1
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Castillo SR, Simone BW, Clark KJ, Devaux P, Ekker SC. Unconstrained precision mitochondrial genome editing with αDdCBEs. Hum Gene Ther 2024. [PMID: 39212664 DOI: 10.1089/hum.2024.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs work in pairs, with each arm composed of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA are predicted to remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5'-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this requirement, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5'-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated DdCBEs containing TALE proteins engineered to recognize all 5' bases. These modified DdCBEs are herein referred to as αDdCBEs. Notably, 5'-T-noncompliant canonical DdCBEs efficiently edited mtDNA at diverse loci. However, they were frequently outperformed by αDdCBEs, which exhibited significant improvements in activity and specificity, regardless of the most 5' bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with the enhanced DddAtox variants DddA6 and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
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Affiliation(s)
- Santiago R Castillo
- Mayo Clinic, Virology and Gene Therapy Graduate Program, Rochester, Minnesota, United States
- Mayo Clinic, Department of Molecular Medicine, Rochester, Minnesota, United States
- Mayo Clinic, Department of Biochemistry and Molecular Biology, Rochester, Minnesota, United States;
| | - Brandon W Simone
- Mayo Clinic, Department of Biochemistry and Molecular Biology, Rochester, Minnesota, United States
- University of Pennsylvania Perelman School of Medicine, Center for Cellular Immunotherapies, Philadelphia, Pennsylvania, United States;
| | - Karl J Clark
- Mayo Clinic, Department of Biochemistry and Molecular Biology, Rochester, Minnesota, United States
- Texas A&M University, Department of Animal Science, College Station, Texas, United States;
| | - Patricia Devaux
- Mayo Clinic, Department of Molecular Medicine, Rochester, Minnesota, United States
- Mayo Clinic, Virology and Gene Therapy Graduate Program, Rochester, Minnesota, United States;
| | - Stephen C Ekker
- Mayo Clinic, Department of Biochemistry and Molecular Biology, Rochester, Minnesota, United States
- The University of Texas at Austin Dell Medical School, Department of Pediatrics and Department of Molecular Biosciences, Austin, Texas, United States;
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2
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Sahu S, Castro M, Muldoon JJ, Asija K, Wyman SK, Krishnappa N, de Onate L, Eyquem J, Nguyen DN, Wilson RC. Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.14.603391. [PMID: 39071446 PMCID: PMC11275745 DOI: 10.1101/2024.07.14.603391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) is a new approach for ex vivo genome editing of primary human cells. PERC uses a single amphiphilic peptide reagent to mediate intracellular delivery of the same pre-formed CRISPR ribonucleoprotein enzymes that are broadly used in research and therapeutics, resulting in high-efficiency editing of stimulated immune cells and cultured hematopoietic stem and progenitor cells (HSPCs). PERC facilitates nuclease-mediated gene knockout, precise transgene knock-in, and base editing. PERC involves mixing the CRISPR ribonucleoprotein enzyme with peptide and then incubating the formulation with cultured cells. For efficient transgene knock-in, adeno-associated virus (AAV) bearing homology-directed repair template DNA may be included. In contrast to electroporation, PERC is appealing as it requires no dedicated hardware and has less impact on cell phenotype and viability. Due to the gentle nature of PERC, delivery can be performed multiple times without substantial impact to cell health or phenotype. Here we report methods for improved PERC-mediated editing of T cells as well as novel methods for PERC-mediated editing of HSPCs, including knockout and precise knock-in. Editing efficiencies can surpass 90% using either Cas9 or Cas12a in primary T cells or HSPCs. Because PERC calls for only three readily available reagents - protein, RNA, and peptide - and does not require dedicated hardware for any step, PERC demands no special expertise and is exceptionally straightforward to adopt. The inherent compatibility of PERC with established cell engineering pipelines makes this approach appealing for rapid deployment in research and clinical settings.
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3
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Maxim DS, Wu DW, Johnson NS, Charu V, Carter JN, Anand S, Church GM, Bhalla V. EditABLE: A Simple Web Application for Designing Genome Editing Experiments. RESEARCH SQUARE 2024:rs.3.rs-4775705. [PMID: 39184070 PMCID: PMC11343172 DOI: 10.21203/rs.3.rs-4775705/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
CRISPR-Cas genome editing is transformative; however, there is no simple tool available for determining the optimal genome editing technology to create specific mutations for experimentation or to correct mutations as a curative therapy for specific diseases. We developed editABLE, an online resource (editable-app.stanford.edu) to provide computationally validated CRISPR editors and guide RNAs based on user provided sequence data. We demonstrate the utility of editABLE by applying it to one of the most common monogenic disorders, autosomal dominant polycystic kidney disease (ADPKD), identifying specific editing tools across the landscape of ADPKD mutations.
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4
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Lu G, Shivalila C, Monian P, Yu H, Harding I, Briem S, Byrne M, Faraone A, Friend S, Huth O, Iwamoto N, Kawamoto T, Kumarasamy J, Lamattina A, Longo K, McCarthy L, McGlynn A, Molski A, Pan Q, Pu T, Purcell-Estabrook E, Rossi J, Standley S, Thomas C, Walen A, Yang H, Kandasamy P, Vargeese C. Rational design of base, sugar and backbone modifications improves ADAR-mediated RNA editing. Nucleic Acids Res 2024:gkae681. [PMID: 39149897 DOI: 10.1093/nar/gkae681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
AIMers are short, chemically modified oligonucleotides that induce A-to-I RNA editing through interaction with endogenous adenosine deaminases acting on RNA (ADAR) enzymes. Here, we describe the development of new AIMer designs with base, sugar and backbone modifications that improve RNA editing efficiency over our previous design. AIMers incorporating a novel pattern of backbone and 2' sugar modifications support enhanced editing efficiency across multiple sequences. Further efficiency gains were achieved through incorporation of an N-3-uridine (N3U), in place of cytidine (C), in the 'orphan base' position opposite the edit site. Molecular modeling suggests that N3U might enhance ADAR catalytic activity by stabilizing the AIMer-ADAR interaction and potentially reducing the energy required to flip the target base into the active site. Supporting this hypothesis, AIMers containing N3U consistently enhanced RNA editing over those containing C across multiple target sequences and multiple nearest neighbor sequence combinations. AIMers combining N3U and the novel pattern of 2' sugar chemistry and backbone modifications improved RNA editing both in vitro and in vivo. We provide detailed N3U synthesis methods and, for the first time, explore the impact of N3U and its analogs on ADAR-mediated RNA editing efficiency and targetable sequence space.
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Affiliation(s)
| | | | | | - Hui Yu
- Wave Life Sciences, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tom Pu
- Wave Life Sciences, Cambridge, MA, USA
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5
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Li XD, Liu LM, Xi YC, Sun QW, Luo Z, Huang HL, Wang XW, Jiang HB, Chen W. Development of a base editor for convenient and multiplex genome editing in cyanobacteria. Commun Biol 2024; 7:994. [PMID: 39143188 PMCID: PMC11324792 DOI: 10.1038/s42003-024-06696-3] [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: 01/02/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
Cyanobacteria are important primary producers, contributing to 25% of the global carbon fixation through photosynthesis. They serve as model organisms to study the photosynthesis, and are important cell factories for synthetic biology. To enable efficient genetic dissection and metabolic engineering in cyanobacteria, effective and accurate genetic manipulation tools are required. However, genetic manipulation in cyanobacteria by the conventional homologous recombination-based method and the recently developed CRISPR-Cas gene editing system require complicated cloning steps, especially during multi-site editing and single base mutation. This restricts the extensive research on cyanobacteria and reduces its application potential. In this study, a highly efficient and convenient cytosine base editing system was developed which allows rapid and precise C → T point mutation and gene inactivation in the genomes of Synechocystis and Anabaena. This base editing system also enables efficient multiplex editing and can be easily cured after editing by sucrose counter-selection. This work will expand the knowledge base regarding the engineering of cyanobacteria. The findings of this study will encourage the biotechnological applications of cyanobacteria.
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Affiliation(s)
- Xing-Da Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling-Mei Liu
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yi-Cao Xi
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Qiao-Wei Sun
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Zhen Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Long Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xin-Wei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Bo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.
| | - Weizhong Chen
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
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Li M, Cai Z, Song S, Yue X, Lu W, Rao S, Zhang C, Xue C. EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms. Nucleic Acids Res 2024; 52:8628-8642. [PMID: 38994565 PMCID: PMC11317134 DOI: 10.1093/nar/gkae612] [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: 10/04/2023] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
Precise gene regulation and programmable RNA editing are vital RNA-level regulatory mechanisms. Gene repression tools grounded in small non-coding RNAs, microRNAs, and CRISPR-dCas proteins, along with RNA editing tools anchored in Adenosine Deaminases acting on RNA (ADARs), have found extensive application in molecular biology and cellular engineering. Here, we introduced a novel approach wherein we developed an EcCas6e mediated crRNA-mRNA annealing system for gene repression in Escherichia coli and RNA editing in Saccharomyces cerevisiae. We found that EcCas6e possesses inherent RNA annealing ability attributed to a secondary positively charged cleft, enhancing crRNA-mRNA hybridization and stability. Based on this, we demonstrated that EcCas6e, along with its cognate crRNA repeat containing a complementary region to the ribosome binding site of a target mRNA, effectively represses gene expression up to 25-fold. Furthermore, we demonstrated that multiple crRNAs can be easily assembled and can simultaneously target up to 13 genes. Lastly, the EcCas6e-crRNA system was developed as an RNA editing tool by fusing it with the ADAR2 deaminase domain. The EcCas6e-crRNA mediated gene repression and RNA editing tools hold broad applications for research and biotechnology.
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Affiliation(s)
- Mutong Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhaohui Cai
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shucheng Song
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinmin Yue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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7
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Li P, Dong D, Gao F, Xie Y, Huang H, Sun S, Ma Z, He C, Lai J, Du X, Wu S. Versatile and efficient mammalian genome editing with Type I-C CRISPR System of Desulfovibrio vulgaris. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2682-5. [PMID: 39126615 DOI: 10.1007/s11427-023-2682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024]
Abstract
CRISPR-Cas tools for mammalian genome editing typically rely on single Cas9 or Cas12a proteins. While type I CRISPR systems in Class I may offer greater specificity and versatility, they are not well-developed for genome editing. Here, we present an alternative type I-C CRISPR system from Desulfovibrio vulgaris (Dvu) for efficient and precise genome editing in mammalian cells and animals. We optimized the Dvu type I-C editing complex to generate precise deletions at multiple loci in various cell lines and pig primary fibroblast cells using a paired PAM-in crRNA strategy. These edited pig cells can serve as donors for generating transgenic cloned piglets. The Dvu type I-C editor also enabled precise large fragment replacements with homology-directed repair. Additionally, we adapted the Dvu-Cascade effector for cytosine and adenine base editing, developing Dvu-CBE and Dvu-ABE systems. These systems efficiently induced C-to-T and A-to-G substitutions in human genes without double-strand breaks. Off-target analysis confirmed the high specificity of the Dvu type I-C editor. Our findings demonstrate the Dvu type I-C editor's potential for diverse mammalian genome editing applications, including deletions, fragment replacement, and base editing, with high efficiency and specificity for biomedicine and agriculture.
