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Zhang H, Kelly K, Lee J, Echeverria D, Cooper D, Panwala R, Amrani N, Chen Z, Gaston N, Wagh A, Newby G, Xie J, Liu DR, Gao G, Wolfe S, Khvorova A, Watts J, Sontheimer E. Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo. Nucleic Acids Res 2024; 52:977-997. [PMID: 38033325 PMCID: PMC10810193 DOI: 10.1093/nar/gkad1125] [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: 03/09/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a 'protecting oligo'), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
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Affiliation(s)
- Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rebecca Panwala
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Atish Wagh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Scot A Wolfe
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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102
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Qi M, Ma S, Liu J, Liu X, Wei J, Lu WJ, Zhang S, Chang Y, Zhang Y, Zhong K, Yan Y, Zhu M, Song Y, Chen Y, Hao G, Wang J, Wang L, Lee AS, Chen X, Wang Y, Lan F. In Vivo Base Editing of Scn5a Rescues Type 3 Long QT Syndrome in Mice. Circulation 2024; 149:317-329. [PMID: 37965733 DOI: 10.1161/circulationaha.123.065624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Pathogenic variants in SCN5A can result in long QT syndrome type 3, a life-threatening genetic disease. Adenine base editors can convert targeted A T base pairs to G C base pairs, offering a promising tool to correct pathogenic variants. METHODS We generated a long QT syndrome type 3 mouse model by introducing the T1307M pathogenic variant into the Scn5a gene. The adenine base editor was split into 2 smaller parts and delivered into the heart by adeno-associated virus serotype 9 (AAV9-ABEmax) to correct the T1307M pathogenic variant. RESULTS Both homozygous and heterozygous T1307M mice showed significant QT prolongation. Carbachol administration induced Torsades de Pointes or ventricular tachycardia for homozygous T1307M mice (20%) but not for heterozygous or wild-type mice. A single intraperitoneal injection of AAV9-ABEmax at postnatal day 14 resulted in up to 99.20% Scn5a transcripts corrected in T1307M mice. Scn5a mRNA correction rate >60% eliminated QT prolongation; Scn5a mRNA correction rate <60% alleviated QT prolongation. Partial Scn5a correction resulted in cardiomyocytes heterogeneity, which did not induce severe arrhythmias. We did not detect off-target DNA or RNA editing events in ABEmax-treated mouse hearts. CONCLUSIONS These findings show that in vivo AAV9-ABEmax editing can correct the variant Scn5a allele, effectively ameliorating arrhythmia phenotypes. Our results offer a proof of concept for the treatment of hereditary arrhythmias.
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Affiliation(s)
- Man Qi
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
- Chinese PLA General Hospital, College of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, Beijing, China (M.Q.)
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China (M.Q., Y. Chen)
| | - Shuhong Ma
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Jingtong Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China (J.L., Y.W.)
| | - Xujie Liu
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China (X.L., F.L.)
| | - Jingjing Wei
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Wen-Jing Lu
- Beijing Laboratory for Cardiovascular Precision Medicine, The Key Laboratory of Biomedical Engineering for Cardiovascular Disease Research, Ministry of Education, Beijing Anzhen Hospital, Capital Medical University, Beijing, China (W.-J.L., S.Z., F.L.)
| | - Siyao Zhang
- Beijing Laboratory for Cardiovascular Precision Medicine, The Key Laboratory of Biomedical Engineering for Cardiovascular Disease Research, Ministry of Education, Beijing Anzhen Hospital, Capital Medical University, Beijing, China (W.-J.L., S.Z., F.L.)
| | - Yun Chang
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Yongshuai Zhang
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Kejia Zhong
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Yuting Yan
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Min Zhu
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Yabing Song
- School of Life Sciences, Tsinghua University, Beijing, China (Y.S., J. Wang)
| | - Yundai Chen
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China (M.Q., Y. Chen)
| | - Guoliang Hao
- Henan Academy of Innovations in Medical Science, Zhengzhou, China (G.H.)
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, China (Y.S., J. Wang)
| | - Li Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Fuwai Hospital, Shenzhen, China (M.Q., S.M., X.L., Y. Chang, Y.Z., Y.Y., M.Z., L.W.)
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
| | - Andrew S Lee
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China (A.S.L.)
| | - Xiangbo Chen
- Hangzhou Rongze Biotechnology Group Co, Ltd, Hangzhou, China (X.C.)
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China (J.L., Y.W.)
| | - Feng Lan
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beijing, China (M.Q., S.M., X.L., J. Wei, Y. Chang, Y.Z., K.Z., Y.Y., M.Z., L.W., F.L.)
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China (X.L., F.L.)
- Beijing Laboratory for Cardiovascular Precision Medicine, The Key Laboratory of Biomedical Engineering for Cardiovascular Disease Research, Ministry of Education, Beijing Anzhen Hospital, Capital Medical University, Beijing, China (W.-J.L., S.Z., F.L.)
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103
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Tang N, Wu Z, Gao Y, Chen W, Wang Z, Su M, Ji W, Ji Q. Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System. ACS Synth Biol 2024; 13:269-281. [PMID: 38061052 DOI: 10.1021/acssynbio.3c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
CRISPR-Cas9 systems have been widely harnessed for diverse genome editing applications because of their ease of use and high efficiency. However, the large molecular sizes and strict PAM requirements of commonly used CRISPR-Cas9 systems restrict their broad applications in therapeutics. Here, we report the molecular basis and genome editing applications of a novel compact type II-A Eubacterium ventriosum CRISPR-Cas9 system (EvCas9) with 1107 residues and distinct 5'-NNGDGN-3' (where D represents A, T, or G) PAM specificity. We determine the cryo-EM structure of EvCas9 in a complex with an sgRNA and a target DNA, revealing the detailed PAM recognition and sgRNA and target DNA association mechanisms. Additionally, we demonstrate the robust genome editing capacity of EvCas9 in bacteria and human cells with superior fidelity compared to SaCas9 and SpCas9, and we engineer it to be efficient base editors by fusing a cytidine or adenosine deaminase. Collectively, our results facilitate further understanding of CRISPR-Cas9 working mechanisms and expand the compact CRISPR-Cas9 toolbox.
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Affiliation(s)
- Na Tang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhaowei Wu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zixiao Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengjiao Su
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenxin Ji
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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104
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Konishi CT, Moulayes N, Butola T, Zhang V, Kagan D, Yang Q, Pressler M, Dirvin BG, Devinsky O, Basu J, Long C. Modeling and Correction of Protein Conformational Disease in iPSC-derived Neurons through Personalized Base Editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576134. [PMID: 38293034 PMCID: PMC10827171 DOI: 10.1101/2024.01.17.576134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Altered protein conformation can cause incurable neurodegenerative disorders. Mutations in SERPINI1 , the gene encoding neuroserpin, alter protein conformation resulting in cytotoxic aggregation in neuronal endoplasmic reticulum. Aggregates cause oxidative stress impairing function, leading to neuronal death. Familial encephalopathy with neuroserpin inclusion bodies (FENIB) is a rare autosomal dominant progressive myoclonic epilepsy. Patients present with seizures and cognitive impairments that progress to dementia and premature death. We developed HEK293T and induced pluripotent stem cell (iPSC) models of FENIB, harboring the patient's pathogenic SERPINI1 variant or stably overexpressing mutant neuroserpin fused to GFP (MUT NS-GFP). FENIB cells form neuroserpin inclusions which increase in size and number. Here, we utilized a personalized adenine base editor (ABE)-mediated approach to efficiently correct the pathogenic variant and to restore neuronal dendritic morphology. ABE-treated MUT NS-GFP cells demonstrated reduced inclusion size and number. Using an inducible MUT NS-GFP neuron system, we identified early prevention of toxic protein expression allowed aggregate clearance, while late prevention halted neuronal impairments. To address several challenges for clinical applications of gene correction, we developed a neuron-specific engineered virus-like particle to optimize neuronal ABE delivery. Preventing mutant protein with altered conformation production improved toxic protein clearance. Our findings provide a targeted strategy and may treat FENIB and potentially other neurodegenerative diseases due to altered protein conformation such as Alzheimer's and Huntington's diseases.
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105
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell 2024; 84:261-276.e18. [PMID: 38176414 PMCID: PMC10872554 DOI: 10.1016/j.molcel.2023.12.003] [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: 05/16/2023] [Revised: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra L Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sem A G Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin N Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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106
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Brooks DL, Whittaker MN, Said H, Dwivedi G, Qu P, Musunuru K, Ahrens-Nicklas RC, Alameh MG, Wang X. A base editing strategy using mRNA-LNPs for in vivo correction of the most frequent phenylketonuria variant. HGG ADVANCES 2024; 5:100253. [PMID: 37922902 PMCID: PMC10800763 DOI: 10.1016/j.xhgg.2023.100253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
The c.1222C>T (p.Arg408Trp) phenylalanine hydroxylase (PAH) variant is the most frequent cause of phenylketonuria (PKU), an autosomal recessive disorder characterized by accumulation of blood phenylalanine (Phe) to neurotoxic levels. Here we devised a therapeutic base editing strategy to correct the variant, using prime-edited hepatocyte cell lines engineered with the c.1222C>T variant to screen a variety of adenine base editors and guide RNAs in vitro, followed by assessment in c.1222C>T humanized mice in vivo. We found that upon delivery of a selected adenine base editor mRNA/guide RNA combination into mice via lipid nanoparticles (LNPs), there was sufficient PAH editing in the liver to fully normalize blood Phe levels within 48 h. This work establishes the viability of a base editing strategy to correct the most common pathogenic variant found in individuals with the most common inborn error of metabolism, albeit with potential limitations compared with other genome editing approaches.
