and clinically relevant phenotypes such as drug resistance. We recently developed a strategy to design nucleic acid-responsive materials using the CRISPR-associated nuclease Cas12a as a user-programmable sensor and material actuator. This approach improves on the sensitivity of current DNA-responsive materials while enabling their rapid repurposing toward new sequence targets. Here, we provide a comprehensive resource for the design, synthesis and actuation of CRISPR-responsive hydrogels. First, we provide guidelines for the synthesis of Cas12a guide RNAs (gRNAs) for in vitro applications. We then outline methods for the synthesis of both polyethylene glycol-DNA (PEG-DNA) and polyacrylamide-DNA (PA-DNA) hydrogels, as well as their controlled degradation using Cas12a for the release of cargos, including small molecules, enzymes, nanoparticles and living cells within hours. Finally, we detail the design and assembly of microfluidic paper-based devices that use Cas12a-sensitive hydrogels to convert DNA inputs into a variety of visual and electronic readouts for use in diagnostics. Following the initial validation of the gRNA and Cas12a components (1 d), the synthesis and testing of either PEG-DNA or PA-DNA hydrogels require 3-4 d of laboratory time. Optional extensions, including the release of primary human cells or the design of the paper-based diagnostic, require an additional 2-3 d each.
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Affiliation(s)
- Raphael V Gayet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena de Puig
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max A English
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luis R Soenksen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Angelo S Mao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Nicolaas M Angenent-Mari
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA.
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Effect of connective tissue growth factor gene editing using adeno-associated virus-mediated CRISPR-Cas9 on rabbit glaucoma filtering surgery outcomes. Gene Ther 2020; 28:277-286. [PMID: 32541929 DOI: 10.1038/s41434-020-0166-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 05/19/2020] [Accepted: 06/03/2020] [Indexed: 01/16/2023]
Abstract
Suppressing excessive wound healing responses is critical to ensure surgical success in glaucoma filtration surgery (GFS). Currently used adjunctive materials can lead to side effects due to the nonselectivity in cell inhibition and may require repeated applications. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system may become a compelling opportunity in glaucoma surgery due to its high selectivity and permanent effect. Connective tissue growth factor (CTGF) is one of the most potent stimulators of tissue fibrosis in the eye. Therefore, we tested the effect of CTGF suppression using the CRISPR-Cas9 system on GFS fibrosis. We used an adeno-associated virus (AAV)-CRISPR-Cas9 system and confirmed successful CTGF suppression was achieved in fibroblasts in vitro through western blot analysis and deep sequencing. In the in vivo intereye-comparison rabbit GFS model, CRISPR-CTGF-treated eyes showed significantly better survival of the surgery site, less subconjunctival fibrosis, limited collagen deposition, and reduced cellularity than untreated eyes. Our results suggest a new possibility of CRISPR-Cas9-mediated CTGF suppression to improve human GFS outcomes.
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Francisella novicida CRISPR-Cas Systems Can Functionally Complement Each Other in DNA Defense while Providing Target Flexibility. J Bacteriol 2020; 202:JB.00670-19. [PMID: 32284320 DOI: 10.1128/jb.00670-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/11/2020] [Indexed: 01/03/2023] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems that facilitate protection of bacteria and archaea against infection by external mobile genetic elements. The model pathogen Francisella novicida encodes a CRISPR-Cas12a (FnoCas12a) system and a CRISPR-Cas9 (FnoCas9) system, the latter of which has an additional and noncanonical function in bacterial virulence. Here, we investigated and compared the functional roles of the FnoCas12a and FnoCas9 systems in transformation inhibition and bacterial virulence. Unlike FnoCas9, FnoCas12a was not required for F. novicida virulence. However, both systems were highly effective at plasmid restriction and acted independently of each other. We further identified a critical protospacer-adjacent motif (PAM) necessary for transformation inhibition by FnoCas12a, demonstrating a greater flexibility for target identification by FnoCas12a than previously appreciated and a specificity that is distinct from that of FnoCas9. The effectors of the two systems exhibited different patterns of expression at the mRNA level, suggesting that they may confer distinct benefits to the bacterium in diverse environments. These data suggest that due to the differences between the two CRISPR-Cas systems, together they may provide F. novicida with a more comprehensive defense against foreign nucleic acids. Finally, we demonstrated that the FnoCas12a and FnoCas9 machineries could be simultaneously engineered to restrict the same nonnative target, thereby expanding the toolset for prokaryotic genome manipulation.IMPORTANCE CRISPR-Cas9 and CRISPR-Cas12a systems have been widely commandeered for genome engineering. However, they originate in prokaryotes, where they function as adaptive immune systems. The details of this activity and relationship between these systems within native host organisms have been minimally explored. The human pathogen Francisella novicida contains both of these systems, with the Cas9 system also exhibiting a second activity, modulating virulence through transcriptional regulation. We compared and contrasted the ability of these two systems to control virulence and restrict DNA within their native host bacterium, highlighting differences and similarities in these two functions. Collectively, our results indicate that these two distinct and reprogrammable endogenous systems provide F. novicida with a more comprehensive defense against mobile genetic elements.