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Affiliation(s)
- Pan Li
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Dingcai Dong
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Fei Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuyang Xie
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Honglin Huang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Siwei Sun
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhao Ma
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Cheng He
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
| | - Sen Wu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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Tonetto E, Cucci A, Follenzi A, Bernardi F, Pinotti M, Balestra D. DNA base editing corrects common hemophilia A mutations and restores factor VIII expression in in vitro and ex vivo models. J Thromb Haemost 2024; 22:2171-2183. [PMID: 38718928 DOI: 10.1016/j.jtha.2024.04.020] [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: 01/22/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Replacement and nonreplacement therapies effectively control bleeding in hemophilia A (HA) but imply lifelong interventions. Authorized gene addition therapy could provide a cure but still poses questions on durability. FVIIIgene correction would definitively restore factor (F)VIII production, as shown in animal models through nuclease-mediated homologous recombination (HR). However, low efficiency and potential off-target double-strand break still limit HR translatability. OBJECTIVES To correct common model single point mutations leading to severe HA through the recently developed double-strand break/HR-independent base editing (BE) and prime editing (PE) approaches. METHODS Screening for efficacy of BE/PE systems in HEK293T cells transiently expressing FVIII variants and validation at DNA (sequencing) and protein (enzyme-linked immunosorbent assay; activated partial thromboplastin time) level in stable clones. Evaluation of rescue in engineered blood outgrowth endothelial cells by lentiviral-mediated delivery of BE. RESULTS Transient assays identified the best-performing BE/PE systems for each variant, with the highest rescue of FVIII expression (up to 25% of wild-type recombinant FVIII) for the p.R2166∗ and p.R2228Q mutations. In stable clones, we demonstrated that the mutation reversion on DNA (∼24%) was consistent with the rescue of FVIII secretion and activity of 20% to 30%. The lentiviral-mediated delivery of the selected BE systems was attempted in engineered blood outgrowth endothelial cells harboring the p.R2166∗ and p.R2228Q variants, which led to an appreciable and dose-dependent rescue of secreted functional FVIII. CONCLUSION Overall data provide the first proof-of-concept for effective BE/PE-mediated correction of HA-causing mutations, which encourage studies in mouse models to develop a personalized cure for large cohorts of patients through a single intervention.
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Affiliation(s)
- Elena Tonetto
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Alessia Cucci
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
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Brödel AK, Charpenay LH, Galtier M, Fuche FJ, Terrasse R, Poquet C, Havránek J, Pignotti S, Krawczyk A, Arraou M, Prevot G, Spadoni D, Yarnall MTN, Hessel EM, Fernandez-Rodriguez J, Duportet X, Bikard D. In situ targeted base editing of bacteria in the mouse gut. Nature 2024; 632:877-884. [PMID: 38987595 PMCID: PMC11338833 DOI: 10.1038/s41586-024-07681-w] [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: 03/17/2023] [Accepted: 06/06/2024] [Indexed: 07/12/2024]
Abstract
Microbiome research is now demonstrating a growing number of bacterial strains and genes that affect our health1. Although CRISPR-derived tools have shown great success in editing disease-driving genes in human cells2, we currently lack the tools to achieve comparable success for bacterial targets in situ. Here we engineer a phage-derived particle to deliver a base editor and modify Escherichia coli colonizing the mouse gut. Editing of a β-lactamase gene in a model E. coli strain resulted in a median editing efficiency of 93% of the target bacterial population with a single dose. Edited bacteria were stably maintained in the mouse gut for at least 42 days following treatment. This was achieved using a non-replicative DNA vector, preventing maintenance and dissemination of the payload. We then leveraged this approach to edit several genes of therapeutic relevance in E. coli and Klebsiella pneumoniae strains in vitro and demonstrate in situ editing of a gene involved in the production of curli in a pathogenic E. coli strain. Our work demonstrates the feasibility of modifying bacteria directly in the gut, offering a new avenue to investigate the function of bacterial genes and opening the door to the design of new microbiome-targeted therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - David Bikard
- Eligo Bioscience, Paris, France.
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France.
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10
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Benavides-Nieto M, Adam F, Martin E, Boussard C, Lagresle-Peyrou C, Callebaut I, Kauskot A, Repérant C, Feng M, Bordet JC, Castelle M, Morelle G, Brouzes C, Zarhrate M, Panikulam P, Lambert N, Picard C, Bodet D, Rouger-Gaudichon J, Revy P, de Villartay JP, Moshous D. Somatic RAP1B gain-of-function variant underlies isolated thrombocytopenia and immunodeficiency. J Clin Invest 2024; 134:e169994. [PMID: 39225097 DOI: 10.1172/jci169994] [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: 03/07/2023] [Accepted: 07/10/2024] [Indexed: 09/04/2024] Open
Abstract
The ubiquitously expressed small GTPase Ras-related protein 1B (RAP1B) acts as a molecular switch that regulates cell signaling, cytoskeletal remodeling, and cell trafficking and activates integrins in platelets and lymphocytes. The residue G12 in the P-loop is required for the RAP1B-GTPase conformational switch. Heterozygous germline RAP1B variants have been described in patients with syndromic thrombocytopenia. However, the causality and pathophysiological impact remained unexplored. We report a boy with neonatal thrombocytopenia, combined immunodeficiency, neutropenia, and monocytopenia caused by a heterozygous de novo single nucleotide substitution, c.35G>A (p.G12E) in RAP1B. We demonstrate that G12E and the previously described G12V and G60R were gain-of-function variants that increased RAP1B activation, talin recruitment, and integrin activation, thereby modifying late responses such as platelet activation, T cell proliferation, and migration. We show that in our patient, G12E was a somatic variant whose allele frequency decreased over time in the peripheral immune compartment, but remained stable in bone marrow cells, suggesting a differential effect in distinct cell populations. Allogeneic hematopoietic stem cell transplantation fully restored the patient's hemato-immunological phenotype. Our findings define monoallelic RAP1B gain-of-function variants as a cause for constitutive immunodeficiency and thrombocytopenia. The phenotypic spectrum ranged from isolated hematological manifestations in our patient with somatic mosaicism to complex syndromic features in patients with reported germline RAP1B variants.
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Affiliation(s)
- Marta Benavides-Nieto
- Université Paris Cité, Paris, France
- Imagine Institute, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, Ligue 2023, INSERM UMR 1163, Paris, France
- General Pediatrics-Infectious Diseases and Internal Medicine, Hôpital Robert Debré, Assistance Publique-Hôpitaux de Paris (AP-HP) Nord, Paris, France
| | - Frédéric Adam
- INSERM UMR S 1176, Laboratory for Hemostasis, Inflammation and Thrombosis (HITh), Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Emmanuel Martin
- Laboratory Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Charlotte Boussard
- Université Paris Cité, Paris, France
- Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
- Laboratory Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Chantal Lagresle-Peyrou
- Biotherapy Clinical Investigation Center, AP-HP, Paris, France
- Laboratory Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Isabelle Callebaut
- Sorbonne University, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Alexandre Kauskot
- INSERM UMR S 1176, Laboratory for Hemostasis, Inflammation and Thrombosis (HITh), Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Christelle Repérant
- INSERM UMR S 1176, Laboratory for Hemostasis, Inflammation and Thrombosis (HITh), Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Miao Feng
- INSERM UMR S 1176, Laboratory for Hemostasis, Inflammation and Thrombosis (HITh), Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Jean-Claude Bordet
- Laboratoire d'Hémostase, Centre de Biologie Est, Hospices Civils de Lyon, Bron, France
| | - Martin Castelle
- Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Guillaume Morelle
- Université Paris Cité, Paris, France
- Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Chantal Brouzes
- Laboratory of Onco-Hematology, Necker-Enfants Malades University Hospital, AP-HP, Paris, France, and INSERM U1151, Institut Necker-Enfants Malades, Paris, France
| | - Mohammed Zarhrate
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 and INSERM US24/CNRS UAR3633, Paris Descartes Sorbonne Paris Cité University, Paris, France
| | - Patricia Panikulam
- Université Paris Cité, Paris, France
- Laboratory "Molecular basis of altered immune homeostasis," INSERM UMR 1163, Imagine Institute, Paris, France
| | - Nathalie Lambert
- Study Center for Primary Immunodeficiencies, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Capucine Picard
- Université Paris Cité, Paris, France
- Laboratory Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
- Centre de Référence des Déficits Immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Damien Bodet
- CHU de Caen Normandie, Onco-Immunohématologie Pédiatrique, Caen, France
| | | | - Patrick Revy
- Université Paris Cité, Paris, France
- Imagine Institute, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, Ligue 2023, INSERM UMR 1163, Paris, France
| | - Jean-Pierre de Villartay
- Université Paris Cité, Paris, France
- Imagine Institute, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, Ligue 2023, INSERM UMR 1163, Paris, France
| | - Despina Moshous
- Université Paris Cité, Paris, France
- Imagine Institute, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, Ligue 2023, INSERM UMR 1163, Paris, France
- Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
- Centre de Référence des Déficits Immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
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11
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Yao Y, Zhou Z, Wang X, Liu Z, Zhai Y, Chi X, Du J, Luo L, Zhao Z, Wang X, Xue C, Rao S. SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution. CELL GENOMICS 2024; 4:100583. [PMID: 38889719 PMCID: PMC11293580 DOI: 10.1016/j.xgen.2024.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/28/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024]
Abstract
CRISPR mutagenesis screens conducted with SpCas9 and other nucleases have identified certain cis-regulatory elements and genetic variants but at a limited resolution due to the absence of protospacer adjacent motif (PAM) sequences. Here, leveraging the broad targeting scope of the near-PAMless SpRY variant, we have demonstrated that saturated SpRY mutagenesis and base editing screens can faithfully identify functional regulatory elements and essential genetic variants for target gene expression at single-base resolution. We further extended this methodology to investigate a genome-wide association study (GWAS) locus at 10q22.1 associated with a red blood cell trait, where we identified potential enhancers regulating HK1 gene expression, despite not all of these enhancers exhibiting typical chromatin signatures. More importantly, our saturated base editing screens pinpoint multiple causal variants within this locus that would otherwise be missed by Bayesian statistical fine-mapping. Our approach is generally applicable to functional interrogation of all non-coding genomic elements while complementing other high-coverage CRISPR screens.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Zhiwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Xiaoling Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Zhirui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Yixin Zhai
- Department of Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiaolin Chi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingyi Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Liheng Luo
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Zhigang Zhao
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Xiaoyue Wang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
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12
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Shirguppe S, Gapinske M, Swami D, Gosstola N, Acharya P, Miskalis A, Joulani D, Szkwarek MG, Bhattacharjee A, Elias G, Stilger M, Winter J, Woods WS, Anand D, Lim CKW, Gaj T, Perez-Pinera P. In vivo CRISPR base editing for treatment of Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602282. [PMID: 39005280 PMCID: PMC11245100 DOI: 10.1101/2024.07.05.602282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Huntington's disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.