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Affiliation(s)
- Dominique L Brooks
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madelynn N Whittaker
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hooda Said
- Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA
| | - Garima Dwivedi
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ping Qu
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Rebecca C Ahrens-Nicklas
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Metabolic Disease Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mohamad-Gabriel Alameh
- Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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107
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Gao S, Guan H, Bloomer H, Wich D, Song D, Khirallah J, Ye Z, Zhao Y, Chen M, Xu C, Liu L, Xu Q. Harnessing non-Watson-Crick's base pairing to enhance CRISPR effectors cleavage activities and enable gene editing in mammalian cells. Proc Natl Acad Sci U S A 2024; 121:e2308415120. [PMID: 38150477 PMCID: PMC10786293 DOI: 10.1073/pnas.2308415120] [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: 05/19/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023] Open
Abstract
Genomic DNA of the cyanophage S-2L virus is composed of 2-aminoadenine (Z), thymine (T), guanine (G), and cytosine (C), forming the genetic alphabet ZTGC, which violates Watson-Crick base pairing rules. The Z-base has an extra amino group on the two position that allows the formation of a third hydrogen bond with thymine in DNA strands. Here, we explored and expanded applications of this non-Watson-Crick base pairing in protein expression and gene editing. Both ZTGC-DNA (Z-DNA) and ZUGC-RNA (Z-RNA) produced in vitro show detectable compatibility and can be decoded in mammalian cells, including Homo sapiens cells. Z-crRNA can guide CRISPR-effectors SpCas9 and LbCas12a to cleave specific DNA through non-Watson-Crick base pairing and boost cleavage activities compared to A-crRNA. Z-crRNA can also allow for efficient gene and base editing in human cells. Together, our results help pave the way for potential strategies for optimizing DNA or RNA payloads for gene editing therapeutics and give insights to understanding the natural Z-DNA genome.
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Affiliation(s)
- Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Huiwen Guan
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Hanan Bloomer
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Douglas Wich
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Jennifer Khirallah
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Mengting Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Chutian Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Lihan Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
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108
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An M, Raguram A, Du SW, Banskota S, Davis JR, Newby GA, Chen PZ, Palczewski K, Liu DR. Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo. Nat Biotechnol 2024:10.1038/s41587-023-02078-y. [PMID: 38191664 PMCID: PMC11228131 DOI: 10.1038/s41587-023-02078-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Prime editing enables precise installation of genomic substitutions, insertions and deletions in living systems. Efficient in vitro and in vivo delivery of prime editing components, however, remains a challenge. Here we report prime editor engineered virus-like particles (PE-eVLPs) that deliver prime editor proteins, prime editing guide RNAs and nicking single guide RNAs as transient ribonucleoprotein complexes. We systematically engineered v3 and v3b PE-eVLPs with 65- to 170-fold higher editing efficiency in human cells compared to a PE-eVLP construct based on our previously reported base editor eVLP architecture. In two mouse models of genetic blindness, single injections of v3 PE-eVLPs resulted in therapeutically relevant levels of prime editing in the retina, protein expression restoration and partial visual function rescue. Optimized PE-eVLPs support transient in vivo delivery of prime editor ribonucleoproteins, enhancing the potential safety of prime editing by reducing off-target editing and obviating the possibility of oncogenic transgene integration.
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Affiliation(s)
- Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samuel W Du
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Paul Z Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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109
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Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [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: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
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Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
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110
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Cho SI, Lim K, Hong S, Lee J, Kim A, Lim CJ, Ryou S, Lee JM, Mok YG, Chung E, Kim S, Han S, Cho SM, Kim J, Kim EK, Nam KH, Oh Y, Choi M, An TH, Oh KJ, Lee S, Lee H, Kim JS. Engineering TALE-linked deaminases to facilitate precision adenine base editing in mitochondrial DNA. Cell 2024; 187:95-109.e26. [PMID: 38181745 DOI: 10.1016/j.cell.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
DddA-derived cytosine base editors (DdCBEs) and transcription activator-like effector (TALE)-linked deaminases (TALEDs) catalyze targeted base editing of mitochondrial DNA (mtDNA) in eukaryotic cells, a method useful for modeling of mitochondrial genetic disorders and developing novel therapeutic modalities. Here, we report that A-to-G-editing TALEDs but not C-to-T-editing DdCBEs induce tens of thousands of transcriptome-wide off-target edits in human cells. To avoid these unwanted RNA edits, we engineered the substrate-binding site in TadA8e, the deoxy-adenine deaminase in TALEDs, and created TALED variants with fine-tuned deaminase activity. Our engineered TALED variants not only reduced RNA off-target edits by >99% but also minimized off-target mtDNA mutations and bystander edits at a target site. Unlike wild-type versions, our TALED variants were not cytotoxic and did not cause developmental arrest of mouse embryos. As a result, we obtained mice with pathogenic mtDNA mutations, associated with Leigh syndrome, which showed reduced heart rates.
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Affiliation(s)
- Sung-Ik Cho
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kayeong Lim
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Seongho Hong
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Jaesuk Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Annie Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | | | | | - Ji Min Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Geun Mok
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; GreenGene Inc., Seoul 08790, Republic of Korea
| | - Eugene Chung
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Sanghun Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seunghun Han
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sang-Mi Cho
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jieun Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Eun-Kyoung Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yeji Oh
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Minkyung Choi
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Tae Hyeon An
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seonghyun Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Edgene, Inc., Seoul 08790, Republic of Korea; Department of MetaBioHealth, Sungkyunkwan University (SKKU), Suwon, Republic of Korea; Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon, Republic of Korea.
| | - Hyunji Lee
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea.
| | - Jin-Soo Kim
- Edgene, Inc., Seoul 08790, Republic of Korea; NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore.
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111
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Lebek S, Caravia XM, Straub LG, Alzhanov D, Tan W, Li H, McAnally JR, Chen K, Xu L, Scherer PE, Liu N, Bassel-Duby R, Olson EN. CRISPR-Cas9 base editing of pathogenic CaMKIIδ improves cardiac function in a humanized mouse model. J Clin Invest 2024; 134:e175164. [PMID: 37856214 PMCID: PMC10760954 DOI: 10.1172/jci175164] [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: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023] Open
Abstract
Cardiovascular diseases are the most common cause of worldwide morbidity and mortality, highlighting the necessity for advanced therapeutic strategies. Ca2+/calmodulin-dependent protein kinase IIδ (CaMKIIδ) is a prominent inducer of various cardiac disorders, which is mediated by 2 oxidation-sensitive methionine residues within the regulatory domain. We have previously shown that ablation of CaMKIIδ oxidation by CRISPR-Cas9 base editing enables the heart to recover function from otherwise severe damage following ischemia/reperfusion (IR) injury. Here, we extended this therapeutic concept toward potential clinical translation. We generated a humanized CAMK2D knockin mouse model in which the genomic sequence encoding the entire regulatory domain was replaced with the human sequence. This enabled comparison and optimization of two different editing strategies for the human genome in mice. To edit CAMK2D in vivo, we packaged the optimized editing components into an engineered myotropic adeno-associated virus (MyoAAV 2A), which enabled efficient delivery at a very low AAV dose into the humanized mice at the time of IR injury. CAMK2D-edited mice recovered cardiac function, showed improved exercise performance, and were protected from myocardial fibrosis, which was otherwise observed in injured control mice after IR. Our findings identify a potentially effective strategy for cardioprotection in response to oxidative damage.
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Affiliation(s)
- Simon Lebek
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Xurde M. Caravia
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Damir Alzhanov
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Wei Tan
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Hui Li
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John R. McAnally
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Ning Liu
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Eric N. Olson
- Department of Molecular Biology and
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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112
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Ye L, Zhao D, Li J, Wang Y, Li B, Yang Y, Hou X, Wang H, Wei Z, Liu X, Li Y, Li S, Liu Y, Zhang X, Bi C. Glycosylase-based base editors for efficient T-to-G and C-to-G editing in mammalian cells. Nat Biotechnol 2024:10.1038/s41587-023-02050-w. [PMID: 38168994 DOI: 10.1038/s41587-023-02050-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 10/27/2023] [Indexed: 01/05/2024]
Abstract
Base editors show promise for treating human genetic diseases, but most current systems use deaminases, which cause off-target effects and are limited in editing type. In this study, we constructed deaminase-free base editors for cytosine (DAF-CBE) and thymine (DAF-TBE), which contain only a cytosine-DNA or a thymine-DNA glycosylase (CDG/TDG) variant, respectively, tethered to a Cas9 nickase. Multiple rounds of mutagenesis by directed evolution in Escherichia coli generated two variants with enhanced base-converting activity-CDG-nCas9 and TDG-nCas9-with efficiencies of up to 58.7% for C-to-A and 54.3% for T-to-A. DAF-BEs achieve C-to-G/T-to-G editing in mammalian cells with minimal Cas9-dependent and Cas9-independent off-target effects as well as minimal RNA off-target effects. Additional engineering resulted in DAF-CBE2/DAF-TBE2, which exhibit altered editing windows from the 5' end to the middle of the protospacer and increased C-to-G/T-to-G editing efficiency of 3.5-fold and 1.2-fold, respectively. Compared to prime editing or CGBEs, DAF-BEs expand conversion types of base editors with similar efficiencies, smaller sizes and lower off-target effects.