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48
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Bai Y, Mansell TJ. Production and Sensing of Butyrate in a Probiotic Escherichia coli Strain. Int J Mol Sci 2020; 21:ijms21103615. [PMID: 32443851 PMCID: PMC7279287 DOI: 10.3390/ijms21103615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The short-chain fatty acid butyrate plays critical roles in human gut health, affecting immunomodulation, cell differentiation, and apoptosis, while also serving as the preferred carbon source for colon cells. In this work, we have engineered a model probiotic organism, Escherichia coli Nissle 1917 (EcN, serotype O6:K5:H1), to produce butyrate from genomic loci up to approximately 1 g/L (11 mM). Then, for real-time monitoring of butyrate production in cultures, we developed a high-throughput biosensor that responds to intracellular butyrate concentrations, with green fluorescent protein as the reporter. This work provides a foundation for studies of butyrate for therapeutic applications.
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Taagen E, Bogdanove AJ, Sorrells ME. Counting on Crossovers: Controlled Recombination for Plant Breeding. TRENDS IN PLANT SCIENCE 2020; 25:455-465. [PMID: 31959421 DOI: 10.1016/j.tplants.2019.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 05/02/2023]
Abstract
Crossovers (COs), that drive genetic exchange between homologous chromosomes, are strongly biased toward subtelomeric regions in plant species. Manipulating the rate and positions of COs to increase the genetic variation accessible to breeders is a longstanding goal. Use of genome editing reagents that induce double-stranded breaks (DSBs) or modify the epigenome at desired sites of recombination, and manipulation of CO factors, are increasingly applicable approaches for achieving this goal. These strategies for 'controlled recombination' have potential to reduce the time and expense associated with traditional breeding, reveal currently inaccessible genetic diversity, and increase control over the inheritance of preferred haplotypes. Considerable challenges to address include translating knowledge from models to crop species and determining the best stages of the breeding cycle at which to control recombination.
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Affiliation(s)
- Ella Taagen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Yang YC, Chen YH, Kao JH, Ching C, Liu IJ, Wang CC, Tsai CH, Wu FY, Liu CJ, Chen PJ, Chen DS, Yang HC. Permanent Inactivation of HBV Genomes by CRISPR/Cas9-Mediated Non-cleavage Base Editing. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 20:480-490. [PMID: 32278307 PMCID: PMC7150432 DOI: 10.1016/j.omtn.2020.03.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Current antiviral therapy fails to cure chronic hepatitis B virus (HBV) infection because of persistent covalently closed circular DNA (cccDNA). CRISPR/Cas9-mediated specific cleavage of cccDNA is a potentially curative strategy for chronic hepatitis B (CHB). However, the CRISPR/Cas system inevitably targets integrated HBV DNA and induces double-strand breaks (DSBs) of host genome, bearing the risk of genomic rearrangement and damage. Herein, we examined the utility of recently developed CRISPR/Cas-mediated "base editors" (BEs) in inactivating HBV gene expression without cleavage of DNA. Candidate target sites of the SpCas9-derived BE and its variants in HBV genomes were screened for generating nonsense mutations of viral genes with individual guide RNAs (gRNAs). SpCas9-BE with certain gRNAs effectively base-edited polymerase and surface genes and reduced HBV gene expression in cells harboring integrated HBV genomes, but induced very few insertions or deletions (indels). Interestingly, some point mutations introduced by base editing resulted in simultaneous suppression of both polymerase and surface genes. Finally, the episomal cccDNA was successfully edited by SpCas9-BE for suppression of viral gene expression in an in vitro HBV infection system. In conclusion, Cas9-mediated base editing is a potential strategy to cure CHB by permanent inactivation of integrated HBV DNA and cccDNA without DSBs of the host genome.
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Affiliation(s)
- Yu-Chan Yang
- Department of Microbiology, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hsiang Chen
- Department of Microbiology, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Research, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi Ching
- Department of Microbiology, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Jung Liu
- Department of Nursing, Cardinal Tien Junior College of Healthcare and Management, New Taipei City, Taiwan
| | - Chih-Chiang Wang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-Hsueh Tsai
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Fang-Yi Wu
- Department of Microbiology, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jen Liu
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Research, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Research, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ding-Shinn Chen
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Research, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Chih Yang
- Department of Microbiology, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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