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Manghrani A, Rangadurai AK, Szekely O, Liu B, Guseva S, Al-Hashimi HM. Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594415. [PMID: 38798635 PMCID: PMC11118333 DOI: 10.1101/2024.05.15.594415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The propensities to form lowly-populated short-lived conformations of DNA could vary with sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging. Using 1 H CEST and 13 C R 1ρ NMR, we measured Watson-Crick to Hoogsteen dynamics for an A-T base pair in thirteen trinucleotide sequence contexts. The Hoogsteen population and exchange rate varied 4-fold and 16-fold, respectively, and were dependent on both the 3'- and 5'-neighbors but only weakly dependent on monovalent ion concentration (25 versus 100 mM NaCl) and pH (6.8 versus 8.0). Flexible TA and CA dinucleotide steps exhibited the highest Hoogsteen populations, and their kinetics rates strongly depended on the 3'-neighbor. In contrast, the stiffer AA and GA steps had the lowest Hoogsteen population, and their kinetics were weakly dependent on the 3'-neighbor. The Hoogsteen lifetime was especially short when G-C neighbors flanked the A-T base pair. The Hoogsteen dynamics had a distinct sequence-dependence compared to duplex stability and minor groove width. Thus, our results uncover a unique source of sequence-specificity hidden within the DNA double helix in the form of A-T Hoogsteen dynamics and establish the utility of 1 H CEST to quantitively measure sequence-dependent DNA dynamics.
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2
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Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, Roukos V. Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol 2024:10.1038/s41587-024-02238-8. [PMID: 38740992 DOI: 10.1038/s41587-024-02238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Cas9 can cleave DNA in both blunt and staggered configurations, resulting in distinct editing outcomes, but what dictates the type of Cas9 incisions is largely unknown. In this study, we developed BreakTag, a versatile method for profiling Cas9-induced DNA double-strand breaks (DSBs) and identifying the determinants of Cas9 incisions. Overall, we assessed cleavage by SpCas9 at more than 150,000 endogenous on-target and off-target sites targeted by approximately 3,500 single guide RNAs. We found that approximately 35% of SpCas9 DSBs are staggered, and the type of incision is influenced by DNA:gRNA complementarity and the use of engineered Cas9 variants. A machine learning model shows that Cas9 incision is dependent on the protospacer sequence and that human genetic variation impacts the configuration of Cas9 cuts and the DSB repair outcome. Matched datasets of Cas9 and engineered variant incisions with repair outcomes show that Cas9-mediated staggered breaks are linked with precise, templated and predictable single-nucleotide insertions, demonstrating that a scission-based gRNA design can be used to correct clinically relevant pathogenic single-nucleotide deletions.
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Affiliation(s)
| | - Sergi Sayols
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Andriana G Kotini
- Department of Biology, Medical School, University of Patras, Patras, Greece
| | - Sabine Heinen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Johannes Gutenberg University (JGU), Mainz, Germany
| | - Vassilis Roukos
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Department of Biology, Medical School, University of Patras, Patras, Greece.
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3
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Zhang C, Xu J, Wu Y, Xu C, Xu P. Base Editors-Mediated Gene Therapy in Hematopoietic Stem Cells for Hematologic Diseases. Stem Cell Rev Rep 2024:10.1007/s12015-024-10715-5. [PMID: 38644403 DOI: 10.1007/s12015-024-10715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
Base editors, developed from the CRISPR/Cas system, consist of components such as deaminase and Cas variants. Since their emergence in 2016, the precision, efficiency, and safety of base editors have been gradually optimized. The feasibility of using base editors in gene therapy has been demonstrated in several disease models. Compared with the CRISPR/Cas system, base editors have shown great potential in hematopoietic stem cells (HSCs) and HSC-based gene therapy, because they do not generate double-stranded breaks (DSBs) while achieving the precise realization of single-base substitutions. This precise editing mechanism allows for the permanent correction of genetic defects directly at their source within HSCs, thus promising a lasting therapeutic effect. Recent advances in base editors are expected to significantly increase the number of clinical trials for HSC-based gene therapies. In this review, we summarize the development and recent progress of DNA base editors, discuss their applications in HSC gene therapy, and highlight the prospects and challenges of future clinical stem cell therapies.
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Affiliation(s)
- Chengpeng Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jinchao Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yikang Wu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Can Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Peng Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China.
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4
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Ho BX, Teo AKK, Ng NHJ. Innovations in bio-engineering and cell-based approaches to address immunological challenges in islet transplantation. Front Immunol 2024; 15:1375177. [PMID: 38650946 PMCID: PMC11033429 DOI: 10.3389/fimmu.2024.1375177] [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: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 04/25/2024] Open
Abstract
Human allogeneic pancreatic islet transplantation is a life-changing treatment for patients with severe Type 1 Diabetes (T1D) who suffer from hypoglycemia unawareness and high risk of severe hypoglycemia. However, intensive immunosuppression is required to prevent immune rejection of the graft, that may in turn lead to undesirable side effects such as toxicity to the islet cells, kidney toxicity, occurrence of opportunistic infections, and malignancies. The shortage of cadaveric human islet donors further limits islet transplantation as a treatment option for widespread adoption. Alternatively, porcine islets have been considered as another source of insulin-secreting cells for transplantation in T1D patients, though xeno-transplants raise concerns over the risk of endogenous retrovirus transmission and immunological incompatibility. As a result, technological advancements have been made to protect transplanted islets from immune rejection and inflammation, ideally in the absence of chronic immunosuppression, to improve the outcomes and accessibility of allogeneic islet cell replacement therapies. These include the use of microencapsulation or macroencapsulation devices designed to provide an immunoprotective environment using a cell-impermeable layer, preventing immune cell attack of the transplanted cells. Other up and coming advancements are based on the use of stem cells as the starting source material for generating islet cells 'on-demand'. These starting stem cell sources include human induced pluripotent stem cells (hiPSCs) that have been genetically engineered to avoid the host immune response, curated HLA-selected donor hiPSCs that can be matched with recipients within a given population, and multipotent stem cells with natural immune privilege properties. These strategies are developed to provide an immune-evasive cell resource for allogeneic cell therapy. This review will summarize the immunological challenges facing islet transplantation and highlight recent bio-engineering and cell-based approaches aimed at avoiding immune rejection, to improve the accessibility of islet cell therapy and enhance treatment outcomes. Better understanding of the different approaches and their limitations can guide future research endeavors towards developing more comprehensive and targeted strategies for creating a more tolerogenic microenvironment, and improve the effectiveness and sustainability of islet transplantation to benefit more patients.