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Affiliation(s)
- Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Yiran Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Bo Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yuanzhao Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xueting Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Huibin Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhandong Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoqi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yaqiu Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yajing Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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113
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Xiao YL, Wu Y, Tang W. An adenine base editor variant expands context compatibility. Nat Biotechnol 2024:10.1038/s41587-023-01994-3. [PMID: 38168987 DOI: 10.1038/s41587-023-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/15/2023] [Indexed: 01/05/2024]
Abstract
Adenine base editors (ABEs) are precise gene-editing agents that convert A:T pairs into G:C through a deoxyinosine intermediate. Existing ABEs function most effectively when the target A is in a TA context. Here we evolve the Escherichia coli transfer RNA-specific adenosine deaminase (TadA) to generate TadA8r, which extends potent deoxyadenosine deamination to RA (R = A or G) and is faster in processing GA than TadA8.20 and TadA8e, the two most active TadA variants reported so far. ABE8r, comprising TadA8r and a Streptococcus pyogenes Cas9 nickase, expands the editing window at the protospacer adjacent motif-distal end and outperforms ABE7.10, ABE8.20 and ABE8e in correcting disease-associated G:C-to-A:T transitions in the human genome, with a controlled off-target profile. We show ABE8r-mediated editing of clinically relevant sites that are poorly accessed by existing editors, including sites in PCSK9, whose disruption reduces low-density lipoprotein cholesterol, and ABCA4-p.Gly1961Glu, the most frequent mutation in Stargardt disease.
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Affiliation(s)
- Yu-Lan Xiao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Yuan Wu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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114
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Lim K. Mitochondrial genome editing: strategies, challenges, and applications. BMB Rep 2024; 57:19-29. [PMID: 38178652 PMCID: PMC10828433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
Mitochondrial DNA (mtDNA), a multicopy genome found in mitochondria, is crucial for oxidative phosphorylation. Mutations in mtDNA can lead to severe mitochondrial dysfunction in tissues and organs with high energy demand. MtDNA mutations are closely associated with mitochondrial and age-related disease. To better understand the functional role of mtDNA and work toward developing therapeutics, it is essential to advance technology that is capable of manipulating the mitochondrial genome. This review discusses ongoing efforts in mitochondrial genome editing with mtDNA nucleases and base editors, including the tools, delivery strategies, and applications. Future advances in mitochondrial genome editing to address challenges regarding their efficiency and specificity can achieve the promise of therapeutic genome editing. [BMB Reports 2024; 57(1): 19-29].
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Affiliation(s)
- Kayeong Lim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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115
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Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, Marson A. Base-editing mutagenesis maps alleles to tune human T cell functions. Nature 2024; 625:805-812. [PMID: 38093011 PMCID: PMC11065414 DOI: 10.1038/s41586-023-06835-6] [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: 05/12/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.
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Affiliation(s)
- Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
| | - Rama Dajani
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zev Armour-Garb
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mineto Ota
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent Allain
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Université Paris Cité, INSERM UMR976, Hôpital Saint-Louis, Paris, France
| | - Rosmely Hernandez
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Layeghi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Galen Xing
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Dmytro Dorovskyi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte Wang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Yan Yi Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, USA
- Arc Institute, Palo Alto, CA, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Stacie E Dodgson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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116
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Shelake RM, Pramanik D, Kim JY. CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution. BMB Rep 2024; 57:30-39. [PMID: 38053292 PMCID: PMC10828429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 12/07/2023] Open
Abstract
Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements. [BMB Reports 2024; 57(1): 30-39].
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
- Division of Life Science, Gyeongsang National University, Jinju 52828, Korea
- R&D Center, Nulla Bio Inc., Jinju 52828, Korea
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117
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Kim JS, Chen J. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol 2024; 25:34-45. [PMID: 37794167 DOI: 10.1038/s41580-023-00663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Mitochondria and chloroplasts are organelles that include their own genomes, which encode key genes for ATP production and carbon dioxide fixation, respectively. Mutations in mitochondrial DNA can cause diverse genetic disorders and are also linked to ageing and age-related diseases, including cancer. Targeted editing of organellar DNA should be useful for studying organellar genes and developing novel therapeutics, but it has been hindered by lack of efficient tools in living cells. Recently, CRISPR-free, protein-only base editors, such as double-stranded DNA deaminase toxin A-derived cytosine base editors (DdCBEs) and adenine base editors (ABEs), have been developed, which enable targeted organellar DNA editing in human cell lines, animals and plants. In this Review, we present programmable deaminases developed for base editing of organellar DNA in vitro and discuss mitochondrial DNA editing in animals, and plastid genome (plastome) editing in plants. We also discuss precision and efficiency limitations of these tools and propose improvements for therapeutic, agricultural and environmental applications.
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Affiliation(s)
- Jin-Soo Kim
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore.
- Edgene, Seoul, South Korea.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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118
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Wang Z, Yuan H, Yang L, Ma L, Zhang Y, Deng J, Li X, Xiao W, Li Z, Qiu J, Ouyang H, Pang D. Decreasing predictable DNA off-target effects and narrowing editing windows of adenine base editors by fusing human Rad18 protein variant. Int J Biol Macromol 2023; 253:127418. [PMID: 37848112 DOI: 10.1016/j.ijbiomac.2023.127418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Adenine base editors, enabling targeted A-to-G conversion in genomic DNA, have enormous potential in therapeutic applications. However, the currently used adenine base editors are limited by wide editing windows and off-target effects in genetic therapy. Here, we report human e18 protein, a RING type E3 ubiquitin ligase variant, fusing with adenine base editors can significantly improve the preciseness and narrow the editing windows compared with ABEmax and ABE8e by diminishing the abundance of base editor protein. As a proof of concept, ABEmax-e18 and ABE8e-e18 dramatically decrease Cas9-dependent and Cas9-independent off-target effects than traditional adenine base editors. Moreover, we utilized ABEmax-e18 to establish syndactyly mouse models and achieve accurate base conversion at human PCSK9 locus in HepG2 cells which exhibited its potential in genetic therapy. Furthermore, a truncated version of base editors-RING (ABEmax-RING or AncBE4max-RING), which fusing the 63 amino acids of e18 protein RING domain to the C terminal of ABEmax or AncBE4max, exhibited similar effect compared to ABEmax-e18 or AncBE4max-e18.In summary, the e18 or RING protein fused with base editors strengthens the precise toolbox in gene modification and maybe works well with various base editing tools with a more applicable to precise genetic therapies in the future.
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Affiliation(s)
- Ziru Wang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Hongming Yuan
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
| | - Lin Yang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lerong Ma
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiacheng Deng
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xueyuan Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wenyu Xiao
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiazhang Qiu
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hongsheng Ouyang
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
| | - Daxin Pang
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
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119
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Xiang J, Xu W, Wu J, Luo Y, Yang B, Chen J. Nucleoside deaminases: the key players in base editing toolkit. BIOPHYSICS REPORTS 2023; 9:325-337. [PMID: 38524700 PMCID: PMC10960570 DOI: 10.52601/bpr.2023.230029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/28/2023] [Indexed: 03/26/2024] Open
Abstract
The development of nucleoside deaminase-containing base editors realized targeted single base change with high efficiency and precision. Such nucleoside deaminases include adenosine and cytidine deaminases, which can catalyze adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) conversion respectively. These nucleoside deaminases are under the spotlight because of their vast application potential in gene editing. Recent advances in the engineering of current nucleoside deaminases and the discovery of new nucleoside deaminases greatly broaden the application scope and improve the editing specificity of base editors. In this review, we cover current knowledge about the deaminases used in base editors, including their key structural features, working mechanisms, optimization, and evolution.
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Affiliation(s)
- Jiangchao Xiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenchao Xu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yaxin Luo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Bei Yang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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120
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Koonin EV, Gootenberg JS, Abudayyeh OO. Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry 2023; 62:3465-3487. [PMID: 37192099 PMCID: PMC10734277 DOI: 10.1021/acs.biochem.3c00159] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Indexed: 05/18/2023]
Abstract
CRISPR systems mediate adaptive immunity in bacteria and archaea through diverse effector mechanisms and have been repurposed for versatile applications in therapeutics and diagnostics thanks to their facile reprogramming with RNA guides. RNA-guided CRISPR-Cas targeting and interference are mediated by effectors that are either components of multisubunit complexes in class 1 systems or multidomain single-effector proteins in class 2. The compact class 2 CRISPR systems have been broadly adopted for multiple applications, especially genome editing, leading to a transformation of the molecular biology and biotechnology toolkit. The diversity of class 2 effector enzymes, initially limited to the Cas9 nuclease, was substantially expanded via computational genome and metagenome mining to include numerous variants of Cas12 and Cas13, providing substrates for the development of versatile, orthogonal molecular tools. Characterization of these diverse CRISPR effectors uncovered many new features, including distinct protospacer adjacent motifs (PAMs) that expand the targeting space, improved editing specificity, RNA rather than DNA targeting, smaller crRNAs, staggered and blunt end cuts, miniature enzymes, promiscuous RNA and DNA cleavage, etc. These unique properties enabled multiple applications, such as harnessing the promiscuous RNase activity of the type VI effector, Cas13, for supersensitive nucleic acid detection. class 1 CRISPR systems have been adopted for genome editing, as well, despite the challenge of expressing and delivering the multiprotein class 1 effectors. The rich diversity of CRISPR enzymes led to rapid maturation of the genome editing toolbox, with capabilities such as gene knockout, base editing, prime editing, gene insertion, DNA imaging, epigenetic modulation, transcriptional modulation, and RNA editing. Combined with rational design and engineering of the effector proteins and associated RNAs, the natural diversity of CRISPR and related bacterial RNA-guided systems provides a vast resource for expanding the repertoire of tools for molecular biology and biotechnology.