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13
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Qin W, Liang F, Lin SJ, Petree C, Huang K, Zhang Y, Li L, Varshney P, Mourrain P, Liu Y, Varshney GK. ABE-ultramax for high-efficiency biallelic adenine base editing in zebrafish. Nat Commun 2024; 15:5613. [PMID: 38965236 PMCID: PMC11224239 DOI: 10.1038/s41467-024-49943-1] [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: 10/27/2023] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
Advancements in CRISPR technology, particularly the development of base editors, revolutionize genetic variant research. When combined with model organisms like zebrafish, base editors significantly accelerate and refine in vivo analysis of genetic variations. However, base editors are restricted by protospacer adjacent motif (PAM) sequences and specific editing windows, hindering their applicability to a broad spectrum of genetic variants. Additionally, base editors can introduce unintended mutations and often exhibit reduced efficiency in living organisms compared to cultured cell lines. Here, we engineer a suite of adenine base editors (ABEs) called ABE-Ultramax (Umax), demonstrating high editing efficiency and low rates of insertions and deletions (indels) in zebrafish. The ABE-Umax suite of editors includes ABEs with shifted, narrowed, or broadened editing windows, reduced bystander mutation frequency, and highly flexible PAM sequence requirements. These advancements have the potential to address previous challenges in disease modeling and advance gene therapy applications.
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Affiliation(s)
- Wei Qin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Fang Liang
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangzhou, Guangdong, 510631, China
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Yu Zhang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Lin Li
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, South China Normal University, 510631, Guangzhou, China
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, 510631, Guangzhou, China
| | - Pratishtha Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, South China Normal University, 510631, Guangzhou, China.
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, 510631, Guangzhou, China.
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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14
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Wu LY, Xu Y, Yu XW. Efficient CRISPR-mediated C-to-T base editing in Komagataella phaffii. Biotechnol J 2024; 19:e2400115. [PMID: 38987223 DOI: 10.1002/biot.202400115] [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: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 07/12/2024]
Abstract
The nonconventional methylotrophic yeast Komagataella phaffii is widely applied in the production of industrial enzymes, pharmaceutical proteins, and various high-value chemicals. The development of robust and versatile genome editing tools for K. phaffii is crucial for the design of increasingly advanced cell factories. Here, we first developed a base editing method for K. phaffii based on the CRISPR-nCas9 system. We engineered 24 different base editor constructs, using a variety of promoters and cytidine deaminases (CDAs). The optimal base editor (PAOX2*-KpA3A-nCas9-KpUGI-DAS1TT) comprised a truncated AOX2 promoter (PAOX2*), a K. phaffii codon-optimized human APOBEC3A CDA (KpA3A), human codon-optimized nCas9 (D10A), and a K. phaffii codon-optimized uracil glycosylase inhibitor (KpUGI). This optimal base editor efficiently performed C-to-T editing in K. phaffii, with single-, double-, and triple-locus editing efficiencies of up to 96.0%, 65.0%, and 5.0%, respectively, within a 7-nucleotide window from C-18 to C-12. To expand the targetable genomic region, we also replaced nCas9 in the optimal base editor with nSpG and nSpRy, and achieved 50.0%-60.0% C-to-T editing efficiency for NGN-protospacer adjacent motif (PAM) sites and 20.0%-93.2% C-to-T editing efficiency for NRN-PAM sites, respectively. Therefore, these constructed base editors have emerged as powerful tools for gene function research, metabolic engineering, genetic improvement, and functional genomics research in K. phaffii.
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Affiliation(s)
- Ling-Yu Wu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiao-Wei Yu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
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15
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [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: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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16
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Lian M, Chen T, Chen M, Peng X, Yang Y, Luo X, Chi Y, Wang J, Tang C, Zhou X, Zhang K, Qin C, Lai L, Zhou J, Zou Q. A modified glycosylase base editor without predictable DNA off-target effects. FEBS Lett 2024. [PMID: 38946058 DOI: 10.1002/1873-3468.14970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
Glycosylase base editor (GBE) can induce C-to-G transversion in mammalian cells, showing great promise for the treatment of human genetic disorders. However, the limited efficiency of transversion and the possibility of off-target effects caused by Cas9 restrict its potential clinical applications. In our recent study, we have successfully developed TaC9-CBE and TaC9-ABE by separating nCas9 and deaminase, which eliminates the Cas9-dependent DNA off-target effects without compromising editing efficiency. We developed a novel GBE called TaC9-GBEYE1, which utilizes the deaminase and UNG-nCas9 guided by TALE and sgRNA, respectively. TaC9-GBEYE1 showed comparable levels of on-target editing efficiency to traditional GBE at 19 target sites, without any off-target effects caused by Cas9 or TALE. The TaC9-GBEYE1 is a safe tool for gene therapy.
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Affiliation(s)
- Meng Lian
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Research Unit of Generation of Large Animal Disease Models, Guangzhou, China
| | - Tao Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaohua Peng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yang Yang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xian Luo
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yue Chi
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Jinling Wang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaoqing Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Kun Zhang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liangxue Lai
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Research Unit of Generation of Large Animal Disease Models, Guangzhou, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jizeng Zhou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
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17
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Chen S, Lo CH, Liu Z, Wang Q, Ning K, Li T, Sun Y. Base editing correction of OCRL in Lowe syndrome: ABE-mediated functional rescue in patient-derived fibroblasts. Hum Mol Genet 2024; 33:1142-1151. [PMID: 38557732 DOI: 10.1093/hmg/ddae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Lowe syndrome, a rare X-linked multisystem disorder presenting with major abnormalities in the eyes, kidneys, and central nervous system, is caused by mutations in OCRL gene (NG_008638.1). Encoding an inositol polyphosphate 5-phosphatase, OCRL catalyzes the hydrolysis of PI(4,5)P2 into PI4P. There are no effective targeted treatments for Lowe syndrome. Here, we demonstrate a novel gene therapy for Lowe syndrome in patient fibroblasts using an adenine base editor (ABE) that can efficiently correct pathogenic point mutations. We show that ABE8e-NG-based correction of a disease-causing mutation in a Lowe patient-derived fibroblast line containing R844X mutation in OCRL gene, restores OCRL expression at mRNA and protein levels. It also restores cellular abnormalities that are hallmarks of OCRL dysfunction, including defects in ciliogenesis, microtubule anchoring, α-actinin distribution, and F-actin network. The study indicates that ABE-mediated gene therapy is a feasible treatment for Lowe syndrome, laying the foundation for therapeutic application of ABE in the currently incurable disease.
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Affiliation(s)
- Siyu Chen
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Chien-Hui Lo
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Zhiquan Liu
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Qing Wang
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Ke Ning
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Tingting Li
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
- Department of Ophthalmology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Pudong district, Shanghai 200120, China
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
- Palo Alto Veterans Administration, 3801 Miranda Avenue, Palo Alto, CA 94304, United States
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18
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Sun Y, Chatterjee S, Lian X, Traylor Z, Sattiraju SR, Xiao Y, Dilliard SA, Sung YC, Kim M, Lee SM, Moore S, Wang X, Zhang D, Wu S, Basak P, Wang J, Liu J, Mann RJ, LePage DF, Jiang W, Abid S, Hennig M, Martinez A, Wustman BA, Lockhart DJ, Jain R, Conlon RA, Drumm ML, Hodges CA, Siegwart DJ. In vivo editing of lung stem cells for durable gene correction in mice. Science 2024; 384:1196-1202. [PMID: 38870301 DOI: 10.1126/science.adk9428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024]
Abstract
In vivo genome correction holds promise for generating durable disease cures; yet, effective stem cell editing remains challenging. In this work, we demonstrate that optimized lung-targeting lipid nanoparticles (LNPs) enable high levels of genome editing in stem cells, yielding durable responses. Intravenously administered gene-editing LNPs in activatable tdTomato mice achieved >70% lung stem cell editing, sustaining tdTomato expression in >80% of lung epithelial cells for 660 days. Addressing cystic fibrosis (CF), NG-ABE8e messenger RNA (mRNA)-sgR553X LNPs mediated >95% cystic fibrosis transmembrane conductance regulator (CFTR) DNA correction, restored CFTR function in primary patient-derived bronchial epithelial cells equivalent to Trikafta for F508del, corrected intestinal organoids and corrected R553X nonsense mutations in 50% of lung stem cells in CF mice. These findings introduce LNP-enabled tissue stem cell editing for disease-modifying genome correction.
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Affiliation(s)
- Yehui Sun
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sumanta Chatterjee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xizhen Lian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zachary Traylor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | | | - Yufen Xiao
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sean A Dilliard
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yun-Chieh Sung
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minjeong Kim
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sang M Lee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stephen Moore
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xu Wang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Di Zhang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shiying Wu
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pratima Basak
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jialu Wang
- ReCode Therapeutics, Menlo Park, CA 94025, USA
| | - Jing Liu
- ReCode Therapeutics, Menlo Park, CA 94025, USA
| | - Rachel J Mann
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - David F LePage
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Weihong Jiang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shadaan Abid
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | | | - Raksha Jain
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ronald A Conlon
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mitchell L Drumm
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Craig A Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Daniel J Siegwart
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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19
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Zhu H, Wang L, Wang Y, Jiang X, Qin Q, Song M, Huang Q. Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e. Cell Mol Life Sci 2024; 81:257. [PMID: 38874784 PMCID: PMC11335294 DOI: 10.1007/s00018-024-05263-7] [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: 03/01/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 06/15/2024]
Abstract
Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.