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Affiliation(s)
- Beatrice Xuan Ho
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- BetaLife Pte Ltd, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Natasha Hui Jin Ng
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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Xiang M, Li H, Zhan Y, Ma D, Gao Q, Fang Y. Functional CRISPR screens in T cells reveal new opportunities for cancer immunotherapies. Mol Cancer 2024; 23:73. [PMID: 38581063 PMCID: PMC10996278 DOI: 10.1186/s12943-024-01987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
T cells are fundamental components in tumour immunity and cancer immunotherapies, which have made immense strides and revolutionized cancer treatment paradigm. However, recent studies delineate the predicament of T cell dysregulation in tumour microenvironment and the compromised efficacy of cancer immunotherapies. CRISPR screens enable unbiased interrogation of gene function in T cells and have revealed functional determinators, genetic regulatory networks, and intercellular interactions in T cell life cycle, thereby providing opportunities to revamp cancer immunotherapies. In this review, we briefly described the central roles of T cells in successful cancer immunotherapies, comprehensively summarised the studies of CRISPR screens in T cells, elaborated resultant master genes that control T cell activation, proliferation, fate determination, effector function, and exhaustion, and highlighted genes (BATF, PRDM1, and TOX) and signalling cascades (JAK-STAT and NF-κB pathways) that extensively engage in multiple branches of T cell responses. In conclusion, this review bridged the gap between discovering element genes to a specific process of T cell activities and apprehending these genes in the global T cell life cycle, deepened the understanding of T cell biology in tumour immunity, and outlined CRISPR screens resources that might facilitate the development and implementation of cancer immunotherapies in the clinic.
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Affiliation(s)
- Minghua Xiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huayi Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yong Fang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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6
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Szekely O, Rangadurai AK, Gu S, Manghrani A, Guseva S, Al-Hashimi HM. NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing. Nucleic Acids Res 2024; 52:2672-2685. [PMID: 38281263 PMCID: PMC10954477 DOI: 10.1093/nar/gkae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024] Open
Abstract
Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T-/U-) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU- formed with a ten-fold higher propensity relative to dT-·rG and dG·dT- and this could be attributed to the lower pKa (ΔpKa ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson-Crick-like G·U- could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
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Affiliation(s)
- Or Szekely
- Department of Biology, Duke University, Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27710, USA
| | | | - Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Serafima Guseva
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
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7
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Botwe G, Fang X, Mukhtar YM, Zhou Y, Tang H, Wang M, Zhang J, Fu M, Jiang P, Gu J, Zhang X. Circular RNAs as biomarkers and therapeutic targets for gastrointestinal cancers. J Gastroenterol Hepatol 2024. [PMID: 38504413 DOI: 10.1111/jgh.16536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/03/2024] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
Circular RNAs are a class of noncoding RNAs with covalently linked 5' and 3' ends that arise from backsplicing events. The absence of a 5' cap and a 3' poly(A) tail makes circular RNAs relatively more stable than their linear counterparts. They are evolutionary conserved and tissue-specific, and some show disease-specific expression patterns. Although their biological functions remain largely unknown, circular RNAs have been shown to play regulatory roles by acting as microRNA sponges, regulators of RNA-binding proteins, alternative splicing, and parental gene expression, and they could even encode proteins. Over the past few decades, circular RNAs have attracted wide attention in oncology owing to their implications in various tumors. Many circular RNAs have been characterized as key players in gastrointestinal cancers and influence cancer growth, progression, metastasis, and therapeutic resistance. Accumulating evidence reveals that their unique characteristics, coupled with their critical roles in tumorigenesis, make circular RNAs promising non-invasive clinical biomarkers for gastrointestinal cancers. In the present review, we summarized the biological roles of the emerging circular RNAs and their potential as biomarkers and therapeutic targets, which may help better understand their clinical significance in the management of gastrointestinal cancers.
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Affiliation(s)
- Godwin Botwe
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinjian Fang
- Department of Oncology, Gaochun Hospital Affiliated to Jiangsu University, Nanjing, Jiangsu, China
| | - Yusif Mohammed Mukhtar
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yue Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haozhou Tang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Maoye Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jiahui Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Fu
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Pengcheng Jiang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jianmei Gu
- Department of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xu Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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8
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Widney KA, Yang DD, Rusch LM, Copley SD. CRISPR-Cas9-assisted genome editing in E. coli elevates the frequency of unintended mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.584922. [PMID: 38562785 PMCID: PMC10983943 DOI: 10.1101/2024.03.19.584922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cas-assisted lambda Red recombineering techniques have rapidly become a mainstay of bacterial genome editing. Such techniques have been used to construct both individual mutants and massive libraries to assess the effects of genomic changes. We have found that a commonly used Cas9-assisted editing method results in unintended mutations elsewhere in the genome in 26% of edited clones. The unintended mutations are frequently found over 200 kb from the intended edit site and even over 10 kb from potential off-target sites. We attribute the high frequency of unintended mutations to error-prone polymerases expressed in response to dsDNA breaks introduced at the edit site. Most unintended mutations occur in regulatory or coding regions and thus may have phenotypic effects. Our findings highlight the risks associated with genome editing techniques involving dsDNA breaks in E. coli and likely other bacteria and emphasize the importance of sequencing the genomes of edited cells to ensure the absence of unintended mutations.
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Affiliation(s)
- Karl A. Widney
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Dong-Dong Yang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Leo M. Rusch
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
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9
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Xu F, Zheng C, Xu W, Zhang S, Liu S, Chen X, Yao K. Breaking genetic shackles: The advance of base editing in genetic disorder treatment. Front Pharmacol 2024; 15:1364135. [PMID: 38510648 PMCID: PMC10953296 DOI: 10.3389/fphar.2024.1364135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The rapid evolution of gene editing technology has markedly improved the outlook for treating genetic diseases. Base editing, recognized as an exceptionally precise genetic modification tool, is emerging as a focus in the realm of genetic disease therapy. We provide a comprehensive overview of the fundamental principles and delivery methods of cytosine base editors (CBE), adenine base editors (ABE), and RNA base editors, with a particular focus on their applications and recent research advances in the treatment of genetic diseases. We have also explored the potential challenges faced by base editing technology in treatment, including aspects such as targeting specificity, safety, and efficacy, and have enumerated a series of possible solutions to propel the clinical translation of base editing technology. In conclusion, this article not only underscores the present state of base editing technology but also envisions its tremendous potential in the future, providing a novel perspective on the treatment of genetic diseases. It underscores the vast potential of base editing technology in the realm of genetic medicine, providing support for the progression of gene medicine and the development of innovative approaches to genetic disease therapy.
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Affiliation(s)
- Fang Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Caiyan Zheng
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shiyao Zhang
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shanshan Liu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaopeng Chen
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
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10
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Sandler SE, Weckman NE, Yorke S, Das A, Chen K, Gutierrez R, Keyser UF. Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores. Nat Biomed Eng 2024; 8:325-334. [PMID: 37550424 DOI: 10.1038/s41551-023-01078-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/30/2023] [Indexed: 08/09/2023]
Abstract
Single-molecule quantification of the strength and sequence specificity of interactions between proteins and nucleic acids would facilitate the probing of protein-DNA binding. Here we show that binding events between the catalytically inactive Cas9 ribonucleoprotein and any pre-defined short sequence of double-stranded DNA can be identified by sensing changes in ionic current as suitably designed barcoded linear DNA nanostructures with Cas9-binding double-stranded DNA overhangs translocate through solid-state nanopores. We designed barcoded DNA nanostructures to study the relationships between DNA sequence and the DNA-binding specificity, DNA-binding efficiency and DNA-mismatch tolerance of Cas9 at the single-nucleotide level. Nanopore-based sensing of DNA-barcoded nanostructures may help to improve the design of efficient and specific ribonucleoproteins for biomedical applications, and could be developed into sensitive protein-sensing assays.