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Affiliation(s)
- Eugene V. Koonin
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Jonathan S. Gootenberg
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Omar O. Abudayyeh
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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121
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Tou CJ, Kleinstiver BP. Recent Advances in Double-Strand Break-Free Kilobase-Scale Genome Editing Technologies. Biochemistry 2023; 62:3493-3499. [PMID: 36049184 PMCID: PMC10239562 DOI: 10.1021/acs.biochem.2c00311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genome editing approaches have transformed the ability to make user-defined changes to genomes in both ex vivo and in vivo contexts. Despite the abundant development of technologies that permit the installation of nucleotide-level changes, until recently, larger-scale sequence edits via technologies independent of DNA double-strand breaks (DSBs) had remained less explored. Here, we review recent advances toward DSB-free technologies that enable kilobase-scale modifications including insertions, deletions, inversions, replacements, and others. These technologies provide new capabilities for users, while offering hope for the simplification of putative therapeutic strategies by moving away from small mutation-specific edits and toward more generalizable kilobase-scale approaches.
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Affiliation(s)
- Connor J. Tou
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
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122
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Ryan D, Diamant-Levi T, Steinfeld I, Taussig D, Visal-Shah S, Thakker S, Lunstad BD, Kaiser RJ, McCaffrey R, Ortiz M, Townsend J, Welch WRW, Singh M, Curry B, Dellinger DJ, Bruhn L. Phosphonoacetate Modifications Enhance the Stability and Editing Yields of Guide RNAs for Cas9 Editors. Biochemistry 2023; 62:3512-3520. [PMID: 35436085 PMCID: PMC10734248 DOI: 10.1021/acs.biochem.1c00768] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CRISPR gene editing and control systems continue to emerge and inspire novel research and clinical applications. Advances in CRISPR performance such as optimizing the duration of activity in cells, tissues, and organisms, as well as limiting off-target activities, have been extremely important for expanding the utility of CRISPR-based systems. By investigating the effects of various chemical modifications in guide RNAs (gRNAs) at defined positions and combinations, we find that 2'-O-methyl-3'-phosphonoacetate (MP) modifications can be substantially more effective than 2'-O-methyl-3'-phosphorothioate (MS) modifications at the 3' ends of single-guide RNAs (sgRNAs) to promote high editing yields, in some instances showing an order of magnitude higher editing yield in human cells. MP-modified 3' ends are especially effective at promoting the activity of guide RNAs cotransfected with Cas messenger RNA (mRNA), as the gRNA must persist in cells until the Cas protein is expressed. We demonstrate such an MP enhancement for sgRNAs cotransfected with a BE4 mRNA for cytidine base editing and also demonstrate that MP at the 3' ends of prime editing guide RNAs (pegRNAs) cotransfected with PE2 mRNA can promote maximal prime editing yields. In the presence of serum, sgRNAs with MP-modified 3' ends showed marked improvements in editing efficiency over sgRNAs with MS-modified 3' ends codelivered with Cas9 mRNA and showed more modest improvements at enhancing the activity of transfected ribonucleoprotein (RNP) complexes. Our results suggest that MP should be considered as a performance-enhancing modification for the 3' ends of synthetic gRNAs, especially in situations where the guide RNAs may be susceptible to exonuclease-mediated degradation.
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Affiliation(s)
- Daniel
E. Ryan
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Tamar Diamant-Levi
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Israel Steinfeld
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - David Taussig
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Savita Visal-Shah
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Suhani Thakker
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | | | - Robert J. Kaiser
- Agilent
Technologies, Santa Clara, California 95051, United States
| | - Ryan McCaffrey
- Agilent
Technologies, Santa Clara, California 95051, United States
| | - Michael Ortiz
- Agilent
Research Laboratories, Boulder, Colorado 80303, United States
| | - Justin Townsend
- Agilent
Research Laboratories, Boulder, Colorado 80303, United States
| | | | - Mandeep Singh
- Agilent
Research Laboratories, Boulder, Colorado 80303, United States
| | - Bo Curry
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | | | - Laurakay Bruhn
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
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123
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Walsh ZH, Shah P, Kothapalli N, Nikolenyi G, Shah SB, Leuzzi G, Mu M, Ho P, Abuzaid S, Brodtman ZD, Vasan N, AlQuraishi M, Milner JD, Ciccia A, Melms JC, Izar B. Massively parallel base editing screens to map variant effects on anti-tumor hallmarks of primary human T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571465. [PMID: 38168306 PMCID: PMC10760091 DOI: 10.1101/2023.12.13.571465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Base editing enables generation of single nucleotide variants, but large-scale screening in primary human T cells is limited due to low editing efficiency, among other challenges 1 . Here, we developed a high-throughput approach for high-efficiency and massively parallel adenine and cytosine base-editor screening in primary human T cells. We performed multiple large-scale screens editing 102 genes with central functions in T cells and full-length tiling mutagenesis of selected genes, and read out variant effects on hallmarks of T cell anti-tumor immunity, including activation, proliferation, and cytokine production. We discovered a broad landscape of gain- and loss-of-function mutations, including in PIK3CD and its regulatory subunit encoded by PIK3R1, LCK , AKT1, CTLA-4 and JAK1 . We identified variants that affected several (e.g., PIK3CD C416R) or only selected (e.g. LCK Y505C) hallmarks of T cell activity, and functionally validated several hits by probing downstream signaling nodes and testing their impact on T cell polyfunctionality and proliferation. Using primary human T cells in which we engineered a T cell receptor (TCR) specific to a commonly presented tumor testis antigen as a model for cellular immunotherapy, we demonstrate that base edits identified in our screens can tune specific or broad T cell functions and ultimately improve tumor elimination while exerting minimal off-target activity. In summary, we present the first large-scale base editing screen in primary human T cells and provide a framework for scalable and targeted base editing at high efficiency. Coupled with multi-modal phenotypic mapping, we accurately nominate variants that produce a desirable T cell state and leverage these synthetic proteins to improve models of cellular cancer immunotherapies.
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124
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Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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125
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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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Bhuyan SJ, Kumar M, Ramrao Devde P, Rai AC, Mishra AK, Singh PK, Siddique KHM. Progress in gene editing tools, implications and success in plants: a review. Front Genome Ed 2023; 5:1272678. [PMID: 38144710 PMCID: PMC10744593 DOI: 10.3389/fgeed.2023.1272678] [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: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.
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Affiliation(s)
- Suman Jyoti Bhuyan
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Pandurang Ramrao Devde
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Avinash Chandra Rai
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | | | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
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Li J, Tang C, Liang G, Tian H, Lai G, Wu Y, Liu S, Zhang W, Liu S, Shao H. Clustered Regularly Interspaced Short Palindromic Repeats and Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 System: Factors Affecting Precision Gene Editing Efficiency and Optimization Strategies. Hum Gene Ther 2023; 34:1190-1203. [PMID: 37642232 DOI: 10.1089/hum.2023.115] [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: 08/31/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) system is a powerful genomic DNA editing tool. The increased applications of gene editing tools, including the CRISPR-Cas system, have contributed to recent advances in biological fields, such as genetic disease therapy, disease-associated gene screening and detection, and cancer therapy. However, the major limiting factor for the wide application of gene editing tools is gene editing efficiency. This review summarizes the recent advances in factors affecting the gene editing efficiency of the CRISPR-Cas9 system and the CRISPR-Cas9 system optimization strategies. The homology-directed repair efficiency-related signal pathways and the form and delivery method of the CRISPR-Cas9 system are the major factors that influence the repair efficiency of gene editing tools. Based on these influencing factors, several strategies have been developed to improve the repair efficiency of gene editing tools. This review provides novel insights for improving the repair efficiency of the CRISPR-Cas9 gene editing system, which may enable the development and improvement of gene editing tools.