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Affiliation(s)
- Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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20
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Naiisseh B, Papasavva PL, Papaioannou NY, Tomazou M, Koniali L, Felekis X, Constantinou CG, Sitarou M, Christou S, Kleanthous M, Lederer CW, Patsali P. Context base editing for splice correction of IVSI-110 β-thalassemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102183. [PMID: 38706633 PMCID: PMC11068610 DOI: 10.1016/j.omtn.2024.102183] [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] [Received: 10/04/2023] [Accepted: 03/28/2024] [Indexed: 05/07/2024]
Abstract
β-Thalassemia is brought about by defective β-globin (HBB [hemoglobin subunit β]) formation and, in severe cases, requires regular blood transfusion and iron chelation for survival. Genome editing of hematopoietic stem cells allows correction of underlying mutations as curative therapy. As potentially safer alternatives to double-strand-break-based editors, base editors (BEs) catalyze base transitions for precision editing of DNA target sites, prompting us to reclone and evaluate two recently published adenine BEs (ABEs; SpRY and SpG) with relaxed protospacer adjacent motif requirements for their ability to correct the common HBBIVSI-110(G>A) splice mutation. Nucleofection of ABE components as RNA into patient-derived CD34+ cells achieved up to 90% editing of upstream sequence elements critical for aberrant splicing, allowing full characterization of the on-target base-editing profile of each ABE and the detection of differences in on-target insertions and deletions. In addition, this study identifies opposing effects on splice correction for two neighboring context bases, establishes the frequency distribution of multiple BE editing events in the editing window, and shows high-efficiency functional correction of HBBIVSI-110(G>A) for our ABEs, including at the levels of RNA, protein, and erythroid differentiation.
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Affiliation(s)
- Basma Naiisseh
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Panayiota L. Papasavva
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Nikoletta Y. Papaioannou
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, Agios Dometios, Nicosia 2371, Cyprus
| | - Lola Koniali
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Xenia Felekis
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Constantina G. Constantinou
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, State Health Services Organization, Larnaca 6301, Cyprus
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, State Health Services Organization, Strovolos, Nicosia 2012, Cyprus
| | - Marina Kleanthous
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Petros Patsali
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
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21
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Christensen CL, Kan SH, Andrade-Heckman P, Rha AK, Harb JF, Wang RY. Base editing rescues acid α-glucosidase function in infantile-onset Pompe disease patient-derived cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102220. [PMID: 38948331 PMCID: PMC11214518 DOI: 10.1016/j.omtn.2024.102220] [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] [Received: 11/21/2023] [Accepted: 05/16/2024] [Indexed: 07/02/2024]
Abstract
Infantile-onset Pompe disease (IOPD) results from pathogenic variants in the GAA gene, which encodes acid α-glucosidase. The correction of pathogenic variants through genome editing may be a valuable one-time therapy for PD and improve upon the current standard of care. We performed adenine base editing in human dermal fibroblasts harboring three transition nonsense variants, c.2227C>T (p.Q743∗; IOPD-1), c.2560C>T (p.R854∗; IOPD-2), and c.2608C>T (p.R870∗; IOPD-3). Up to 96% adenine deamination of target variants was observed, with minimal editing across >50 off-target sites. Post-base editing, expressed GAA protein was up to 0.66-fold normal (unaffected fibroblasts), an improvement over affected fibroblasts wherein GAA was undetectable. GAA enzyme activity was between 81.91 ± 13.51 and 129.98 ± 9.33 units/mg protein at 28 days post-transfection, which falls within the normal range (50-200 units/mg protein). LAMP2 protein was significantly decreased in the most robustly edited cell line, IOPD-3, indicating reduced lysosomal burden. Taken together, the findings reported herein demonstrate that base editing results in efficacious adenine deamination, restoration of GAA expression and activity, and reduction in lysosomal burden in the most robustly edited cells. Future work will assess base editing outcomes and the impact on Pompe pathology in two mouse models, Gaa c.2227C>T and Gaa c.2560C>T.
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Affiliation(s)
| | - Shih-Hsin Kan
- CHOC Children’s Research Institute, Orange, CA 92868, USA
| | | | | | - Jerry F. Harb
- CHOC Children’s Research Institute, Orange, CA 92868, USA
| | - Raymond Y. Wang
- Division of Metabolic Disorders, CHOC Children’s Specialists, Orange, CA 92868, USA
- Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, CA 92697, USA
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22
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Prasad K, Devaraju N, George A, Ravi NS, Paul J, Mahalingam G, Rajendiran V, Panigrahi L, Venkatesan V, Lakhotiya K, Periyasami Y, Pai AA, Nakamura Y, Kurita R, Balasubramanian P, Thangavel S, Velayudhan SR, Newby GA, Marepally S, Srivastava A, Mohankumar KM. Precise correction of a spectrum of β-thalassemia mutations in coding and non-coding regions by base editors. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102205. [PMID: 38817682 PMCID: PMC11137594 DOI: 10.1016/j.omtn.2024.102205] [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] [Received: 04/28/2023] [Accepted: 04/26/2024] [Indexed: 06/01/2024]
Abstract
β-thalassemia/HbE results from mutations in the β-globin locus that impede the production of functional adult hemoglobin. Base editors (BEs) could facilitate the correction of the point mutations with minimal or no indel creation, but its efficiency and bystander editing for the correction of β-thalassemia mutations in coding and non-coding regions remains unexplored. Here, we screened BE variants in HUDEP-2 cells for their ability to correct a spectrum of β-thalassemia mutations that were integrated into the genome as fragments of HBB. The identified targets were introduced into their endogenous genomic location using BEs and Cas9/homology-directed repair (HDR) to create cellular models with β-thalassemia/HbE. These β-thalassemia/HbE models were then used to assess the efficiency of correction in the native locus and functional β-globin restoration. Most bystander edits produced near target sites did not interfere with adult hemoglobin expression and are not predicted to be pathogenic. Further, the effectiveness of BE was validated for the correction of the pathogenic HbE variant in severe β0/βE-thalassaemia patient cells. Overall, our study establishes a novel platform to screen and select optimal BE tools for therapeutic genome editing by demonstrating the precise, efficient, and scarless correction of pathogenic point mutations spanning multiple regions of HBB including the promoter, intron, and exons.
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Affiliation(s)
- Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Vigneshwaran Venkatesan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Kartik Lakhotiya
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Boston MA 02111, USA
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 3050074, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Poonkuzhali Balasubramanian
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Shaji R. Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Gregory A. Newby
- Departments of Genetic Medicine and Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Kumarasamypet M. Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
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23
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Zhang L, Li K, Liu Z, An L, Wei H, Pang S, Cao Z, Huang X, Jin X, Ma X. Restoring T and B cell generation in X-linked severe combined immunodeficiency mice through hematopoietic stem cells adenine base editing. Mol Ther 2024; 32:1658-1671. [PMID: 38532630 PMCID: PMC11184316 DOI: 10.1016/j.ymthe.2024.03.028] [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: 07/18/2023] [Revised: 01/15/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
Base editing of hematopoietic stem/progenitor cells (HSPCs) is an attractive strategy for treating immunohematologic diseases. However, the feasibility of using adenine-base-edited HSPCs for treating X-linked severe combined immunodeficiency (SCID-X1), the influence of dose-response relationships on immune cell generation, and the potential risks have not been demonstrated in vivo. Here, a humanized SCID-X1 mouse model was established, and 86.67% ± 2.52% (n = 3) of mouse hematopoietic stem cell (HSC) pathogenic mutations were corrected, with no single-guide-RNA (sgRNA)-dependent off-target effects detected. Analysis of peripheral blood over 16 weeks post-transplantation in mice with different immunodeficiency backgrounds revealed efficient immune cell generation following transplantation of different amounts of modified HSCs. Therefore, a large-scale infusion of gene-corrected HSCs within a safe range can achieve rapid, stable, and durable immune cell regeneration. Tissue-section staining further demonstrated the restoration of immune organ tissue structures, with no tumor formation in multiple organs. Collectively, these data suggest that base-edited HSCs are a potential therapeutic approach for SCID-X1 and that a threshold infusion dose of gene-corrected cells is required for immune cell regeneration. This study lays a theoretical foundation for the clinical application of base-edited HSCs in treating SCID-X1.
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Affiliation(s)
- Lu Zhang
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Lisha An
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Haikun Wei
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Shanshan Pang
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Zongfu Cao
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaohua Jin
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China.
| | - Xu Ma
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China.
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24
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Garaudé S, Marone R, Lepore R, Devaux A, Beerlage A, Seyres D, Dell' Aglio A, Juskevicius D, Zuin J, Burgold T, Wang S, Katta V, Manquen G, Li Y, Larrue C, Camus A, Durzynska I, Wellinger LC, Kirby I, Van Berkel PH, Kunz C, Tamburini J, Bertoni F, Widmer CC, Tsai SQ, Simonetta F, Urlinger S, Jeker LT. Selective haematological cancer eradication with preserved haematopoiesis. Nature 2024; 630:728-735. [PMID: 38778101 PMCID: PMC11186773 DOI: 10.1038/s41586-024-07456-3] [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: 08/07/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Haematopoietic stem cell (HSC) transplantation (HSCT) is the only curative treatment for a broad range of haematological malignancies, but the standard of care relies on untargeted chemotherapies and limited possibilities to treat malignant cells after HSCT without affecting the transplanted healthy cells1. Antigen-specific cell-depleting therapies hold the promise of much more targeted elimination of diseased cells, as witnessed in the past decade by the revolution of clinical practice for B cell malignancies2. However, target selection is complex and limited to antigens expressed on subsets of haematopoietic cells, resulting in a fragmented therapy landscape with high development costs2-5. Here we demonstrate that an antibody-drug conjugate (ADC) targeting the pan-haematopoietic marker CD45 enables the antigen-specific depletion of the entire haematopoietic system, including HSCs. Pairing this ADC with the transplantation of human HSCs engineered to be shielded from the CD45-targeting ADC enables the selective eradication of leukaemic cells with preserved haematopoiesis. The combination of CD45-targeting ADCs and engineered HSCs creates an almost universal strategy to replace a diseased haematopoietic system, irrespective of disease aetiology or originating cell type. We propose that this approach could have broad implications beyond haematological malignancies.