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Affiliation(s)
- Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Nicole E Weckman
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Institute for Studies in Transdisciplinary Engineering Education & Practice, Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
| | - Sarah Yorke
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, Cambridge, UK
| | - Akashaditya Das
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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11
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Sun X, Liang C, Chen Y, Cui T, Han J, Dai M, Zhang Y, Zhou Q, Li W. Knockout and Replacement Gene Surgery to Treat Rhodopsin-Mediated Autosomal Dominant Retinitis Pigmentosa. Hum Gene Ther 2024; 35:151-162. [PMID: 38368562 DOI: 10.1089/hum.2023.201] [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: 02/19/2024] Open
Abstract
Mutations in the rhodopsin (RHO) gene are the predominant causes of autosomal dominant retinitis pigmentosa (adRP). Given the diverse gain-of-function mutations, therapeutic strategies targeting specific sequences face significant challenges. Here, we provide a universal approach to conquer this problem: we have devised a CRISPR-Cas12i-based, mutation-independent gene knockout and replacement compound therapy carried by a dual AAV2/8 system. In this study, we successfully delayed the progression of retinal degeneration in the classic mouse disease model RhoP23H, and also RhoP347S, a new native mouse mutation model we developed. Our research expands the horizon of potential options for future treatments of RHO-mediated adRP.
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Affiliation(s)
- Xuehan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China; and
| | - Chen Liang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China; and
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jiabao Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China; and
| | - Moyu Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China; and
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China; and
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China; and
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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12
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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13
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Berríos KN, Barka A, Gill J, Serrano JC, Bailer PF, Parker JB, Evitt NH, Gajula KS, Shi J, Kohli RM. Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Res 2024; 52:2078-2090. [PMID: 38261989 PMCID: PMC10899762 DOI: 10.1093/nar/gkae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding of how Cas9 and DNA deaminases collaborate to shape base editor (BE) outcomes has been lacking. Here, we support a novel mechanistic model of base editing by deriving a range of hyperactive activation-induced deaminase (AID) base editors (hBEs) and exploiting their characteristic diversifying activity. Our model involves multiple layers of previously underappreciated cooperativity in BE steps including: (i) Cas9 binding can potentially expose both DNA strands for 'capture' by the deaminase, a feature that is enhanced by guide RNA mismatches; (ii) after strand capture, the intrinsic activity of the DNA deaminase can tune window size and base editing efficiency; (iii) Cas9 defines the boundaries of editing on each strand, with deamination blocked by Cas9 binding to either the PAM or the protospacer and (iv) non-canonical edits on the guide RNA bound strand can be further elicited by changing which strand is nicked by Cas9. Leveraging insights from our mechanistic model, we create novel hBEs that can remarkably generate simultaneous C > T and G > A transitions over >65 bp with significant potential for targeted gene diversification.
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Affiliation(s)
- Kiara N Berríos
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aleksia Barka
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jasleen Gill
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juan C Serrano
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter F Bailer
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jared B Parker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Niklaus H Evitt
- Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kiran S Gajula
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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14
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Zhang Y, Wu ZY. Gene therapy for monogenic disorders: challenges, strategies, and perspectives. J Genet Genomics 2024; 51:133-143. [PMID: 37586590 DOI: 10.1016/j.jgg.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Monogenic disorders refer to a group of human diseases caused by mutations in single genes. While disease-modifying therapies have offered some relief from symptoms and delayed progression for some monogenic diseases, most of these diseases still lack effective treatments. In recent decades, gene therapy has emerged as a promising therapeutic strategy for genetic disorders. Researchers have developed various gene manipulation tools and gene delivery systems to treat monogenic diseases. Despite this progress, concerns about inefficient delivery, persistent expression, immunogenicity, toxicity, capacity limitation, genomic integration, and limited tissue specificity still need to be addressed. This review gives an overview of commonly used gene therapy and delivery tools, along with the challenges they face and potential strategies to counter them.
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Affiliation(s)
- Yi Zhang
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang 310009, China
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang 310009, China.
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15
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Evmenov K, Pustogarov N, Panteleev D, Safin A, Alkalaeva E. An Efficient Expression and Purification Protocol for SpCas9 Nuclease and Evaluation of Different Delivery Methods of Ribonucleoprotein. Int J Mol Sci 2024; 25:1622. [PMID: 38338898 PMCID: PMC10855156 DOI: 10.3390/ijms25031622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system is a revolutionary tool for precise genome editing across various cell types. Ribonucleoproteins (RNPs), encompassing the Cas9 protein and guide RNA (gRNA), have emerged as a promising technique due to their increased specificity and reduced off-target effects. This method eliminates the need for plasmid DNA introduction, thereby preventing potential integration of foreign DNA into the target cell genome. Given the requirement for large quantities of highly purified protein in various Cas9 studies, we present an efficient and simple method for the preparation of recombinant Streptococcus pyogenes Cas9 (SpCas9) protein. This method leverages the Small Ubiquitin Like Modifier(SUMO) tag system, which includes metal-affinity chromatography followed by anion-exchange chromatography purification. Furthermore, we compare two methods of CRISPR-Cas9 system delivery into cells: transfection with plasmid DNA encoding the CRISPR-Cas9 system and RNP transfection with the Cas9-gRNA complex. We estimate the efficiency of genomic editing and protein lifespan post-transfection. Intriguingly, we found that RNP treatment of cells, even in the absence of a transfection system, is a relatively efficient method for RNP delivery into cell culture. This discovery is particularly promising as it can significantly reduce cytotoxicity, which is crucial for certain cell cultures such as induced pluripotent stem cells (iPSCs).
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Affiliation(s)
- Konstantin Evmenov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (K.E.); (N.P.)
| | - Nikolay Pustogarov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (K.E.); (N.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Dmitri Panteleev
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia;
| | - Artur Safin
- Department of Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (K.E.); (N.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
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16
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Molina Vargas A, Sinha S, Osborn R, Arantes P, Patel A, Dewhurst S, Hardy D, Cameron A, Palermo G, O’Connell M. New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity. Nucleic Acids Res 2024; 52:921-939. [PMID: 38033324 PMCID: PMC10810210 DOI: 10.1093/nar/gkad1132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
An increasingly pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are sensitive, fast, and inexpensive, and that can be deployed at point-of-care. Recently, the RNA-guided ribonuclease CRISPR-Cas13 has been successfully harnessed for such purposes. However, developing assays for detection of genetic variability, for example single-nucleotide polymorphisms, is still challenging and previously described design strategies are not always generalizable. Here, we expanded our characterization of LbuCas13a RNA-detection specificity by performing a combination of experimental RNA mismatch tolerance profiling, molecular dynamics simulations, protein, and crRNA engineering. We found certain positions in the crRNA-target-RNA duplex that are particularly sensitive to mismatches and establish the effect of RNA concentration in mismatch tolerance. Additionally, we determined that shortening the crRNA spacer or modifying the direct repeat of the crRNA leads to stricter specificities. Furthermore, we harnessed our understanding of LbuCas13a allosteric activation pathways through molecular dynamics and structure-guided engineering to develop novel Cas13a variants that display increased sensitivities to single-nucleotide mismatches. We deployed these Cas13a variants and crRNA design strategies to achieve superior discrimination of SARS-CoV-2 strains compared to wild-type LbuCas13a. Together, our work provides new design criteria and Cas13a variants to use in future easier-to-implement Cas13-based RNA detection applications.