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Affiliation(s)
- Jiawen Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Chuxi Tang
- School of Pharmacy & Clinical Pharmacy (School of Integrative Pharmacy), Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Guozheng Liang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Huiqun Tian
- The Second People's Hospital of China Three Gorges University, Yichang, People's Republic of China
| | - Guanxi Lai
- School of Pharmacy & Clinical Pharmacy (School of Integrative Pharmacy), Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Yixiang Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- School of Pharmacy & Clinical Pharmacy (School of Integrative Pharmacy), Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Shiwen Liu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- School of Pharmacy & Clinical Pharmacy (School of Integrative Pharmacy), Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Wenfeng Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Song Liu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- School of Pharmacy & Clinical Pharmacy (School of Integrative Pharmacy), Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hongwei Shao
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
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Tan J, Shen M, Chai N, Liu Q, Liu YG, Zhu Q. Genome editing for plant synthetic metabolic engineering and developmental regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154141. [PMID: 38016350 DOI: 10.1016/j.jplph.2023.154141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Plant metabolism and development are a reflection of the orderly expression of genetic information intertwined with the environment interactions. Genome editing is the cornerstone for scientists to modify endogenous genes or introduce exogenous functional genes and metabolic pathways, holding immense potential applications in molecular breeding and biosynthesis. Over the course of nearly a decade of development, genome editing has advanced significantly beyond the simple cutting of double-stranded DNA, now enabling precise base and fragment replacements, regulation of gene expression and translation, as well as epigenetic modifications. However, the utilization of genome editing in plant synthetic metabolic engineering and developmental regulation remains exploratory. Here, we provide an introduction and a comprehensive overview of the editing attributes associated with various CRISPR/Cas tools, along with diverse strategies for the meticulous control of plant metabolic pathways and developments. Furthermore, we discuss the limitations of current approaches and future prospects for genome editing-driven plant breeding.
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Affiliation(s)
- Jiantao Tan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Mengyuan Shen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Lin Y, Kwok S, Hein AE, Thai BQ, Alabi Y, Ostrowski MS, Wu K, Floor SN. RNA molecular recording with an engineered RNA deaminase. Nat Methods 2023; 20:1887-1899. [PMID: 37857907 DOI: 10.1038/s41592-023-02046-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 09/13/2023] [Indexed: 10/21/2023]
Abstract
RNA deaminases are powerful tools for base editing and RNA molecular recording. However, the enzymes used in currently available RNA molecular recorders such as TRIBE, DART or STAMP have limitations due to RNA structure and sequence dependence. We designed a platform for directed evolution of RNA molecular recorders. We engineered an RNA A-to-I deaminase (an RNA adenosine base editor, rABE) that has high activity, low bias and low background. Using rABE, we present REMORA (RNA-encoded molecular recording in adenosines), wherein deamination by rABE writes a molecular record of RNA-protein interactions. By combining rABE with the C-to-U deaminase APOBEC1 and long-read RNA sequencing, we measured binding by two RNA-binding proteins on single messenger RNAs. Orthogonal RNA molecular recording of mammalian Pumilio proteins PUM1 and PUM2 shows that PUM1 competes with PUM2 for a subset of sites in cells. Furthermore, we identify transcript isoform-specific RNA-protein interactions driven by isoform changes distal to the binding site. The genetically encodable RNA deaminase rABE enables single-molecule identification of RNA-protein interactions with cell type specificity.
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Affiliation(s)
- Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Samentha Kwok
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Abigail E Hein
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Bao Quoc Thai
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- MSTP Program, University of Arizona, Tuscon, AZ, USA
| | - Yewande Alabi
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Megan S Ostrowski
- Gladstone Institute for Data Science and Biotechnology, San Francisco, CA, USA
| | - Ke Wu
- Gladstone Institute for Data Science and Biotechnology, San Francisco, CA, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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Zhang A, Shan T, Sun Y, Chen Z, Hu J, Hu Z, Ming Z, Zhu Z, Li X, He J, Liu S, Jiang L, Dong X, Wu Y, Wang Y, Liu Y, Li C, Wan J. Directed evolution rice genes with randomly multiplexed sgRNAs assembly of base editors. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2597-2610. [PMID: 37571976 PMCID: PMC10651138 DOI: 10.1111/pbi.14156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
CRISPR-based directed evolution is an effective breeding biotechnology to improve agronomic traits in plants. However, its gene diversification is still limited using individual single guide RNA. We described here a multiplexed orthogonal base editor (MoBE), and a randomly multiplexed sgRNAs assembly strategy to maximize gene diversification. MoBE could induce efficiently orthogonal ABE (<36.6%), CBE (<36.0%), and A&CBE (<37.6%) on different targets, while the sgRNA assembling strategy randomized base editing events on various targets. With respective 130 and 84 targets from each strand of the 34th exon of rice acetyl-coenzyme A carboxylase (OsACC), we observed the target-scaffold combination types up to 27 294 in randomly dual and randomly triple sgRNA libraries. We further performed directed evolution of OsACC using MoBE and randomly dual sgRNA libraries in rice, and obtained single or linked mutations of stronger herbicide resistance. These strategies are useful for in situ directed evolution of functional genes and may accelerate trait improvement in rice.
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Affiliation(s)
- Ao Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Tiaofeng Shan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Yan Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Zhipeng Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Jianjian Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Zhichao Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Ziheng Ming
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Zhitao Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Xue Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Jun He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Shijia Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Ling Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome EditingInstitute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesBeijingChina
| | - Yuqiang Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Chao Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
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Yoon DE, Kim NR, Park SJ, Jeong TY, Eun B, Cho Y, Lim SY, Lee H, Seong JK, Kim K. Precise base editing without unintended indels in human cells and mouse primary myoblasts. Exp Mol Med 2023; 55:2586-2595. [PMID: 38036737 PMCID: PMC10766602 DOI: 10.1038/s12276-023-01128-4] [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: 05/03/2023] [Revised: 08/09/2023] [Accepted: 09/21/2023] [Indexed: 12/02/2023] Open
Abstract
Base editors are powerful tools for making precise single-nucleotide changes in the genome. However, they can lead to unintended insertions and deletions at the target sites, which is a significant limitation for clinical applications. In this study, we aimed to eliminate unwanted indels at the target sites caused by various evolved base editors. Accordingly, we applied dead Cas9 instead of nickase Cas9 in the base editors to induce accurate substitutions without indels. Additionally, we tested the use of chromatin-modulating peptides in the base editors to improve nucleotide conversion efficiency. We found that using both dead Cas9 and chromatin-modulating peptides in base editing improved the nucleotide substitution efficiency without unintended indel mutations at the desired target sites in human cell lines and mouse primary myoblasts. Furthermore, the proposed scheme had fewer off-target effects than conventional base editors at the DNA level. These results indicate that the suggested approach is promising for the development of more accurate and safer base editing techniques for use in clinical applications.
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Affiliation(s)
- Da Eun Yoon
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Medicine, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Na-Rae Kim
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Soo-Ji Park
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Medicine, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Tae Yeong Jeong
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Medicine, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Bokkee Eun
- Core Laboratory for Convergent Translational Research, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Yongcheol Cho
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Soo-Yeon Lim
- Korea Mouse Phenotyping Center, Seoul National University, 08826, Seoul, Republic of Korea
| | - Hyunji Lee
- Department of Medicine, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, 28116, Cheongju, Republic of Korea
| | - Je Kyoung Seong
- Korea Mouse Phenotyping Center, Seoul National University, 08826, Seoul, Republic of Korea
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, 08826, Seoul, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
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Liu Y, Li Q, Yan T, Chen H, Wang J, Wang Y, Yang Y, Xiang L, Chi Z, Ren K, Lin B, Lin G, Li J, Liu Y, Gu F. Adenine base editor-mediated splicing remodeling activates noncanonical splice sites. J Biol Chem 2023; 299:105442. [PMID: 37949222 PMCID: PMC10704375 DOI: 10.1016/j.jbc.2023.105442] [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: 05/18/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
Adenine base editors (ABEs) are genome-editing tools that have been harnessed to introduce precise A•T to G•C conversion. The discovery of split genes revealed that all introns contain two highly conserved dinucleotides, canonical "AG" (acceptor) and "GT" (donor) splice sites. ABE can directly edit splice acceptor sites of the adenine (A) base, leading to aberrant gene splicing, which may be further adopted to remodel splicing. However, spliced isoforms triggered with ABE have not been well explored. To address it, we initially generated a cell line harboring C-terminal enhanced GFP (eGFP)-tagged β-actin (ACTB), in which the eGFP signal can track endogenous β-actin expression. Expectedly, after the editing of splice acceptor sites, we observed a dramatical decrease in the percentage of eGFP-positive cells and generation of splicing products with the noncanonical splice site. Furthermore, we manipulated Peroxidasin in mouse embryos with ABE, in which a noncanonical acceptor was activated to remodel splicing, successfully generating a mouse disease model of anophthalmia and severely malformed microphthalmia. Collectively, we demonstrate that ABE-mediated splicing remodeling can activate a noncanonical acceptor to manipulate human and mouse genomes, which will facilitate the investigation of basic and translational medicine studies.
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Affiliation(s)
- Yuanyuan Liu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China; Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University, Changsha, China
| | - Qing Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tong Yan
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Haoran Chen
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Jiahua Wang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Yingyi Wang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Yeqin Yang
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lue Xiang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Zailong Chi
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Kaiqun Ren
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University, Changsha, China
| | - Bin Lin
- School of Optometry, Hong Kong Polytechnic University, Hong Kong, China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Yong Liu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China.
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China; Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University, Changsha, China; Guangxiu Hospital Affiliated with Hunan Normal University (Hunan Guangxiu Hospital), Changsha, China.