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Affiliation(s)
- Simon Garaudé
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Rosalba Lepore
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
- Cimeio Therapeutics, Basel, Switzerland
| | - Anna Devaux
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Astrid Beerlage
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
- Department of Hematology, Basel University Hospital, Basel, Switzerland
| | - Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Alessandro Dell' Aglio
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Darius Juskevicius
- Department of Laboratory Medicine, Diagnostic Hematology, Basel University Hospital, Basel, Switzerland
| | - Jessica Zuin
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Thomas Burgold
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Sisi Wang
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Varun Katta
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Garret Manquen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Clément Larrue
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
| | | | | | | | | | | | | | - Jérôme Tamburini
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Corinne C Widmer
- Department of Hematology, Basel University Hospital, Basel, Switzerland
- Department of Laboratory Medicine, Diagnostic Hematology, Basel University Hospital, Basel, Switzerland
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Federico Simonetta
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland.
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland.
- Innovation Focus Cell Therapy, Basel University Hospital, Basel, Switzerland.
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25
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Kennedy PH, Alborzian Deh Sheikh A, 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 CG, Alarcón S, Newby GA, Myers SA. Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput. Nat Methods 2024; 21:1033-1043. [PMID: 38684783 DOI: 10.1038/s41592-024-02256-z] [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: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
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 the high-throughput, functional assessment of phosphorylation sites 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 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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Affiliation(s)
- Patrick H Kennedy
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Amin Alborzian Deh Sheikh
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Alexander C Jones
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | | | - Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria I Matias
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Natan Pirete
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajan Burt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Levy
- 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
| | - Tamia Little
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Patrick G Hogan
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Program in Immunology, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, 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
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzie Alarcón
- La Jolla Institute for Immunology, La Jolla, CA, USA
- AUGenomics, San Diego, CA, 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
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA.
- Program in Immunology, University of California San Diego, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA.
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26
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Fiumara M, Ferrari S, Omer-Javed A, Beretta S, Albano L, Canarutto D, Varesi A, Gaddoni C, Brombin C, Cugnata F, Zonari E, Naldini MM, Barcella M, Gentner B, Merelli I, Naldini L. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat Biotechnol 2024; 42:877-891. [PMID: 37679541 PMCID: PMC11180610 DOI: 10.1038/s41587-023-01915-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/26/2023] [Indexed: 09/09/2023]
Abstract
Base and prime editors (BEs and PEs) may provide more precise genetic engineering than nuclease-based approaches because they bypass the dependence on DNA double-strand breaks. However, little is known about their cellular responses and genotoxicity. Here, we compared state-of-the-art BEs and PEs and Cas9 in human hematopoietic stem and progenitor cells with respect to editing efficiency, cytotoxicity, transcriptomic changes and on-target and genome-wide genotoxicity. BEs and PEs induced detrimental transcriptional responses that reduced editing efficiency and hematopoietic repopulation in xenotransplants and also generated DNA double-strand breaks and genotoxic byproducts, including deletions and translocations, at a lower frequency than Cas9. These effects were strongest for cytidine BEs due to suboptimal inhibition of base excision repair and were mitigated by tailoring delivery timing and editor expression through optimized mRNA design. However, BEs altered the mutational landscape of hematopoietic stem and progenitor cells across the genome by increasing the load and relative proportions of nucleotide variants. These findings raise concerns about the genotoxicity of BEs and PEs and warrant further investigation in view of their clinical application.
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Affiliation(s)
- Martina Fiumara
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Attya Omer-Javed
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Canarutto
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelica Varesi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Gaddoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Brombin
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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27
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Walsh ZH, Shah P, Kothapalli N, Shah SB, Nikolenyi G, Brodtman DZ, Leuzzi G, Rogava M, Mu M, Ho P, Abuzaid S, Vasan N, AlQuraishi M, Milner JD, Ciccia A, Melms JC, Izar B. Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens. Nat Biotechnol 2024:10.1038/s41587-024-02235-x. [PMID: 38783148 DOI: 10.1038/s41587-024-02235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Single-nucleotide variants (SNVs) in key T cell genes can drive clinical pathologies and could be repurposed to improve cellular cancer immunotherapies. Here, we perform massively parallel base-editing screens to generate thousands of variants at gene loci annotated with known or potential clinical relevance. We discover a broad landscape of putative gain-of-function (GOF) and loss-of-function (LOF) mutations, including in PIK3CD and the gene encoding its regulatory subunit, PIK3R1, LCK, SOS1, AKT1 and RHOA. Base editing of PIK3CD and PIK3R1 variants in T cells with an engineered T cell receptor specific to a melanoma epitope or in different generations of CD19 chimeric antigen receptor (CAR) T cells demonstrates that discovered GOF variants, but not LOF or silent mutation controls, enhanced signaling, cytokine production and lysis of cognate melanoma and leukemia cell models, respectively. Additionally, we show that generations of CD19 CAR T cells engineered with PIK3CD GOF mutations demonstrate enhanced antigen-specific signaling, cytokine production and leukemia cell killing, including when benchmarked against other recent strategies.
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Affiliation(s)
- Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Parin Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Neeharika Kothapalli
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gergo Nikolenyi
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - D Zack Brodtman
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Meri Rogava
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Sinan Abuzaid
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Mohammed AlQuraishi
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Johannes C Melms
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Benjamin Izar
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA.
- Columbia Center for Translational Immunology, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
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28
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Chapus F, Giraud G, Huchon P, Rodà M, Grand X, Charre C, Goldsmith C, Roca Suarez AA, Martinez MG, Fresquet J, Diederichs A, Locatelli M, Polvèche H, Scholtès C, Chemin I, Hernandez Vargas H, Rivoire M, Bourgeois CF, Zoulim F, Testoni B. Helicases DDX5 and DDX17 promote heterogeneity in HBV transcription termination in infected human hepatocytes. J Hepatol 2024:S0168-8278(24)00351-9. [PMID: 38782119 DOI: 10.1016/j.jhep.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/28/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND & AIMS Transcription termination fine-tunes gene expression and contributes to the specification of RNA function in eukaryotic cells. Transcription termination of HBV is subject to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. However, the regulation of this cPAS and its impact on viral gene expression and replication is currently unknown. METHODS To unravel the regulation of HBV transcript termination, we implemented a 3' RACE (rapid amplification of cDNA ends)-PCR assay coupled to single molecule sequencing both in in vitro-infected hepatocytes and in chronically infected patients. RESULTS The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. Gene expression downregulation experiments demonstrated a role for the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, in turn, associated with HBV RNA destabilization and decreased HBx protein expression. RNA and chromatin immunoprecipitation, together with mutation of the cPAS sequence, suggested a direct role of DDX5 and DDX17 in functionally linking cPAS recognition to transcriptional readthrough, HBV RNA stability and replication. CONCLUSIONS Our findings identify DDX5 and DDX17 as crucial determinants of HBV transcriptional fidelity and as host restriction factors for HBV replication. IMPACT AND IMPLICATIONS HBV covalently closed circular (ccc)DNA degradation or functional inactivation remains the holy grail for the achievement of HBV cure. Transcriptional fidelity is a cornerstone in the regulation of gene expression. Here, we demonstrate that two helicases, DDX5 and DDX17, inhibit recognition of the HBV polyadenylation signal and thereby transcriptional termination, thus decreasing HBV RNA stability and acting as restriction factors for efficient cccDNA transcription and viral replication. The observation that DDX5 and DDX17 are downregulated in patients chronically infected with HBV suggests a role for these helicases in HBV persistence in vivo. These results open new perspectives for researchers aiming at identifying new targets to neutralise cccDNA transcription.
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Affiliation(s)
- Fleur Chapus
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France
| | - Guillaume Giraud
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Pélagie Huchon
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Mélanie Rodà
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Xavier Grand
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Caroline Charre
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; Department of Virology, Croix Rousse Hospital, Hospices Civils de Lyon, Lyon, France
| | | | - Armando Andres Roca Suarez
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Maria-Guadalupe Martinez
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France
| | - Judith Fresquet
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Audrey Diederichs
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Maëlle Locatelli
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France
| | - Hélène Polvèche
- CECS/AFM, I-Stem, Corbeil-Essonnes, 91100, France; University Claude Bernard of Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 69007, Lyon, France
| | - Caroline Scholtès
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; Department of Virology, Croix Rousse Hospital, Hospices Civils de Lyon, Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Isabelle Chemin
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | | | - Michel Rivoire
- INSERM U1032, Centre Léon Bérard (CLB), 69008 Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Cyril F Bourgeois
- University Claude Bernard of Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 69007, Lyon, France
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; Department of Hepatology, Hospices Civils de Lyon, France; The Lyon Hepatology Institute EVEREST, France.
| | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France.
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29
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Bulcaen M, Kortleven P, Liu RB, Maule G, Dreano E, Kelly M, Ensinck MM, Thierie S, Smits M, Ciciani M, Hatton A, Chevalier B, Ramalho AS, Casadevall I Solvas X, Debyser Z, Vermeulen F, Gijsbers R, Sermet-Gaudelus I, Cereseto A, Carlon MS. Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. Cell Rep Med 2024; 5:101544. [PMID: 38697102 PMCID: PMC11148721 DOI: 10.1016/j.xcrm.2024.101544] [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: 07/26/2023] [Revised: 01/16/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved modulator therapies. We show that, upon DNA correction of the CFTR gene, the complex glycosylation, localization, and, most importantly, function of the CFTR protein are restored in HEK293T and 16HBE cell lines. These findings were subsequently validated in patient-derived rectal organoids and human nasal epithelial cells. Through analysis of predicted and experimentally identified candidate off-target sites in primary stem cells, we confirm previous reports on the high prime editor (PE) specificity and its potential for a curative CF gene editing therapy. To facilitate future screening of genetic strategies in a translational CF model, a machine learning algorithm was developed for dynamic quantification of CFTR function in organoids (DETECTOR: "detection of targeted editing of CFTR in organoids").
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Affiliation(s)
- Mattijs Bulcaen
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium.
| | - Phéline Kortleven
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Ronald B Liu
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; School of Engineering, University of Edinburgh, EH9 3JL Edinburgh, UK
| | - Giulia Maule
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Elise Dreano
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Mairead Kelly
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Marjolein M Ensinck
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Sam Thierie
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Maxime Smits
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Matteo Ciciani
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Aurelie Hatton
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Benoit Chevalier
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Anabela S Ramalho
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | | | - Zeger Debyser
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - François Vermeulen
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; Department of Pediatrics, UZ Leuven, 3000 Leuven, Belgium
| | - Rik Gijsbers
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Sermet-Gaudelus
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France; Cystic Fibrosis National Pediatric Reference Center, Pneumo-Allergologie Pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), 75015 Paris, France; European Reference Network, ERN-Lung CF, 60596 Frankfurt am Mein, Germany
| | - Anna Cereseto
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Marianne S Carlon
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium.