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Affiliation(s)
- Adrian M Molina Vargas
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Souvik Sinha
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Raven Osborn
- Clinical and Translational Sciences Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Amun Patel
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Stephen Dewhurst
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Dwight J Hardy
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Mitchell R O’Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
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17
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Yaish O, Malle A, Cohen E, Orenstein Y. SWOffinder: Efficient and versatile search of CRISPR off-targets with bulges by Smith-Waterman alignment. iScience 2024; 27:108557. [PMID: 38169993 PMCID: PMC10758973 DOI: 10.1016/j.isci.2023.108557] [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: 10/25/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
CRISPR/Cas9 technology is revolutionizing the field of gene editing. While this technology enables the targeting of any gene, it may also target unplanned loci, termed off-target sites (OTS), which are a few mismatches, insertions, and deletions from the target. While existing methods for finding OTS up to a given mismatch threshold are efficient, other methods considering insertions and deletions are limited by long runtimes, incomplete OTS lists, and partial support of versatile thresholds. Here, we developed SWOffinder, an efficient method based on Smith-Waterman alignment to find all OTS up to some edit distance. We implemented an original trace-back approach to find OTS under versatile criteria, such as separate limits on the number of insertions, deletions, and mismatches. Compared to state-of-the-art methods, only SWOffinder finds all OTS in the genome in just a few minutes. SWOffinder enables accurate and efficient genomic search of OTS, which will lead to safer gene editing.
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Affiliation(s)
- Ofir Yaish
- School of Electrical and Computer Engineering, Ben-Gurion University the Negev, Beer Sheba 8410501, Israel
| | - Amichai Malle
- School of Electrical and Computer Engineering, Ben-Gurion University the Negev, Beer Sheba 8410501, Israel
| | - Eliav Cohen
- School of Electrical and Computer Engineering, Ben-Gurion University the Negev, Beer Sheba 8410501, Israel
| | - Yaron Orenstein
- Department of Computer Science, Bar-Ilan University, Ramat Gan 5290002, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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18
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Badon IW, Oh Y, Kim HJ, Lee SH. Recent application of CRISPR-Cas12 and OMEGA system for genome editing. Mol Ther 2024; 32:32-43. [PMID: 37952084 PMCID: PMC10787141 DOI: 10.1016/j.ymthe.2023.11.013] [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: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
In 2012, it was discovered that precise gene editing could be induced in target DNA using the reprogrammable characteristics of the CRISPR system. Since then, several studies have investigated the potential of the CRISPR system to edit various biological organisms. For the typical CRISPR system obtained from bacteria and archaea, many application studies have been conducted and have spread to various fields. To date, orthologs with various characteristics other than CRISPR-Cas9 have been discovered and are being intensively studied in the field of gene editing. CRISPR-Cas12 and its varied orthologs are representative examples of genome editing tools and have superior properties in terms of in vivo target gene editing compared with Cas9. Recently, TnpB and Fanzor of the OMEGA (obligate mobile element guided activity) system were identified to be the ancestor of CRISPR-Cas12 on the basis of phylogenetic analysis. Notably, the compact sizes of Cas12 and OMEGA endonucleases allow adeno-associated virus (AAV) delivery; hence, they are set to challenge Cas9 for in vivo gene therapy. This review is focused on these RNA-guided reprogrammable endonucleases: their structure, biochemistry, off-target effects, and applications in therapeutic gene editing.
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Affiliation(s)
- Isabel Wen Badon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ho-Joong Kim
- Department of Chemistry, Chosun University, Gwangju 61452, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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19
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Becker HJ, Yamazaki S. Understanding genetic heterogeneity in gene-edited hematopoietic stem cell products. Exp Hematol 2024; 129:104133. [PMID: 38036097 DOI: 10.1016/j.exphem.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
CRISPR/Cas gene editing has transformed genetic research and is poised to drive the next generation of gene therapies targeting hematopoietic stem cells (HSCs). However, the installation of the "desired" edit is most often only achieved in a minor subset of alleles. The array of cellular pathways triggered by gene editing tools produces a broad spectrum of "undesired" editing outcomes, including short insertions and deletions (indels) and chromosome rearrangements, leading to considerable genetic heterogeneity in gene-edited HSC populations. This heterogeneity may undermine the effect of the genetic intervention since only a subset of cells will carry the intended modification. Also, undesired mutations represent a potential safety concern as gene editing advances toward broader clinical use. Here, we will review the different sources of "undesired" edits and will discuss strategies for their mitigation and control.
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Affiliation(s)
- Hans Jiro Becker
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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20
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Lee Y, Oh Y, Lee SH. Recent advances in genome engineering by CRISPR technology. BMB Rep 2024; 57:12-18. [PMID: 38053294 PMCID: PMC10828434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 12/07/2023] Open
Abstract
Due to the development of CRISPR technology, the era of effective editing of target genes has arrived. However, the offtarget problem that occurs when recognizing target DNA due to the inherent nature of CRISPR components remains the biggest task to be overcome in the future. In this review, the principle of inducing such unintended off-target editing is analyzed from the structural aspect of CRISPR, and the methodology that has been developed to reduce off-target editing until now is summarized. [BMB Reports 2024; 57(1): 12-18].
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Affiliation(s)
- Youngsik Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
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21
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Karpov DS, Sosnovtseva AO, Pylina SV, Bastrich AN, Petrova DA, Kovalev MA, Shuvalova AI, Eremkina AK, Mokrysheva NG. Challenges of CRISPR/Cas-Based Cell Therapy for Type 1 Diabetes: How Not to Engineer a "Trojan Horse". Int J Mol Sci 2023; 24:17320. [PMID: 38139149 PMCID: PMC10743607 DOI: 10.3390/ijms242417320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Type 1 diabetes mellitus (T1D) is an autoimmune disease caused by the destruction of insulin-producing β-cells in the pancreas by cytotoxic T-cells. To date, there are no drugs that can prevent the development of T1D. Insulin replacement therapy is the standard care for patients with T1D. This treatment is life-saving, but is expensive, can lead to acute and long-term complications, and results in reduced overall life expectancy. This has stimulated the research and development of alternative treatments for T1D. In this review, we consider potential therapies for T1D using cellular regenerative medicine approaches with a focus on CRISPR/Cas-engineered cellular products. However, CRISPR/Cas as a genome editing tool has several drawbacks that should be considered for safe and efficient cell engineering. In addition, cellular engineering approaches themselves pose a hidden threat. The purpose of this review is to critically discuss novel strategies for the treatment of T1D using genome editing technology. A well-designed approach to β-cell derivation using CRISPR/Cas-based genome editing technology will significantly reduce the risk of incorrectly engineered cell products that could behave as a "Trojan horse".