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Xue C, Qiu F, Wang Y, Li B, Zhao KT, Chen K, Gao C. Tuning plant phenotypes by precise, graded downregulation of gene expression. Nat Biotechnol 2023; 41:1758-1764. [PMID: 36894598 DOI: 10.1038/s41587-023-01707-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
The ability to control gene expression and generate quantitative phenotypic changes is essential for breeding new and desired traits into crops. Here we report an efficient, facile method for downregulating gene expression to predictable, desired levels by engineering upstream open reading frames (uORFs). We used base editing or prime editing to generate de novo uORFs or to extend existing uORFs by mutating their stop codons. By combining these approaches, we generated a suite of uORFs that incrementally downregulate the translation of primary open reading frames (pORFs) to 2.5-84.9% of the wild-type level. By editing the 5' untranslated region of OsDLT, which encodes a member of the GRAS family and is involved in the brassinosteroid transduction pathway, we obtained, as predicted, a series of rice plants with varied plant heights and tiller numbers. These methods offer an efficient way to obtain genome-edited plants with graded expression of traits.
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Affiliation(s)
- Chenxiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fengti Qiu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuxiang Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Wang J, Lin J, Chen Y, Liu J, Zheng Q, Deng M, Wang R, Zhang Y, Feng S, Xu Z, Ye W, Hu Y, Duan J, Lin Y, Dai J, Chen Y, Li Y, Luo T, Chen Q, Lu Z. An ultra-compact promoter drives widespread neuronal expression in mouse and monkey brains. Cell Rep 2023; 42:113348. [PMID: 37910509 DOI: 10.1016/j.celrep.2023.113348] [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: 10/18/2022] [Revised: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Promoters are essential tools for basic and translational neuroscience research. An ideal promoter should possess the shortest possible DNA sequence with cell-type selectivity. However, whether ultra-compact promoters can offer neuron-specific expression is unclear. Here, we report the development of an extremely short promoter that enables selective gene expression in neurons, but not glial cells, in the brain. The promoter sequence originates from the human CALM1 gene and is only 120 bp in size. The CALM1 promoter (pCALM1) embedded in an adeno-associated virus (AAV) genome directed broad reporter expression in excitatory and inhibitory neurons in mouse and monkey brains. Moreover, pCALM1, when inserted into an all-in-one AAV vector expressing SpCas9 and sgRNA, drives constitutive and conditional in vivo gene editing in neurons and elicits functional alterations. These data demonstrate the ability of pCALM1 to conduct restricted neuronal gene expression, illustrating the feasibility of ultra-miniature promoters for targeting brain-cell subtypes.
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Affiliation(s)
- Jingyi Wang
- Department of Anesthesiology, Peking University Shenzhen Hospital, Shenzhen 518034, China; Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbang Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yefei Chen
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jing Liu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China
| | - Qiongping Zheng
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mao Deng
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Ruiqi Wang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yujing Zhang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shijing Feng
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhenyan Xu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weiyi Ye
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Yu Hu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiamei Duan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yunping Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Dai
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yu Chen
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuantao Li
- Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China
| | - Tao Luo
- Department of Anesthesiology, Peking University Shenzhen Hospital, Shenzhen 518034, China
| | - Qian Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Zhonghua Lu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen 518055, China.
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135
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Sahu S, Poplawska M, Lim SH, Dutta D. CRISPR-based precision medicine for hematologic disorders: Advancements, challenges, and prospects. Life Sci 2023; 333:122165. [PMID: 37832631 DOI: 10.1016/j.lfs.2023.122165] [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: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
The development of programmable nucleases to introduce defined alterations in genomic sequences has been a powerful tool for precision medicine. While several nucleases such as zinc-finger nucleases (ZFN), transcriptor activator-like effector nucleases (TALEN), and meganucleases have been explored, the advent of CRISPR/Cas9 technology has revolutionized the field of genome engineering. In addition to disease modeling, the CRISPR/Cas9 technology has contributed to safer and more effective treatment strategies for hematologic diseases and personalized T-cell-based therapies. Here we discuss the applications of the CRISPR technology in the treatment of hematologic diseases, their efficacy, and ongoing clinical trials. We examine the obstacles to their successful use and the approaches investigated to overcome these challenges. Finally, we provide our perspectives to improve this genome editing tool for targeted therapies.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Building 560, Room 32-04, Frederick, MD 21702, USA.
| | - Maria Poplawska
- Department of Medicine (Division of Hematology and Oncology), State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Seah H Lim
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA
| | - Dibyendu Dutta
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA.
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Kennedy PH, Deh Sheikh AA, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer C, Alarcón S, Newby G, Myers SA. Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566649. [PMID: 38014346 PMCID: PMC10680671 DOI: 10.1101/2023.11.11.566649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe "signaling-to-transcription network" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of the phosphatase PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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137
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Zhao D, Gao X, Zhou J, Li J, Qian Y, Wang D, Niu W, Zhang T, Hu M, Xiong H, Lai L, Li Z. Engineered domain-inlaid Nme2Cas9 adenine base editors with increased on-target DNA editing and targeting scope. BMC Biol 2023; 21:250. [PMID: 37946200 PMCID: PMC10636962 DOI: 10.1186/s12915-023-01754-4] [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: 07/04/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Nme2ABE8e has been constructed and characterized as a compact, accurate adenine base editor with a less restrictive dinucleotide protospacer-adjacent motif (PAM: N4CC) but low editing efficiency at challenging loci in human cells. Here, we engineered a subset of domain-inlaid Nme2Cas9 base editors to bring the deaminase domain closer to the nontarget strand to improve editing efficiency. RESULTS Our results demonstrated that Nme2ABE8e-797 with adenine deaminase inserted between amino acids 797 and 798 has a significantly increased editing efficiency with a wide editing window ranging from 4 to 18 bases in mammalian cells, especially at the sites that were difficult to edit by Nme2ABE8e. In addition, by swapping the PAM-interacting domain of Nme2ABE8e-797 with that of SmuCas9 or introducing point mutations of eNme2-C in Nme2ABE8e-797, we created Nme2ABE8e-797Smu and Nme2ABE8e-797-C, respectively, which exhibited robust activities at a wide range of sites with N4CN PAMs in human cells. Moreover, the modified domain-inlaid Nme2ABE8e can efficiently restore or install disease-related loci in Neuro-2a cells and mice. CONCLUSIONS These novel Nme2ABE8es with increased on-target DNA editing and expanded PAM compatibility will expand the base editing toolset for efficient gene modification and therapeutic applications.
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Affiliation(s)
- Ding Zhao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xun Gao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jiale Zhou
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jinze Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yuqiang Qian
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Di Wang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Wenchao Niu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Tao Zhang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Mingyang Hu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Haoyang Xiong
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangzhou Regenerative Medicine and Health Guang Dong Laboratory (GRMH-GDL), Guangzhou, 510005, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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138
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [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: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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139
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Lebek S, Caravia XM, Chemello F, Tan W, McAnally JR, Chen K, Xu L, Liu N, Bassel-Duby R, Olson EN. Elimination of CaMKIIδ Autophosphorylation by CRISPR-Cas9 Base Editing Improves Survival and Cardiac Function in Heart Failure in Mice. Circulation 2023; 148:1490-1504. [PMID: 37712250 PMCID: PMC10842988 DOI: 10.1161/circulationaha.123.065117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Cardiovascular diseases are the main cause of worldwide morbidity and mortality, highlighting the need for new therapeutic strategies. Autophosphorylation and subsequent overactivation of the cardiac stress-responsive enzyme CaMKIIδ (Ca2+/calmodulin-dependent protein kinase IIδ) serves as a central driver of multiple cardiac disorders. METHODS To develop a comprehensive therapy for heart failure, we used CRISPR-Cas9 adenine base editing to ablate the autophosphorylation site of CaMKIIδ. We generated mice harboring a phospho-resistant CaMKIIδ mutation in the germline and subjected these mice to severe transverse aortic constriction, a model for heart failure. Cardiac function, transcriptional changes, apoptosis, and fibrosis were assessed by echocardiography, RNA sequencing, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and standard histology, respectively. Specificity toward CaMKIIδ gene editing was assessed using deep amplicon sequencing. Cellular Ca2+ homeostasis was analyzed using epifluorescence microscopy in Fura-2-loaded cardiomyocytes. RESULTS Within 2 weeks after severe transverse aortic constriction surgery, 65% of all wild-type mice died, and the surviving mice showed dramatically impaired cardiac function. In contrast to wild-type mice, CaMKIIδ phospho-resistant gene-edited mice showed a mortality rate of only 11% and exhibited substantially improved cardiac function after severe transverse aortic constriction. Moreover, CaMKIIδ phospho-resistant mice were protected from heart failure-related aberrant changes in cardiac gene expression, myocardial apoptosis, and subsequent fibrosis, which were observed in wild-type mice after severe transverse aortic constriction. On the basis of identical mouse and human genome sequences encoding the autophosphorylation site of CaMKIIδ, we deployed the same editing strategy to modify this pathogenic site in human induced pluripotent stem cells. It is notable that we detected a >2000-fold increased specificity for editing of CaMKIIδ compared with other CaMKII isoforms, which is an important safety feature. While wild-type cardiomyocytes showed impaired Ca2+ transients and an increased frequency of arrhythmias after chronic β-adrenergic stress, CaMKIIδ-edited cardiomyocytes were protected from these adverse responses. CONCLUSIONS Ablation of CaMKIIδ autophosphorylation by adenine base editing may offer a potential broad-based therapeutic concept for human cardiac disease.