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30
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Selgrade DF, Fullenkamp DE, Chychula IA, Li B, Dellefave-Castillo L, Dubash AD, Ohiri J, Monroe TO, Blancard M, Tomar G, Holgren C, Burridge PW, George AL, Demonbreun AR, Puckelwartz MJ, George SA, Efimov IR, Green KJ, McNally EM. Susceptibility to innate immune activation in genetically mediated myocarditis. J Clin Invest 2024; 134:e180254. [PMID: 38768074 PMCID: PMC11213508 DOI: 10.1172/jci180254] [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: 02/12/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Myocarditis is clinically characterized by chest pain, arrhythmias, and heart failure, and treatment is often supportive. Mutations in DSP, a gene encoding the desmosomal protein desmoplakin, have been increasingly implicated in myocarditis. To model DSP-associated myocarditis and assess the role of innate immunity, we generated engineered heart tissues (EHTs) using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from patients with heterozygous DSP truncating variants (DSPtvs) and a gene-edited homozygous deletion cell line (DSP-/-). At baseline, DSP-/- EHTs displayed a transcriptomic signature of innate immune activation, which was mirrored by cytokine release. Importantly, DSP-/- EHTs were hypersensitive to Toll-like receptor (TLR) stimulation, demonstrating more contractile dysfunction compared with isogenic controls. Relative to DSP-/- EHTs, heterozygous DSPtv EHTs had less functional impairment. DSPtv EHTs displayed heightened sensitivity to TLR stimulation, and when subjected to strain, DSPtv EHTs developed functional deficits, indicating reduced contractile reserve compared with healthy controls. Colchicine or NF-κB inhibitors improved strain-induced force deficits in DSPtv EHTs. Genomic correction of DSP p.R1951X using adenine base editing reduced inflammatory biomarker release from EHTs. Thus, EHTs replicate electrical and contractile phenotypes seen in human myocarditis, implicating cytokine release as a key part of the myogenic susceptibility to inflammation. The heightened innate immune activation and sensitivity are targets for clinical intervention.
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Affiliation(s)
| | - Dominic E. Fullenkamp
- Center for Genetic Medicine and
- Bluhm Cardiovascular Institute, Department of Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Binjie Li
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois, USA
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine and
- Bluhm Cardiovascular Institute, Department of Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Adi D. Dubash
- Department of Biology, Furman University, Greenville, South Carolina, USA
- Department of Pathology
| | | | | | | | | | | | | | | | | | | | - Sharon A. George
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois, USA
| | - Igor R. Efimov
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois, USA
| | - Kathleen J. Green
- Department of Pathology
- Department of Dermatology, and
- R.H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elizabeth M. McNally
- Center for Genetic Medicine and
- Bluhm Cardiovascular Institute, Department of Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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31
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Castillo SR, Simone BW, Clark KJ, Devaux P, Ekker SC. Unconstrained Precision Mitochondrial Genome Editing with αDdCBEs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593977. [PMID: 38798498 PMCID: PMC11118498 DOI: 10.1101/2024.05.13.593977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
DddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs are often deployed as pairs, with each arm comprised of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5'-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this constraint, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5'-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated αDdCBEs that contain modified TALE proteins engineered to recognize all 5' bases. Notably, 5'-T-noncompliant, canonical DdCBEs efficiently edited mtDNA at diverse loci. However, DdCBEs were frequently outperformed by αDdCBEs, which consistently displayed significant improvements in activity and specificity, regardless of the 5'-most bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with DddA tox and its derivatives DddA6, and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes at a single target site. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
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Zhang D, Boch J. Development of TALE-adenine base editors in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1067-1077. [PMID: 37997697 PMCID: PMC11022790 DOI: 10.1111/pbi.14246] [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: 12/21/2022] [Revised: 10/10/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Base editors enable precise nucleotide changes at targeted genomic loci without requiring double-stranded DNA breaks or repair templates. TALE-adenine base editors (TALE-ABEs) are genome editing tools, composed of a DNA-binding domain from transcription activator-like effectors (TALEs), an engineered adenosine deaminase (TadA8e), and a cytosine deaminase domain (DddA), that allow A•T-to-G•C editing in human mitochondrial DNA. However, the editing ability of TALE-ABEs in plants apart from chloroplast DNA has not been described, so far, and the functional role how DddA enhances TadA8e is still unclear. We tested a series of TALE-ABEs with different deaminase fusion architectures in Nicotiana benthamiana and rice. The results indicate that the double-stranded DNA-specific cytosine deaminase DddA can boost the activities of single-stranded DNA-specific deaminases (TadA8e or APOBEC3A) on double-stranded DNA. We analysed A•T-to-G•C editing efficiencies in a β-glucuronidase reporter system and showed precise adenine editing in genomic regions with high product purity in rice protoplasts. Furthermore, we have successfully regenerated rice plants with A•T-to-G•C mutations in the chloroplast genome using TALE-ABE. Consequently, TALE-adenine base editors provide alternatives for crop improvement and gene therapy by editing nuclear or organellar genomes.
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Affiliation(s)
- Dingbo Zhang
- Institute of Plant GeneticsLeibniz Universität HannoverHannoverGermany
| | - Jens Boch
- Institute of Plant GeneticsLeibniz Universität HannoverHannoverGermany
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Chen TY, Lin SP, Huang DF, Huang HS, Tsai FC, Lee LJ, Lin HY, Huang HP. Mature neurons from iPSCs unveil neurodegeneration-related pathways in mucopolysaccharidosis type II: GSK-3β inhibition for therapeutic potential. Cell Death Dis 2024; 15:302. [PMID: 38684682 PMCID: PMC11058230 DOI: 10.1038/s41419-024-06692-9] [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: 01/11/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Mucopolysaccharidosis (MPS) type II is caused by a deficiency of iduronate-2-sulfatase and is characterized by the accumulation of glycosaminoglycans (GAGs). Without effective therapy, the severe form of MPS II causes progressive neurodegeneration and death. This study generated multiple clones of induced pluripotent stem cells (iPSCs) and their isogenic controls (ISO) from four patients with MPS II neurodegeneration. MPS II-iPSCs were successfully differentiated into cortical neurons with characteristic biochemical and cellular phenotypes, including axonal beadings positive for phosphorylated tau, and unique electrophysiological abnormalities, which were mostly rescued in ISO-iPSC-derived neurons. RNA sequencing analysis uncovered dysregulation in three major signaling pathways, including Wnt/β-catenin, p38 MAP kinase, and calcium pathways, in mature MPS II neurons. Further mechanistic characterization indicated that the dysregulation in calcium signaling led to an elevated intracellular calcium level, which might be linked to compromised survival of neurons. Based on these dysregulated pathways, several related chemicals and drugs were tested using this mature MPS II neuron-based platform and a small-molecule glycogen synthase kinase-3β inhibitor was found to significantly rescue neuronal survival, neurite morphology, and electrophysiological abnormalities in MPS II neurons. Our results underscore that the MPS II-iPSC-based platform significantly contributes to unraveling the mechanisms underlying the degeneration and death of MPS II neurons and assessing potential drug candidates. Furthermore, the study revealed that targeting the specific dysregulation of signaling pathways downstream of GAG accumulation in MPS II neurons with a well-characterized drug could potentially ameliorate neuronal degeneration.
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Affiliation(s)
- Tzu-Yu Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shuan-Pei Lin
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
| | - De-Fong Huang
- Graduate Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Feng-Chiao Tsai
- Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Jen Lee
- Graduate Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
| | - Hsiang-Po Huang
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan.
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Capin J, Harrison A, Raele RA, Yadav SKN, Baiwir D, Mazzucchelli G, Quinton L, Satchwell T, Toye A, Schaffitzel C, Berger I, Aulicino F. An engineered baculoviral protein and DNA co-delivery system for CRISPR-based mammalian genome editing. Nucleic Acids Res 2024; 52:3450-3468. [PMID: 38412306 PMCID: PMC11014373 DOI: 10.1093/nar/gkae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
CRISPR-based DNA editing technologies enable rapid and accessible genome engineering of eukaryotic cells. However, the delivery of genetically encoded CRISPR components remains challenging and sustained Cas9 expression correlates with higher off-target activities, which can be reduced via Cas9-protein delivery. Here we demonstrate that baculovirus, alongside its DNA cargo, can be used to package and deliver proteins to human cells. Using protein-loaded baculovirus (pBV), we demonstrate delivery of Cas9 or base editors proteins, leading to efficient genome and base editing in human cells. By implementing a reversible, chemically inducible heterodimerization system, we show that protein cargoes can selectively and more efficiently be loaded into pBVs (spBVs). Using spBVs we achieved high levels of multiplexed genome editing in a panel of human cell lines. Importantly, spBVs maintain high editing efficiencies in absence of detectable off-targets events. Finally, by exploiting Cas9 protein and template DNA co-delivery, we demonstrate up to 5% site-specific targeted integration of a 1.8 kb heterologous DNA payload using a single spBV in a panel of human cell lines. In summary, we demonstrate that spBVs represent a versatile, efficient and potentially safer alternative for CRISPR applications requiring co-delivery of DNA and protein cargoes.
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Affiliation(s)
- Julien Capin
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Alexandra Harrison
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Renata A Raele
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Sathish K N Yadav
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liege, B-4000 Liege, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Loic Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Timothy J Satchwell
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Ashley M Toye
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | | | - Imre Berger
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Francesco Aulicino
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
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Jalil S, Keskinen T, Juutila J, Sartori Maldonado R, Euro L, Suomalainen A, Lapatto R, Kuuluvainen E, Hietakangas V, Otonkoski T, Hyvönen ME, Wartiovaara K. Genetic and functional correction of argininosuccinate lyase deficiency using CRISPR adenine base editors. Am J Hum Genet 2024; 111:714-728. [PMID: 38579669 PMCID: PMC11023919 DOI: 10.1016/j.ajhg.2024.03.004] [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: 08/23/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024] Open
Abstract
Argininosuccinate lyase deficiency (ASLD) is a recessive metabolic disorder caused by variants in ASL. In an essential step in urea synthesis, ASL breaks down argininosuccinate (ASA), a pathognomonic ASLD biomarker. The severe disease forms lead to hyperammonemia, neurological injury, and even early death. The current treatments are unsatisfactory, involving a strict low-protein diet, arginine supplementation, nitrogen scavenging, and in some cases, liver transplantation. An unmet need exists for improved, efficient therapies. Here, we show the potential of a lipid nanoparticle-mediated CRISPR approach using adenine base editors (ABEs) for ASLD treatment. To model ASLD, we first generated human-induced pluripotent stem cells (hiPSCs) from biopsies of individuals homozygous for the Finnish founder variant (c.1153C>T [p.Arg385Cys]) and edited this variant using the ABE. We then differentiated the hiPSCs into hepatocyte-like cells that showed a 1,000-fold decrease in ASA levels compared to those of isogenic non-edited cells. Lastly, we tested three different FDA-approved lipid nanoparticle formulations to deliver the ABE-encoding RNA and the sgRNA targeting the ASL variant. This approach efficiently edited the ASL variant in fibroblasts with no apparent cell toxicity and minimal off-target effects. Further, the treatment resulted in a significant decrease in ASA, to levels of healthy donors, indicating restoration of the urea cycle. Our work describes a highly efficient approach to editing the disease-causing ASL variant and restoring the function of the urea cycle. This method relies on RNA delivered by lipid nanoparticles, which is compatible with clinical applications, improves its safety profile, and allows for scalable production.