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Affiliation(s)
- Dmitry S. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (A.O.S.); (M.A.K.); (A.I.S.)
| | - Anastasiia O. Sosnovtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (A.O.S.); (M.A.K.); (A.I.S.)
| | - Svetlana V. Pylina
- Endocrinology Research Centre, 115478 Moscow, Russia; (S.V.P.); (A.N.B.); (D.A.P.); (A.K.E.)
| | - Asya N. Bastrich
- Endocrinology Research Centre, 115478 Moscow, Russia; (S.V.P.); (A.N.B.); (D.A.P.); (A.K.E.)
| | - Darya A. Petrova
- Endocrinology Research Centre, 115478 Moscow, Russia; (S.V.P.); (A.N.B.); (D.A.P.); (A.K.E.)
| | - Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (A.O.S.); (M.A.K.); (A.I.S.)
| | - Anastasija I. Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (A.O.S.); (M.A.K.); (A.I.S.)
| | - Anna K. Eremkina
- Endocrinology Research Centre, 115478 Moscow, Russia; (S.V.P.); (A.N.B.); (D.A.P.); (A.K.E.)
| | - Natalia G. Mokrysheva
- Endocrinology Research Centre, 115478 Moscow, Russia; (S.V.P.); (A.N.B.); (D.A.P.); (A.K.E.)
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22
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Chen Q, Chuai G, Zhang H, Tang J, Duan L, Guan H, Li W, Li W, Wen J, Zuo E, Zhang Q, Liu Q. Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints. Nat Commun 2023; 14:7521. [PMID: 37980345 PMCID: PMC10657421 DOI: 10.1038/s41467-023-42695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/19/2023] [Indexed: 11/20/2023] Open
Abstract
The powerful CRISPR genome editing system is hindered by its off-target effects, and existing computational tools achieved limited performance in genome-wide off-target prediction due to the lack of deep understanding of the CRISPR molecular mechanism. In this study, we propose to incorporate molecular dynamics (MD) simulations in the computational analysis of CRISPR system, and present CRISOT, an integrated tool suite containing four related modules, i.e., CRISOT-FP, CRISOT-Score, CRISOT-Spec, CRISORT-Opti for RNA-DNA molecular interaction fingerprint generation, genome-wide CRISPR off-target prediction, sgRNA specificity evaluation and sgRNA optimization of Cas9 system respectively. Our comprehensive computational and experimental tests reveal that CRISOT outperforms existing tools with extensive in silico validations and proof-of-concept experimental validations. In addition, CRISOT shows potential in accurately predicting off-target effects of the base editors and prime editors, indicating that the derived RNA-DNA molecular interaction fingerprint captures the underlying mechanisms of RNA-DNA interaction among distinct CRISPR systems. Collectively, CRISOT provides an efficient and generalizable framework for genome-wide CRISPR off-target prediction, evaluation and sgRNA optimization for improved targeting specificity in CRISPR genome editing.
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Affiliation(s)
- Qinchang Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Haihang Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jin Tang
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Liwen Duan
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Huan Guan
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Wenhui Li
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Wannian Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiaying Wen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Qing Zhang
- Roche R&D Center (China) Ltd., China Innovation Center of Roche, Shanghai, 201203, China.
- Ailomics Therapeutics, Shanghai, 201203, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
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23
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O’Brien A, Bauer DC, Burgio G. Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning. PLoS One 2023; 18:e0292924. [PMID: 37847697 PMCID: PMC10581463 DOI: 10.1371/journal.pone.0292924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas technology has revolutionized many fields in biology. Beyond Cas9 nucleases, Cas12a (formerly Cpf1) has emerged as a promising alternative to Cas9 for editing AT-rich genomes. Despite the promises, guide RNA efficiency prediction through computational tools search still lacks accuracy. Through a computational meta-analysis, here we report that Cas12a target and off-target cleavage behavior are a factor of nucleotide bias combined with nucleotide mismatches relative to the protospacer adjacent motif (PAM) site. These features helped to train a Random Forest machine learning model to improve the accuracy by at least 15% over existing algorithms to predict guide RNA efficiency for the Cas12a enzyme. Despite the progresses, our report underscores the need for more representative datasets and further benchmarking to reliably and accurately predict guide RNA efficiency and off-target effects for Cas12a enzymes.
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Affiliation(s)
- Aidan O’Brien
- Division of Genome Science and Cancer and The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research (CSIRO) Health and Biosecurity, Adelaide, SA, Australia
| | - Denis C. Bauer
- Commonwealth Scientific and Industrial Research (CSIRO) Health and Biosecurity, Adelaide, SA, Australia
- Faculty of Medicine and Health Science, Department of Biomedical Sciences, Macquarie University, Macquarie Park, Australia
- Faculty of Science and Engineering, Applied BioSciences, Macquarie University, Macquarie Park, Australia
| | - Gaetan Burgio
- Division of Genome Science and Cancer and The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
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24
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Newton MD, Losito M, Smith QM, Parnandi N, Taylor BJ, Akcakaya P, Maresca M, van Eijk P, Reed SH, Boulton SJ, King GA, Cuomo ME, Rueda DS. Negative DNA supercoiling induces genome-wide Cas9 off-target activity. Mol Cell 2023; 83:3533-3545.e5. [PMID: 37802026 DOI: 10.1016/j.molcel.2023.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/30/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an important consideration for therapeutic applications. We have previously shown that force-stretching DNA induces off-target activity and hypothesized that distortions of the DNA topology in vivo, such as negative DNA supercoiling, could reduce Cas9 specificity. Using single-molecule optical-tweezers, we demonstrate that negative supercoiling λ-DNA induces sequence-specific Cas9 off-target binding at multiple sites, even at low forces. Using an adapted CIRCLE-seq approach, we detect over 10,000 negative-supercoiling-induced Cas9 off-target double-strand breaks genome-wide caused by increased mismatch tolerance. We further demonstrate in vivo that directed local DNA distortion increases off-target activity in cells and that induced off-target events can be detected during Cas9 genome editing. These data demonstrate that Cas9 off-target activity is regulated by DNA topology in vitro and in vivo, suggesting that cellular processes, such as transcription and replication, could induce off-target activity at previously overlooked sites.
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Affiliation(s)
- Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK; DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Marialucrezia Losito
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK; Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Quentin M Smith
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK
| | - Nishita Parnandi
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Benjamin J Taylor
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Patrick van Eijk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4AW, UK
| | - Simon H Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4AW, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
| | | | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK.
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25
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Molugu K, Khajanchi N, Lazzarotto CR, Tsai SQ, Saha K. Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells. CRISPR J 2023; 6:473-485. [PMID: 37676985 PMCID: PMC10611976 DOI: 10.1089/crispr.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Genome-edited human-induced pluripotent stem cells (iPSCs) have broad applications in disease modeling, drug discovery, and regenerative medicine. Despite the development of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system, the gene editing process is inefficient and can take several weeks to months to generate edited iPSC clones. We developed a strategy to improve the efficiency of the iPSC gene editing process via application of a small-molecule, trichostatin A (TSA), a Class I and II histone deacetylase inhibitor. We observed that TSA decreased global chromatin condensation and further resulted in increased gene-editing efficiency of iPSCs by twofold to fourfold while concurrently ensuring no increased off-target effects. The edited iPSCs could be clonally expanded while maintaining genomic integrity and pluripotency. The rapid generation of therapeutically relevant gene-edited iPSCs could be enabled by these findings.