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Affiliation(s)
- Simon Lebek
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
- Department of Internal Medicine II, University Hospital Regensburg; Regensburg, Germany
| | - Xurde M. Caravia
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Wei Tan
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - John R. McAnally
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center; Dallas, TX USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center; Dallas, TX USA
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Schmitt LT, Schneider A, Posorski J, Lansing F, Jelicic M, Jain M, Sayed S, Buchholz F, Sürün D. Quantification of evolved DNA-editing enzymes at scale with DEQSeq. Genome Biol 2023; 24:254. [PMID: 37932818 PMCID: PMC10626641 DOI: 10.1186/s13059-023-03097-3] [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: 04/06/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length sequences, editing efficiencies, and specificities from thousands of evolved enzymes simultaneously, DEQSeq streamlines the process of identifying the most valuable variants for further study and application. We apply DEQSeq to evolved libraries of Cas12f-ABEs and designer-recombinases, identifying variants with improved properties for future applications. Our results demonstrate that DEQSeq is a powerful tool for accelerating enzyme discovery and advancing genome editing research.
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Affiliation(s)
- Lukas Theo Schmitt
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
- Present Address: Seamless Therapeutics GmbH, Tatzberg 47/49, 01307, Dresden, Germany
| | - Aksana Schneider
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
- Present Address: Seamless Therapeutics GmbH, Tatzberg 47/49, 01307, Dresden, Germany
| | - Jonas Posorski
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
- Present Address: Seamless Therapeutics GmbH, Tatzberg 47/49, 01307, Dresden, Germany
| | - Milica Jelicic
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Manavi Jain
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Shady Sayed
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany.
| | - Duran Sürün
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany.
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141
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Li H, Ma T, Remsberg JR, Won SJ, DeMeester KE, Njomen E, Ogasawara D, Zhao KT, Huang TP, Lu B, Simon GM, Melillo B, Schreiber SL, Lykke-Andersen J, Liu DR, Cravatt BF. Assigning functionality to cysteines by base editing of cancer dependency genes. Nat Chem Biol 2023; 19:1320-1330. [PMID: 37783940 PMCID: PMC10698195 DOI: 10.1038/s41589-023-01428-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/24/2023] [Indexed: 10/04/2023]
Abstract
Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse human proteins. Determining which of these covalent binding events affect protein function, however, remains challenging. Here we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cancer cell proliferation. The resulting atlas, which covers more than 13,800 cysteines on more than 1,750 cancer dependency proteins, confirms the essentiality of cysteines targeted by covalent drugs and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines in more than 160 cancer dependency proteins. We further show that a stereoselective and site-specific ligand targeting an essential cysteine in TOE1 inhibits the nuclease activity of this protein through an apparent allosteric mechanism. Our findings thus describe a versatile method and valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.
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Affiliation(s)
- Haoxin Li
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | - Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Sang Joon Won
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | - Kevin T Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Bingwen Lu
- Vividion Therapeutics, San Diego, CA, USA
| | | | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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142
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Xiong X, Liu K, Li Z, Xia FN, Ruan XM, He X, Li JF. Split complementation of base editors to minimize off-target edits. NATURE PLANTS 2023; 9:1832-1847. [PMID: 37845337 DOI: 10.1038/s41477-023-01540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Base editors (BEs) empower the efficient installation of beneficial or corrective point mutations in crop and human genomes. However, conventional BEs can induce unpredictable guide RNA (gRNA)-independent off-target edits in the genome and transcriptome due to spurious activities of BE-enclosing deaminases, and current improvements mostly rely on deaminase-specific mutagenesis or exogenous regulators. Here we developed a split deaminase for safe editing (SAFE) system applicable to BEs containing distinct cytidine or adenosine deaminases, with no need of external regulators. In SAFE, a BE was properly split at a deaminase domain embedded inside a Cas9 nickase, simultaneously fragmenting and deactivating both the deaminase and the Cas9 nickase. The gRNA-conditioned BE reassembly conferred robust on-target editing in plant, human and yeast cells, while minimizing both gRNA-independent and gRNA-dependent off-target DNA/RNA edits. SAFE also substantially increased product purity by eliminating indels. Altogether, SAFE provides a generalizable solution for BEs to suppress off-target editing and improve on-target performance.
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Affiliation(s)
- Xiangyu Xiong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kehui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Zhenxiang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xue-Ming Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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143
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Ting WW, Ng IS. Tunable T7 Promoter Orthogonality on T7RNAP for cis-Aconitate Decarboxylase Evolution via Base Editor and Screening from Itaconic Acid Biosensor. ACS Synth Biol 2023; 12:3020-3029. [PMID: 37750409 PMCID: PMC10595973 DOI: 10.1021/acssynbio.3c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Indexed: 09/27/2023]
Abstract
The deaminase-fused T7 RNA polymerase (T7RNAP) presents a promising toolkit for in vivo target-specific enzyme evolution, offering the unique advantage of simultaneous DNA modification and screening. Previous studies have reported the mutation efficiency of base editors relying on different resources. In contrast, the mechanism underlying the T7RNAP/T7 system is well-understood. Therefore, this study aimed to establish a new platform, termed dT7-Muta, by tuning the binding efficiency between T7RNAP and the T7 promoter for gene mutagenesis. The strategy for proof-of-concept involves alterations in the fluorescence distribution through dT7-Muta and screening of the mutants via flow cytometry. The cis-aconitate decarboxylase from Aspergillus terreus (AtCadA) was evolved and screened via an itaconate-induced biosensor as proof-of-function of enzyme evolution. First, the degenerated codons were designed within the binding and initial region of T7 promoters (dT7s), including upstream (U), central (C), and downstream (D) regions. Three strength variants of dT7 promoter from each design, i.e., strong (S), medium (M), and weak (W), were used for evaluation. Mutation using dT7s of varying strength resulted in a broader fluorescence distribution in sfGFP mutants from the promoters CW and DS. On the other hand, broader fluorescence distribution was observed in the AtCadA mutants from the original promoter T7, UW, and DS, with the highest fluorescence and itaconic acid titer at 860 a.u. and 0.51 g/L, respectively. The present platform introduces a novel aspect of the deaminase-based mutagenesis, emphasizing the potential of altering the binding efficiency between T7RNAP and the T7 promoter for further efforts in enzyme evolution.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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144
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Hong S, Kim S, Kim K, Lee H. Clinical Approaches for Mitochondrial Diseases. Cells 2023; 12:2494. [PMID: 37887337 PMCID: PMC10605124 DOI: 10.3390/cells12202494] [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: 09/26/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Mitochondria are subcontractors dedicated to energy production within cells. In human mitochondria, almost all mitochondrial proteins originate from the nucleus, except for 13 subunit proteins that make up the crucial system required to perform 'oxidative phosphorylation (OX PHOS)', which are expressed by the mitochondria's self-contained DNA. Mitochondrial DNA (mtDNA) also encodes 2 rRNA and 22 tRNA species. Mitochondrial DNA replicates almost autonomously, independent of the nucleus, and its heredity follows a non-Mendelian pattern, exclusively passing from mother to children. Numerous studies have identified mtDNA mutation-related genetic diseases. The consequences of various types of mtDNA mutations, including insertions, deletions, and single base-pair mutations, are studied to reveal their relationship to mitochondrial diseases. Most mitochondrial diseases exhibit fatal symptoms, leading to ongoing therapeutic research with diverse approaches such as stimulating the defective OXPHOS system, mitochondrial replacement, and allotropic expression of defective enzymes. This review provides detailed information on two topics: (1) mitochondrial diseases caused by mtDNA mutations, and (2) the mechanisms of current treatments for mitochondrial diseases and clinical trials.
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Affiliation(s)
- Seongho Hong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea;
- Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Sanghun Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea;
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kyoungmi Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hyunji Lee
- Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
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145
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Haldrup J, Andersen S, Labial AR, Wolff JH, Frandsen F, Skov T, Rovsing A, Nielsen I, Jakobsen TS, Askou A, Thomsen M, Corydon T, Thomsen E, Mikkelsen J. Engineered lentivirus-derived nanoparticles (LVNPs) for delivery of CRISPR/Cas ribonucleoprotein complexes supporting base editing, prime editing and in vivo gene modification. Nucleic Acids Res 2023; 51:10059-10074. [PMID: 37678882 PMCID: PMC10570023 DOI: 10.1093/nar/gkad676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/07/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023] Open
Abstract
Implementation of therapeutic in vivo gene editing using CRISPR/Cas relies on potent delivery of gene editing tools. Administration of ribonucleoprotein (RNP) complexes consisting of Cas protein and single guide RNA (sgRNA) offers short-lived editing activity and safety advantages over conventional viral and non-viral gene and RNA delivery approaches. By engineering lentivirus-derived nanoparticles (LVNPs) to facilitate RNP delivery, we demonstrate effective administration of SpCas9 as well as SpCas9-derived base and prime editors (BE/PE) leading to gene editing in recipient cells. Unique Gag/GagPol protein fusion strategies facilitate RNP packaging in LVNPs, and refinement of LVNP stoichiometry supports optimized LVNP yield and incorporation of therapeutic payload. We demonstrate near instantaneous target DNA cleavage and complete RNP turnover within 4 days. As a result, LVNPs provide high on-target DNA cleavage and lower levels of off-target cleavage activity compared to standard RNP nucleofection in cultured cells. LVNPs accommodate BE/sgRNA and PE/epegRNA RNPs leading to base editing with reduced bystander editing and prime editing without detectable indel formation. Notably, in the mouse eye, we provide the first proof-of-concept for LVNP-directed in vivo gene disruption. Our findings establish LVNPs as promising vehicles for delivery of RNPs facilitating donor-free base and prime editing without formation of double-stranded DNA breaks.