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Affiliation(s)
- Sami Jalil
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Keskinen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Rocio Sartori Maldonado
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Liliya Euro
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Suomalainen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Risto Lapatto
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Emilia Kuuluvainen
- Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mervi E Hyvönen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kirmo Wartiovaara
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Clinical Genetics, Helsinki University Hospital, Helsinki, Finland.
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Vishy CE, Thomas C, Vincent T, Crawford DK, Goddeeris MM, Freedman BS. Genetics of cystogenesis in base-edited human organoids reveal therapeutic strategies for polycystic kidney disease. Cell Stem Cell 2024; 31:537-553.e5. [PMID: 38579684 PMCID: PMC11325856 DOI: 10.1016/j.stem.2024.03.005] [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: 02/21/2023] [Revised: 12/19/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
In polycystic kidney disease (PKD), microscopic tubules expand into macroscopic cysts. Among the world's most common genetic disorders, PKD is inherited via heterozygous loss-of-function mutations but is theorized to require additional loss of function. To test this, we establish human pluripotent stem cells in allelic series representing four common nonsense mutations, using CRISPR base editing. When differentiated into kidney organoids, homozygous mutants spontaneously form cysts, whereas heterozygous mutants (original or base corrected) express no phenotype. Using these, we identify eukaryotic ribosomal selective glycosides (ERSGs) as PKD therapeutics enabling ribosomal readthrough of these same nonsense mutations. Two different ERSGs not only prevent cyst initiation but also limit growth of pre-formed cysts by partially restoring polycystin expression. Furthermore, glycosides accumulate in cyst epithelia in organoids and mice. Our findings define the human polycystin threshold as a surmountable drug target for pharmacological or gene therapy interventions, with relevance for understanding disease mechanisms and future clinical trials.
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Affiliation(s)
- Courtney E Vishy
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Chardai Thomas
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Thomas Vincent
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA
| | - Daniel K Crawford
- Eloxx Pharmaceuticals, Inc., 950 Winter Street, Waltham, MA 02451, USA
| | | | - Benjamin S Freedman
- Division of Nephrology, Department of Medicine, Institute for Stem Cell and Regenerative Medicine, and Kidney Research Institute, University of Washington, Seattle, WA 98109, USA; Plurexa, 1209 6th Ave. N., Seattle, WA 98109, USA.
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37
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Wang M, Krueger JB, Gilkey AK, Stelljes EM, Kluesner MG, Pomeroy EJ, Skeate JG, Slipek NJ, Lahr WS, Vázquez PNC, Zhao Y, Eaton EJ, Laoharawee K, Webber BR, Moriarity BS. Precision Enhancement of CAR-NK Cells through Non-Viral Engineering and Highly Multiplexed Base Editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.582637. [PMID: 38496503 PMCID: PMC10942345 DOI: 10.1101/2024.03.05.582637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Natural killer (NK) cells' unique ability to kill transformed cells expressing stress ligands or lacking major histocompatibility complexes (MHC) has prompted their development for immunotherapy. However, NK cells have demonstrated only moderate responses against cancer in clinical trials and likely require advanced genome engineering to reach their full potential as a cancer therapeutic. Multiplex genome editing with CRISPR/Cas9 base editors (BE) has been used to enhance T cell function and has already entered clinical trials but has not been reported in human NK cells. Here, we report the first application of BE in primary NK cells to achieve both loss-of-function and gain-of-function mutations. We observed highly efficient single and multiplex base editing, resulting in significantly enhanced NK cell function. Next, we combined multiplex BE with non-viral TcBuster transposon-based integration to generate IL-15 armored CD19 CAR-NK cells with significantly improved functionality in a highly suppressive model of Burkitt's lymphoma both in vitro and in vivo. The use of concomitant non-viral transposon engineering with multiplex base editing thus represents a highly versatile and efficient platform to generate CAR-NK products for cell-based immunotherapy and affords the flexibility to tailor multiple gene edits to maximize the effectiveness of the therapy for the cancer type being treated.
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Affiliation(s)
- Minjing Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Joshua B Krueger
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Alexandria K Gilkey
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Erin M Stelljes
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Molecular and Cellular Biology Graduate Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Joseph G Skeate
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Patricia N Claudio Vázquez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Yueting Zhao
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Ella J Eaton
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Kanut Laoharawee
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
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Rajendiran V, Devaraju N, Haddad M, Ravi NS, Panigrahi L, Paul J, Gopalakrishnan C, Wyman S, Ariudainambi K, Mahalingam G, Periyasami Y, Prasad K, George A, Sukumaran D, Gopinathan S, Pai AA, Nakamura Y, Balasubramanian P, Ramalingam R, Thangavel S, Velayudhan SR, Corn JE, Mackay JP, Marepally S, Srivastava A, Crossley M, Mohankumar KM. Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression. Mol Ther 2024; 32:663-677. [PMID: 38273654 PMCID: PMC10928131 DOI: 10.1016/j.ymthe.2024.01.023] [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: 04/28/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for β-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.
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Affiliation(s)
- Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mahdi Haddad
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Chandrasekar Gopalakrishnan
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA
| | | | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Dhiyaneshwaran Sukumaran
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Sandhiya Gopinathan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Rajasekaran Ramalingam
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Jacon E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA; Institute of Molecular Health Sciences, Department of Biology, Zurich, Switzerland
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India.
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39
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Yarra R, Krysan PJ. An SpG-Cas9-based cytosine base editor expands the scope of genome editing in carrot plants. PLANT CELL REPORTS 2024; 43:82. [PMID: 38441656 DOI: 10.1007/s00299-024-03173-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/09/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE SpG Cas9 significantly expands the genome editing scope in carrot with NGN PAM recognition.
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Affiliation(s)
- Rajesh Yarra
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, 53706, USA
| | - Patrick J Krysan
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, 53706, USA.
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40
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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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41
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Baudrier L, Benamozig O, Langley J, Chopra S, Kalashnikova T, Benaoudia S, Singh G, Mahoney DJ, Wright NAM, Billon P. One-pot DTECT enables rapid and efficient capture of genetic signatures for precision genome editing and clinical diagnostics. CELL REPORTS METHODS 2024; 4:100698. [PMID: 38301655 PMCID: PMC10921016 DOI: 10.1016/j.crmeth.2024.100698] [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: 08/25/2023] [Revised: 12/05/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
The detection of genomic sequences and their alterations is crucial for basic research and clinical diagnostics. However, current methodologies are costly and time-consuming and require outsourcing sample preparation, processing, and analysis to genomic companies. Here, we establish One-pot DTECT, a platform that expedites the detection of genetic signatures, only requiring a short incubation of a PCR product in an optimized one-pot mixture. One-pot DTECT enables qualitative, quantitative, and visual detection of biologically relevant variants, such as cancer mutations, and nucleotide changes introduced by prime editing and base editing into cancer cells and human primary T cells. Notably, One-pot DTECT achieves quantification accuracy for targeted genetic signatures comparable with Sanger and next-generation sequencing. Furthermore, its effectiveness as a diagnostic platform is demonstrated by successfully detecting sickle cell variants in blood and saliva samples. Altogether, One-pot DTECT offers an efficient, versatile, adaptable, and cost-effective alternative to traditional methods for detecting genomic signatures.
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Affiliation(s)
- Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Jethro Langley
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Sanchit Chopra
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Tatiana Kalashnikova
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Sacha Benaoudia
- Arnie Charbonneau Cancer Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Gurpreet Singh
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Douglas J Mahoney
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada; Snyder Institute for Chronic Disease, Calgary, AB, Canada; Department of Microbiology, Immunology and Infectious Disease, Calgary, AB, Canada
| | - Nicola A M Wright
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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42
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Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O’Brien KA, Vasquez CA, Cowan QT, Bruck PT, Mercader K, Alotaibi M, Long T, Hall JE, Moya EA, Bauk MA, Reeves JJ, Kong MC, Salem RM, Vizcardo-Galindo G, Macarlupu JL, Figueroa-Mujíca R, Bermudez D, Corante N, Gaio E, Fox KP, Salomaa V, Havulinna AS, Murray AJ, Malhotra A, Powel FL, Jain M, Komor AC, Cavalleri GL, Huff CD, Villafuerte FC, Simonson TS. Functional EPAS1/ HIF2A missense variant is associated with hematocrit in Andean highlanders. SCIENCE ADVANCES 2024; 10:eadj5661. [PMID: 38335297 PMCID: PMC10857371 DOI: 10.1126/sciadv.adj5661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.
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Affiliation(s)
- Elijah S. Lawrence
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecilia Anza-Ramirez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Amy M. Cole
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James J. Yu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica C. Heinrich
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Katie A. O’Brien
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T. Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Patrick T. Bruck
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Kysha Mercader
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Tao Long
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - James E. Hall
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marco A. Bauk
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer J. Reeves
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mitchell C. Kong
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rany M. Salem
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gustavo Vizcardo-Galindo
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jose-Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Rómulo Figueroa-Mujíca
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Daniela Bermudez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Noemi Corante
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Eduardo Gaio
- Laboratório de Fisiologia Respiratória, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Keolu P. Fox
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLIFE), Helsinki, Finland
| | - Andrew J. Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frank L. Powel
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco C. Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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43
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Sun Y, Chen Q, Cheng Y, Wang X, Deng Z, Zhou F, Sun Y. Design and Engineering of Light-Induced Base Editors Facilitating Genome Editing with Enhanced Fidelity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305311. [PMID: 38039441 PMCID: PMC10837352 DOI: 10.1002/advs.202305311] [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: 08/01/2023] [Revised: 10/27/2023] [Indexed: 12/03/2023]
Abstract
Base editors, which enable targeted locus nucleotide conversion in genomic DNA without double-stranded breaks, have been engineered as powerful tools for biotechnological and clinical applications. However, the application of base editors is limited by their off-target effects. Continuously expressed deaminases used for gene editing may lead to unwanted base alterations at unpredictable genomic locations. In the present study, blue-light-activated base editors (BLBEs) are engineered based on the distinct photoswitches magnets that can switch from a monomer to dimerization state in response to blue light. By fusing the N- and C-termini of split DNA deaminases with photoswitches Magnets, efficient A-to-G and C-to-T base editing is achieved in response to blue light in prokaryotic and eukaryotic cells. Furthermore, the results showed that BLBEs can realize precise blue light-induced gene editing across broad genomic loci with low off-target activity at the DNA- and RNA-level. Collectively, these findings suggest that the optogenetic utilization of base editing and optical base editors may provide powerful tools to promote the development of optogenetic genome engineering.