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Affiliation(s)
- Kaivalya Molugu
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Namita Khajanchi
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Biomedical and Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Biomedical and Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and St Jude Children's Research Hospital, Memphis, Tennessee, USA
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26
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Khan A, Paneerselvam N, Lawson BR. Antiretrovirals to CCR5 CRISPR/Cas9 gene editing - A paradigm shift chasing an HIV cure. Clin Immunol 2023; 255:109741. [PMID: 37611838 PMCID: PMC10631514 DOI: 10.1016/j.clim.2023.109741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
The evolution of drug-resistant viral strains and anatomical and cellular reservoirs of HIV pose significant clinical challenges to antiretroviral therapy. CCR5 is a coreceptor critical for HIV host cell fusion, and a homozygous 32-bp gene deletion (∆32) leads to its loss of function. Interestingly, an allogeneic HSCT from an HIV-negative ∆32 donor to an HIV-1-infected recipient demonstrated a curative approach by rendering the recipient's blood cells resistant to viral entry. Ex vivo gene editing tools, such as CRISPR/Cas9, hold tremendous promise in generating allogeneic HSC grafts that can potentially replace allogeneic ∆32 HSCTs. Here, we review antiretroviral therapeutic challenges, clinical successes, and failures of allogeneic and allogeneic ∆32 HSCTs, and newer exciting developments within CCR5 editing using CRISPR/Cas9 in the search to cure HIV.
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Affiliation(s)
- Amber Khan
- The Scintillon Research Institute, 6868 Nancy Ridge Drive, San Diego, CA 92121, USA
| | | | - Brian R Lawson
- The Scintillon Research Institute, 6868 Nancy Ridge Drive, San Diego, CA 92121, USA.
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27
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Hryhorowicz M, Lipiński D, Zeyland J. Evolution of CRISPR/Cas Systems for Precise Genome Editing. Int J Mol Sci 2023; 24:14233. [PMID: 37762535 PMCID: PMC10532350 DOI: 10.3390/ijms241814233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
The bacteria-derived CRISPR/Cas (an acronym for regularly interspaced short palindromic repeats/CRISPR-associated protein) system is currently the most widely used, versatile, and convenient tool for genome engineering. CRISPR/Cas-based technologies have been applied to disease modeling, gene therapies, transcriptional modulation, and diagnostics. Nevertheless, some challenges remain, such as the risk of immunological reactions or off-target effects. To overcome these problems, many new methods and CRISPR/Cas-based tools have been developed. In this review, we describe the current classification of CRISPR systems and new precise genome-editing technologies, summarize the latest applications of this technique in several fields of research, and, finally, discuss CRISPR/Cas system limitations, ethical issues, and challenges.
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Affiliation(s)
- Magdalena Hryhorowicz
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (D.L.); (J.Z.)
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28
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Goldberg GW, Kogenaru M, Keegan S, Haase MAB, Kagermazova L, Arias MA, Onyebeke K, Adams S, Fenyö D, Noyes MB, Boeke JD. Engineered transcription-associated Cas9 targeting in eukaryotic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558319. [PMID: 37781609 PMCID: PMC10541143 DOI: 10.1101/2023.09.18.558319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT). Engineered TraCT is enabled when suboptimal PAM interactions limit basal activity in vivo and when one or more nascent RNA substrates are still tethered to the actively transcribing target DNA in cis. We further show that this phenomenon can be exploited for selective editing at one of two identical targets in distinct gene loci, or, in diploid allelic loci that are differentially transcribed. Our work demonstrates that temporal control over Cas9's targeting activity at specific DNA sites may be engineered without modifying Cas9's core domains and guide RNA components or their expression levels. More broadly, it establishes RNA binding in cis as a mechanism that can conditionally stimulate CRISPR-Cas DNA targeting in eukaryotes.
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Affiliation(s)
- Gregory W. Goldberg
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Manjunatha Kogenaru
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Denotes equivalent contribution to the work
| | - Max A. B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Denotes equivalent contribution to the work
| | - Larisa Kagermazova
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mauricio A. Arias
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Kenenna Onyebeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Samantha Adams
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Marcus B. Noyes
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn NY 11201
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29
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Kulcsár PI, Tálas A, Ligeti Z, Tóth E, Rakvács Z, Bartos Z, Krausz SL, Welker Á, Végi VL, Huszár K, Welker E. A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets. Nat Commun 2023; 14:5746. [PMID: 37717069 PMCID: PMC10505190 DOI: 10.1038/s41467-023-41393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/04/2023] [Indexed: 09/18/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) has been employed as a genome engineering tool with a promising potential within therapeutics. However, its off-target effects present major safety concerns for applications requiring high specificity. Approaches developed to date to mitigate this effect, including any of the increased-fidelity (i.e., high-fidelity) SpCas9 variants, only provide efficient editing on a relatively small fraction of targets without detectable off-targets. Upon addressing this problem, we reveal a rather unexpected cleavability ranking of target sequences, and a cleavage rule that governs the on-target and off-target cleavage of increased-fidelity SpCas9 variants but not that of SpCas9-NG or xCas9. According to this rule, for each target, an optimal variant with matching fidelity must be identified for efficient cleavage without detectable off-target effects. Based on this insight, we develop here an extended set of variants, the CRISPRecise set, with increased fidelity spanning across a wide range, with differences in fidelity small enough to comprise an optimal variant for each target, regardless of its cleavability ranking. We demonstrate efficient editing with maximum specificity even on those targets that have not been possible in previous studies.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zsófia Rakvács
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zsuzsa Bartos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Ágnes Welker
- Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Vanessza Laura Végi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary.
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30
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination. Nucleic Acids Res 2023; 51:8730-8743. [PMID: 37522352 PMCID: PMC10484686 DOI: 10.1093/nar/gkad636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The finding sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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Affiliation(s)
- Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Kevin G Liu
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Aleique Allen
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Jiang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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31
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Bestas B, Wimberger S, Degtev D, Madsen A, Rottner AK, Karlsson F, Naumenko S, Callahan M, Touza JL, Francescatto M, Möller CI, Badertscher L, Li S, Cerboni S, Selfjord N, Ericson E, Gordon E, Firth M, Chylinski K, Taheri-Ghahfarokhi A, Bohlooly-Y M, Snowden M, Pangalos M, Nuttall B, Akcakaya P, Sienski G, Maresca M. A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo. Nat Commun 2023; 14:5474. [PMID: 37673883 PMCID: PMC10482872 DOI: 10.1038/s41467-023-41240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes.