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Affiliation(s)
- Jakob Haldrup
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Sofie Andersen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | | | | | | | | | | | - Ian Nielsen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Thomas Stax Jakobsen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Aarhus N, Denmark
| | - Anne Louise Askou
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Aarhus N, Denmark
| | | | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Aarhus N, Denmark
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146
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Zhao L, Koseki SRT, Silverstein RA, Amrani N, Peng C, Kramme C, Savic N, Pacesa M, Rodríguez TC, Stan T, Tysinger E, Hong L, Yudistyra V, Ponnapati MR, Jacobson JM, Church GM, Jakimo N, Truant R, Jinek M, Kleinstiver BP, Sontheimer EJ, Chatterjee P. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 2023; 14:6175. [PMID: 37794046 PMCID: PMC10550912 DOI: 10.1038/s41467-023-41829-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.
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Affiliation(s)
- Lin Zhao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Christina Peng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christian Kramme
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Natasha Savic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Tomás C Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Teodora Stan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emma Tysinger
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lauren Hong
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Vivian Yudistyra
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Joseph M Jacobson
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Noah Jakimo
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Pranam Chatterjee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
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147
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Kabra M, Shahi PK, Wang Y, Sinha D, Spillane A, Newby GA, Saxena S, Tong Y, Chang Y, Abdeen AA, Edwards KL, Theisen CO, Liu DR, Gamm DM, Gong S, Saha K, Pattnaik BR. Nonviral base editing of KCNJ13 mutation preserves vision in a model of inherited retinal channelopathy. J Clin Invest 2023; 133:e171356. [PMID: 37561581 PMCID: PMC10541187 DOI: 10.1172/jci171356] [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: 04/11/2023] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
Clinical genome editing is emerging for rare disease treatment, but one of the major limitations is the targeting of CRISPR editors' delivery. We delivered base editors to the retinal pigmented epithelium (RPE) in the mouse eye using silica nanocapsules (SNCs) as a treatment for retinal degeneration. Leber congenital amaurosis type 16 (LCA16) is a rare pediatric blindness caused by point mutations in the KCNJ13 gene, a loss of function inwardly rectifying potassium channel (Kir7.1) in the RPE. SNCs carrying adenine base editor 8e (ABE8e) mRNA and sgRNA precisely and efficiently corrected the KCNJ13W53X/W53X mutation. Editing in both patient fibroblasts (47%) and human induced pluripotent stem cell-derived RPE (LCA16-iPSC-RPE) (17%) showed minimal off-target editing. We detected functional Kir7.1 channels in the edited LCA16-iPSC-RPE. In the LCA16 mouse model (Kcnj13W53X/+ΔR), RPE cells targeted SNC delivery of ABE8e mRNA preserved normal vision, measured by full-field electroretinogram (ERG). Moreover, multifocal ERG confirmed the topographic measure of electrical activity primarily originating from the edited retinal area at the injection site. Preserved retina structure after treatment was established by optical coherence tomography (OCT). This preclinical validation of targeted ion channel functional rescue, a challenge for pharmacological and genomic interventions, reinforced the effectiveness of nonviral genome-editing therapy for rare inherited disorders.
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Affiliation(s)
- Meha Kabra
- Department of Pediatrics
- McPherson Eye Research Institute
| | - Pawan K. Shahi
- Department of Pediatrics
- McPherson Eye Research Institute
| | - Yuyuan Wang
- Department of Biomedical Engineering
- Wisconsin Institute of Discovery, and
| | - Divya Sinha
- McPherson Eye Research Institute
- Waisman Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | | | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute and
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Shivani Saxena
- McPherson Eye Research Institute
- Department of Biomedical Engineering
- Wisconsin Institute of Discovery, and
| | - Yao Tong
- Department of Biomedical Engineering
- Wisconsin Institute of Discovery, and
| | | | - Amr A. Abdeen
- McPherson Eye Research Institute
- Department of Biomedical Engineering
- Wisconsin Institute of Discovery, and
| | - Kimberly L. Edwards
- McPherson Eye Research Institute
- Waisman Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Cole O. Theisen
- Waisman Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute and
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - David M. Gamm
- McPherson Eye Research Institute
- Waisman Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Ophthalmology and Visual Sciences and
| | - Shaoqin Gong
- McPherson Eye Research Institute
- Department of Biomedical Engineering
- Wisconsin Institute of Discovery, and
- Department of Ophthalmology and Visual Sciences and
| | - Krishanu Saha
- Department of Pediatrics
- McPherson Eye Research Institute
- Department of Biomedical Engineering
- Wisconsin Institute of Discovery, and
- Center for Human Genomics and Precision Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Bikash R. Pattnaik
- Department of Pediatrics
- McPherson Eye Research Institute
- Department of Ophthalmology and Visual Sciences and
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148
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Xia K, Wang F, Tan Z, Zhang S, Lai X, Ou W, Yang C, Chen H, Peng H, Luo P, Hu A, Tu X, Wang T, Ke Q, Deng C, Xiang AP. Precise Correction of Lhcgr Mutation in Stem Leydig Cells by Prime Editing Rescues Hereditary Primary Hypogonadism in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300993. [PMID: 37697644 PMCID: PMC10582410 DOI: 10.1002/advs.202300993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/20/2023] [Indexed: 09/13/2023]
Abstract
Hereditary primary hypogonadism (HPH), caused by gene mutation related to testosterone synthesis in Leydig cells, usually impairs male sexual development and spermatogenesis. Genetically corrected stem Leydig cells (SLCs) transplantation may provide a new approach for treating HPH. Here, a novel nonsense-point-mutation mouse model (LhcgrW495X ) is first generated based on a gene mutation relative to HPH patients. To verify the efficacy and feasibility of SLCs transplantation in treating HPH, wild-type SLCs are transplanted into LhcgrW495X mice, in which SLCs obviously rescue HPH phenotypes. Through comparing several editing strategies, optimized PE2 protein (PEmax) system is identified as an efficient and precise approach to correct the pathogenic point mutation in Lhcgr. Furthermore, delivering intein-split PEmax system via lentivirus successfully corrects the mutation in SLCs from LhcgrW495X mice ex vivo. Gene-corrected SLCs from LhcgrW495X mice exert ability to differentiate into functional Leydig cells in vitro. Notably, the transplantation of gene-corrected SLCs effectively regenerates Leydig cells, recovers testosterone production, restarts sexual development, rescues spermatogenesis, and produces fertile offspring in LhcgrW495X mice. Altogether, these results suggest that PE-based gene editing in SLCs ex vivo is a promising strategy for HPH therapy and is potentially leveraged to address more hereditary diseases in reproductive system.
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Affiliation(s)
- Kai Xia
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Fulin Wang
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Zhipeng Tan
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Suyuan Zhang
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Xingqiang Lai
- Cardiovascular DepartmentThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdong518033China
| | - Wangsheng Ou
- State Key Laboratory of Ophthalmology Zhong Shan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouGuangdong510000China
| | - Cuifeng Yang
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Hong Chen
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Hao Peng
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Peng Luo
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Anqi Hu
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Xiang'an Tu
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Tao Wang
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Qiong Ke
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Chunhua Deng
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
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149
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Jewel D, Pham Q, Chatterjee A. Virus-assisted directed evolution of biomolecules. Curr Opin Chem Biol 2023; 76:102375. [PMID: 37542745 PMCID: PMC10870257 DOI: 10.1016/j.cbpa.2023.102375] [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: 03/27/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 08/07/2023]
Abstract
Directed evolution is a powerful technique that uses principles of natural evolution to enable the development of biomolecules with novel functions. However, the slow pace of natural evolution does not support the demand for rapidly generating new biomolecular functions in the laboratory. Viruses offer a unique path to design fast laboratory evolution experiments, owing to their innate ability to evolve much more rapidly than most living organisms, facilitated by a smaller genome size that tolerate a high frequency of mutations, as well as a fast rate of replication. These attributes offer a great opportunity to evolve various biomolecules by linking their activity to the replication of a suitable virus. This review highlights the recent advances in the application of virus-assisted directed evolution of designer biomolecules in both prokaryotic and eukaryotic cells.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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Cui Y, Cao Q, Li Y, He M, Liu X. Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5441-5457. [PMID: 37402253 DOI: 10.1093/jxb/erad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
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Affiliation(s)
- Yue Cui
- College of Teacher Education, Molecular and Cellular Postdoctoral Research Station, Hebei Normal University, Shijiazhuang 050024, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiao Cao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mingqi He
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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