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Affiliation(s)
- Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dmitrii Degtev
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Alexandra Madsen
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Antje K Rottner
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Sergey Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - Megan Callahan
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Julia Liz Touza
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Margherita Francescatto
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Carl Ivar Möller
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Niklas Selfjord
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Elke Ericson
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | | | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Snowden
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Barrett Nuttall
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Grzegorz Sienski
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
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32
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Li Y, Cooper BH, Liu Y, Wu D, Zhang X, Rohs R, Qin PZ. CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid. Biochemistry 2023; 62:2541-2548. [PMID: 37552860 PMCID: PMC10578059 DOI: 10.1021/acs.biochem.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
CRISPR-Cas9 has been adapted as a readily programmable genome manipulation agent, and continuing technological advances rely on an in-depth mechanistic understanding of Cas9 target discrimination. Cas9 interrogates a target by unwinding the DNA duplex to form an R-loop, where the RNA guide hybridizes with one of the DNA strands. It has been shown that RNA guides shorter than the normal length of 20-nucleotide (-nt) support Cas9 cleavage activity by enabling partial unwinding beyond the RNA/DNA hybrid. To investigate whether DNA segment beyond the RNA/DNA hybrid can impact Cas9 target discrimination with truncated guides, Cas9 double-stranded DNA cleavage rates (kcat) were measured with 16-nt guides on targets with varying sequences at +17 to +20 positions distal to the protospacer-adjacent-motif (PAM). The data reveal a log-linear inverse correlation between kcat and the PAM+(17-20) DNA duplex dissociation free energy (ΔGNN(17-20)0), with sequences having smaller ΔGNN(17-20)0 showing faster cleavage and a higher degree of unwinding. The results indicate that, with a 16-nt guide, "peripheral" DNA sequences beyond the RNA/DNA hybrid contribute to target discrimination by tuning the cleavage reaction transition state through the modulation of PAM-distal unwinding. The finding provides mechanistic insights for the further development of strategies that use RNA guide truncation to enhance Cas9 specificity.
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Affiliation(s)
- Yue Li
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Brendon H Cooper
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Yukang Liu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Difei Wu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Szekely O, Rangadurai AK, Gu S, Manghrani A, Guseva S, Al-Hashimi HM. NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: Implications for the fidelity of transcription and CRISPR/Cas9 gene editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554670. [PMID: 37662220 PMCID: PMC10473728 DOI: 10.1101/2023.08.24.554670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G•T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R 1ρ experiments, we show that dG•rU and dT•rG mismatches in two RNA:DNA hybrids transiently form tautomeric (G enol •T/U ⇄G•T enol /U enol ) and anionic (G•T - /U - ) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG•rU - formed with a ten-fold higher propensity relative to dT - •rG and dG•dT - and this could be attributed to the lower pK a (Δ pK a ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G•T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G•U versus G•T, and indicate that anionic Watson-Crick-like G•U - could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
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Vargas AMM, Osborn R, Sinha S, Arantes PR, Patel A, Dewhurst S, Palermo G, O'Connell MR. New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550755. [PMID: 37547020 PMCID: PMC10402140 DOI: 10.1101/2023.07.26.550755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are sensitive, fast, and inexpensive, and that can be deployed at point-of-care. Recently, the RNA-guided ribonuclease CRISPR-Cas13 has been successfully harnessed for such purposes. However, developing assays for detection of genetic variability, for example single-nucleotide polymorphisms, is still challenging and previously described design strategies are not always generalizable. Here, we expanded our characterization of LbuCas13a RNA-detection specificity by performing a combination of experimental RNA mismatch tolerance profiling, molecular dynamics simulations, protein, and crRNA engineering. We found certain positions in the crRNA-target-RNA duplex that are particularly sensitive to mismatches and establish the effect of RNA concentration in mismatch tolerance. Additionally, we determined that shortening the crRNA spacer or modifying the direct repeat of the crRNA leads to stricter specificities. Furthermore, we harnessed our understanding of LbuCas13a allosteric activation pathways through molecular dynamics and structure-guided engineering to develop novel Cas13a variants that display increased sensitivities to single-nucleotide mismatches. We deployed these Cas13a variants and crRNA design strategies to achieve superior discrimination of SARS-CoV-2 strains compared to wild-type LbuCas13a. Together, our work provides new design criteria and new Cas13a variants for easier-to-implement Cas13-based diagnostics. KEY POINTS Certain positions in the Cas13a crRNA-target-RNA duplex are particularly sensitive to mismatches.Understanding Cas13a's allosteric activation pathway allowed us to develop novel high-fidelity Cas13a variants.These Cas13a variants and crRNA design strategies achieve superior discrimination of SARS-CoV-2 strains. GRAPHICAL ABSTRACT
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Hao N, Donnelly AJ, Dodd IB, Shearwin KE. When push comes to shove - RNA polymerase and DNA-bound protein roadblocks. Biophys Rev 2023; 15:355-366. [PMID: 37396453 PMCID: PMC10310618 DOI: 10.1007/s12551-023-01064-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 07/04/2023] Open
Abstract
In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Alana J. Donnelly
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Ian B. Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
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36
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541046. [PMID: 37292754 PMCID: PMC10245671 DOI: 10.1101/2023.05.16.541046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The data sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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37
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Zhou L, Yao S. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. MOLECULAR BIOMEDICINE 2023; 4:10. [PMID: 37027099 PMCID: PMC10080534 DOI: 10.1186/s43556-023-00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 derived editing tools had significantly improved our ability to make desired changes in the genome. Wild-type Cas9 protein recognizes the target genomic loci and induced local double strand breaks (DSBs) in the guidance of small RNA molecule. In mammalian cells, the DSBs are mainly repaired by endogenous non-homologous end joining (NHEJ) pathway, which is error prone and results in the formation of indels. The indels can be harnessed to interrupt gene coding sequences or regulation elements. The DSBs can also be fixed by homology directed repair (HDR) pathway to introduce desired changes, such as base substitution and fragment insertion, when proper donor templates are provided, albeit in a less efficient manner. Besides making DSBs, Cas9 protein can be mutated to serve as a DNA binding platform to recruit functional modulators to the target loci, performing local transcriptional regulation, epigenetic remolding, base editing or prime editing. These Cas9 derived editing tools, especially base editors and prime editors, can introduce precise changes into the target loci at a single-base resolution and in an efficient and irreversible manner. Such features make these editing tools very promising for therapeutic applications. This review focuses on the evolution and mechanisms of CRISPR-Cas9 derived editing tools and their applications in the field of gene therapy.
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Affiliation(s)
- Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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38
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Sinha S, Pindi C, Ahsan M, Arantes PR, Palermo G. Machines on Genes through the Computational Microscope. J Chem Theory Comput 2023; 19:1945-1964. [PMID: 36947696 PMCID: PMC10104023 DOI: 10.1021/acs.jctc.2c01313] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Macromolecular machines acting on genes are at the core of life's fundamental processes, including DNA replication and repair, gene transcription and regulation, chromatin packaging, RNA splicing, and genome editing. Here, we report the increasing role of computational biophysics in characterizing the mechanisms of "machines on genes", focusing on innovative applications of computational methods and their integration with structural and biophysical experiments. We showcase how state-of-the-art computational methods, including classical and ab initio molecular dynamics to enhanced sampling techniques, and coarse-grained approaches are used for understanding and exploring gene machines for real-world applications. As this review unfolds, advanced computational methods describe the biophysical function that is unseen through experimental techniques, accomplishing the power of the "computational microscope", an expression coined by Klaus Schulten to highlight the extraordinary capability of computer simulations. Pushing the frontiers of computational biophysics toward a pragmatic representation of large multimegadalton biomolecular complexes is instrumental in bridging the gap between experimentally obtained macroscopic observables and the molecular principles playing at the microscopic level. This understanding will help harness molecular machines for medical, pharmaceutical, and biotechnological purposes.
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39
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Guo C, Ma X, Gao F, Guo Y. Off-target effects in CRISPR/Cas9 gene editing. Front Bioeng Biotechnol 2023; 11:1143157. [PMID: 36970624 PMCID: PMC10034092 DOI: 10.3389/fbioe.2023.1143157] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Gene editing stands for the methods to precisely make changes to a specific nucleic acid sequence. With the recent development of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, gene editing has become efficient, convenient and programmable, leading to promising translational studies and clinical trials for both genetic and non-genetic diseases. A major concern in the applications of the CRISPR/Cas9 system is about its off-target effects, namely the deposition of unexpected, unwanted, or even adverse alterations to the genome. To date, many methods have been developed to nominate or detect the off-target sites of CRISPR/Cas9, which laid the basis for the successful upgrades of CRISPR/Cas9 derivatives with enhanced precision. In this review, we summarize these technological advancements and discuss about the current challenges in the management of off-target effects for future gene therapy.
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Affiliation(s)
- Congting Guo
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Institute of Cardiovascular Sciences, Beijing, China
| | - Xiaoteng Ma
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Fei Gao
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
- *Correspondence: Fei Gao, ; Yuxuan Guo,
| | - Yuxuan Guo
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Institute of Cardiovascular Sciences, Beijing, China
- Ministry of Education Key Laboratory of Molecular Cardiovascular Science, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
- *Correspondence: Fei Gao, ; Yuxuan Guo,
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40
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Nierzwicki Ł, Ahsan M, Palermo G. The Electronic Structure of Genome Editors from the First Principles. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2023; 5:014003. [PMID: 36926635 PMCID: PMC10016068 DOI: 10.1088/2516-1075/acb410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
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41
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Bhattacharya S, Satpati P. Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:1817-1837. [PMID: 36687047 PMCID: PMC9850488 DOI: 10.1021/acsomega.2c05583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The CRISPR/Cas9 system is a popular genome-editing tool with immense therapeutic potential. It is a simple two-component system (Cas9 protein and RNA) that recognizes the DNA sequence on the basis of RNA:DNA complementarity, and the Cas9 protein catalyzes the double-stranded break in the DNA. In the past decade, near-atomic resolution structures at various stages of the CRISPR/Cas9 DNA editing pathway have been reported along with numerous experimental and computational studies. Such studies have boosted knowledge of the genome-editing mechanism. Despite such advancements, the application of CRISPR/Cas9 in therapeutics is still limited, primarily due to off-target effects. Several studies aim at engineering high-fidelity Cas9 to minimize the off-target effects. Molecular Dynamics (MD) simulations have been an excellent complement to the experimental studies for investigating the mechanism of CRISPR/Cas9 editing in terms of structure, thermodynamics, and kinetics. MD-based studies have uncovered several important molecular aspects of Cas9, such as nucleotide binding, catalytic mechanism, and off-target effects. In this Review, the contribution of MD simulation to understand the CRISPR/Cas9 mechanism has been discussed, preceded by an overview of the history, mechanism, and structural aspects of the CRISPR/Cas9 system. These studies are important for the rational design of highly specific Cas9 and will also be extremely promising for achieving more accurate genome editing in the future.
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42
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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43
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Kohabir KAV, Nooi LO, Brink A, Brakenhoff RH, Sistermans EA, Wolthuis RMF. In Vitro CRISPR-Cas12a-Based Detection of Cancer-Associated TP53 Hotspot Mutations Beyond the crRNA Seed Region. CRISPR J 2023; 6:127-139. [PMID: 36637878 PMCID: PMC10123810 DOI: 10.1089/crispr.2022.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cost-effective and time-efficient detection of oncogenic mutations supports improved presymptomatic cancer diagnostics and post-treatment disease monitoring. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a is an RNA-guided endonuclease that, upon protospacer adjacent motif (PAM)-dependent recognition of target DNA in cis, exhibits indiscriminate ssDNase activity in trans, which can be harnessed for diagnostics. TP53, one of the most frequently mutated tumor suppressor genes in cancer, displays recurring point mutations at so-called "hotspots." In this study, we optimized Cas12a-based assay conditions for in vitro detection of six TP53 hotspot mutations at the codon for p.R273, located outside the Cas12a seed region, and evaluated the specificities of four commercial Cas12a variants. We found that nonengineered LbCas12a significantly outperformed the other tested nucleases specifically in distinguishing mutant p.R273 codons in synthetic DNA, mock cell-free DNA, and tissue biopsies, despite the suboptimal PAM-distal positioning of the corresponding mutations. Future clinical Cas12a-based applications may include point-of-care tumor analysis, cost-effective mutation screening, and improved monitoring of individual cancer patients.
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Affiliation(s)
- Kavish A V Kohabir
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Embryonic & Fetal Development, Amsterdam Reproduction & Development, Amsterdam, The Netherlands.,Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Lars O Nooi
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjen Brink
- Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Otolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ruud H Brakenhoff
- Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Otolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Embryonic & Fetal Development, Amsterdam Reproduction & Development, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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44
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Kurishev AO, Karpov DS, Nadolinskaia NI, Goncharenko AV, Golimbet VE. CRISPR/Cas-Based Approaches to Study Schizophrenia and Other Neurodevelopmental Disorders. Int J Mol Sci 2022; 24:ijms24010241. [PMID: 36613684 PMCID: PMC9820593 DOI: 10.3390/ijms24010241] [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: 11/12/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The study of diseases of the central nervous system (CNS) at the molecular level is challenging because of the complexity of neural circuits and the huge number of specialized cell types. Moreover, genomic association studies have revealed the complex genetic architecture of schizophrenia and other genetically determined mental disorders. Investigating such complex genetic architecture to decipher the molecular basis of CNS pathologies requires the use of high-throughput models such as cells and their derivatives. The time is coming for high-throughput genetic technologies based on CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)/Cas systems to manipulate multiple genomic targets. CRISPR/Cas systems provide the desired complexity, versatility, and flexibility to create novel genetic tools capable of both altering the DNA sequence and affecting its function at higher levels of genetic information flow. CRISPR/Cas tools make it possible to find and investigate the intricate relationship between the genotype and phenotype of neuronal cells. The purpose of this review is to discuss innovative CRISPR-based approaches for studying the molecular mechanisms of CNS pathologies using cellular models.
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Affiliation(s)
| | - Dmitry S. Karpov
- Mental Health Research Center, Kashirskoe sh. 34, 115522 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Nonna I. Nadolinskaia
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna V. Goncharenko
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vera E. Golimbet
- Mental Health Research Center, Kashirskoe sh. 34, 115522 Moscow, Russia
- Correspondence:
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45
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Bravo JP, Hibshman GN, Taylor DW. Constructing next-generation CRISPR-Cas tools from structural blueprints. Curr Opin Biotechnol 2022; 78:102839. [PMID: 36371895 DOI: 10.1016/j.copbio.2022.102839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats - CRISPR-associated protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive immune response. Since the discovery that they can be reengineered as programmable RNA-guided nucleases, there has been significant interest in using these systems to perform diverse and precise genetic manipulations. Here, we outline recent advances in the mechanistic understanding of CRISPR-Cas9, how these findings have been leveraged in the rational redesign of Cas9 variants with altered activities, and how these novel tools can be exploited for biotechnology and therapeutics. We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight how future structural studies will bolster these technologies.
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Affiliation(s)
- Jack Pk Bravo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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