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Affiliation(s)
- Yangning Sun
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Qi Chen
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Yanbing Cheng
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Xi Wang
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Zixin Deng
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Fuling Zhou
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Yuhui Sun
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
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44
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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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45
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Lau KEH, Nguyen NT, Kesavan JC, Langa E, Fanning K, Brennan GP, Sanz-Rodriguez A, Villegas-Salmerón J, Yan Y, Venø MT, Mills JD, Rosenow F, Bauer S, Kjems J, Henshall DC. Differential microRNA editing may drive target pathway switching in human temporal lobe epilepsy. Brain Commun 2024; 6:fcad355. [PMID: 38204971 PMCID: PMC10781512 DOI: 10.1093/braincomms/fcad355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
MicroRNAs have emerged as important regulators of the gene expression landscape in temporal lobe epilepsy. The mechanisms that control microRNA levels and influence target choice remain, however, poorly understood. RNA editing is a post-transcriptional mechanism mediated by the adenosine acting on RNA (ADAR) family of proteins that introduces base modification that diversifies the gene expression landscape. RNA editing has been studied for the mRNA landscape but the extent to which microRNA editing occurs in human temporal lobe epilepsy is unknown. Here, we used small RNA-sequencing data to characterize the identity and extent of microRNA editing in human temporal lobe epilepsy brain samples. This detected low-to-high editing in over 40 of the identified microRNAs. Among microRNA exhibiting the highest editing was miR-376a-3p, which was edited in the seed region and this was predicted to significantly change the target pool. The edited form was expressed at lower levels in human temporal lobe epilepsy samples. We modelled the shift in editing levels of miR-376a-3p in human-induced pluripotent stem cell-derived neurons. Reducing levels of the edited form of miR-376a-3p using antisense oligonucleotides resulted in extensive gene expression changes, including upregulation of mitochondrial and metabolism-associated pathways. Together, these results show that differential editing of microRNAs may re-direct targeting and result in altered functions relevant to the pathophysiology of temporal lobe epilepsy and perhaps other disorders of neuronal hyperexcitability.
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Affiliation(s)
- Kelvin E How Lau
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Ngoc T Nguyen
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Jaideep C Kesavan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Elena Langa
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Kevin Fanning
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Gary P Brennan
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Amaya Sanz-Rodriguez
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Javier Villegas-Salmerón
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway H91 TK33, Ireland
| | - Yan Yan
- Omiics ApS, 8200 Aarhus N, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Morten T Venø
- Omiics ApS, 8200 Aarhus N, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - James D Mills
- Department of Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
- Chalfont Centre for Epilepsy, Chalfont St.Peter SL9 0RJ, UK
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Felix Rosenow
- Goethe-University Frankfurt, Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, University Hospital, 60590 Frankfurt, Germany
- Goethe-University Frankfurt, LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60590 Frankfurt, Germany
| | - Sebastian Bauer
- Goethe-University Frankfurt, Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, University Hospital, 60590 Frankfurt, Germany
- Goethe-University Frankfurt, LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60590 Frankfurt, Germany
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
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46
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Marayati BF, Thompson MG, Holley CL, Horner SM, Meyer KD. Programmable protein expression using a genetically encoded m 6A sensor. Nat Biotechnol 2024:10.1038/s41587-023-01978-3. [PMID: 38168988 PMCID: PMC11217150 DOI: 10.1038/s41587-023-01978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/01/2023] [Indexed: 01/05/2024]
Abstract
The N6-methyladenosine (m6A) modification is found in thousands of cellular mRNAs and is a critical regulator of gene expression and cellular physiology. m6A dysregulation contributes to several human diseases, and the m6A methyltransferase machinery has emerged as a promising therapeutic target. However, current methods for studying m6A require RNA isolation and do not provide a real-time readout of mRNA methylation in living cells. Here we present a genetically encoded m6A sensor (GEMS) technology, which couples a fluorescent signal with cellular mRNA methylation. GEMS detects changes in m6A caused by pharmacological inhibition of the m6A methyltransferase, giving it potential utility for drug discovery efforts. Additionally, GEMS can be programmed to achieve m6A-dependent delivery of custom protein payloads in cells. Thus, GEMS is a versatile platform for m6A sensing that provides both a simple readout for m6A methylation and a system for m6A-coupled protein expression.
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Affiliation(s)
- Bahjat F Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Christopher L Holley
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
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47
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Mohajerani F, Tehrankhah ZM, Rahmani S, Afsordeh N, Shafiee S, Pourgholami MH, Soltani BM, Sadeghizadeh M. CLEC19A overexpression inhibits tumor cell proliferation/migration and promotes apoptosis concomitant suppression of PI3K/AKT/NF-κB signaling pathway in glioblastoma multiforme. BMC Cancer 2024; 24:19. [PMID: 38167030 PMCID: PMC10763001 DOI: 10.1186/s12885-023-11755-9] [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: 10/20/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND GBM is the most frequent malignant primary brain tumor in humans. The CLEC19A is a member of the C-type lectin family, which has a high expression in brain tissue. Herein, we sought to carry out an in-depth analysis to pinpoint the role of CLEC19A expression in GBM. METHODS To determine the localization of CLEC19A, this protein was detected using Western blot, Immunocytochemistry/Immunofluorescence, and confocal microscopy imaging. CLEC19A expression in glioma cells and tissues was evaluated by qRT-PCR. Cell viability, proliferation, migration, and apoptosis were examined through MTT assay, CFSE assay, colony formation, wound healing assay, transwell test, and flow cytometry respectively after CLEC19A overexpression. The effect of CLEC19A overexpression on the PI3K/AKT/NF-κB signaling pathway was investigated using Western blot. An in vivo experiment substantiated the in vitro results using the glioblastoma rat models. RESULTS Our in-silico analysis using TCGA data and measuring CLEC19A expression level by qRT-PCR determined significantly lower expression of CLEC19A in human glioma tissues compared to healthy brain tissues. By employment of ICC/IF, confocal microscopy imaging, and Western blot we could show that CLEC19A is plausibly a secreted protein. Results obtained from several in vitro readouts showed that CLEC19A overexpression in U87 and C6 glioma cell lines is associated with the inhibition of cell proliferation, viability, and migration. Further, qRT-PCR and Western blot analysis showed CLEC19A overexpression could reduce the expression levels of PI3K, VEGFα, MMP2, and NF-κB and increase PTEN, TIMP3, RECK, and PDCD4 expression levels in glioma cell lines. Furthermore, flow cytometry results revealed that CLEC19A overexpression was associated with significant cell cycle arrest and promotion of apoptosis in glioma cell lines. Interestingly, using a glioma rat model we could substantiate that CLEC19A overexpression suppresses glioma tumor growth. CONCLUSIONS To our knowledge, this is the first report providing in-silico, molecular, cellular, and in vivo evidences on the role of CLEC19A as a putative tumor suppressor gene in GBM. These results enhance our understanding of the role of CLEC19A in glioma and warrant further exploration of CLEC19A as a potential therapeutic target for GBM.
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Affiliation(s)
- Fatemeh Mohajerani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal AleAhmad Highway, Tehran, Iran
| | - Zahra Moazezi Tehrankhah
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal AleAhmad Highway, Tehran, Iran
| | - Saeid Rahmani
- School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Nastaran Afsordeh
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sajad Shafiee
- Department of Neurosurgery, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Bahram M Soltani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal AleAhmad Highway, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal AleAhmad Highway, Tehran, Iran.
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48
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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: 8] [Impact Index Per Article: 8.0] [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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49
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Chiaramida A, Obwar SG, Nordstrom AEH, Ericsson M, Saldanha A, Ivanova EV, Griffin GK, Khan DH, Belizaire R. Sensitivity to targeted UBA1 inhibition in a myeloid cell line model of VEXAS syndrome. Blood Adv 2023; 7:7445-7456. [PMID: 38091008 PMCID: PMC10758730 DOI: 10.1182/bloodadvances.2023010531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 12/18/2023] Open
Abstract
Somatic UBA1 mutations in hematopoietic cells are a hallmark of Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) syndrome, which is a late-onset inflammatory disease associated with bone marrow failure and high mortality. The majority of UBA1 mutations in VEXAS syndrome comprise hemizygous mutations affecting methionine-41 (M41), leading to the expression of UBA1M41T, UBA1M41V, or UBA1M41L and globally reduced protein polyubiquitination. Here, we used CRISPR-Cas9 to engineer isogenic 32D mouse myeloid cell lines expressing hemizygous Uba1WT or Uba1M41L from the endogenous locus. Consistent with prior analyses of patients with VEXAS syndrome samples, hemizygous Uba1M41L expression was associated with loss of the UBA1b protein isoform, gain of the UBA1c protein isoform, reduced polyubiquitination, abnormal cytoplasmic vacuoles, and increased production of interleukin-1β and inflammatory chemokines. Vacuoles in Uba1M41L cells contained a variety of endolysosomal membranes, including small vesicles, multivesicular bodies, and multilamellar lysosomes. Uba1M41L cells were more sensitive to the UBA1 inhibitor TAK243. TAK243 treatment promoted apoptosis in Uba1M41L cells and led to preferential loss of Uba1M41L cells in competition assays with Uba1WT cells. Knock-in of a TAK243-binding mutation, Uba1A580S, conferred TAK243 resistance. In addition, overexpression of catalytically active UBA1b in Uba1M41L cells restored polyubiquitination and increased TAK243 resistance. Altogether, these data indicate that loss of UBA1b underlies a key biochemical phenotype associated with VEXAS syndrome and renders cells with reduced UBA1 activity vulnerable to targeted UBA1 inhibition. Our Uba1M41L knock-in cell line is a useful model of VEXAS syndrome that will aid in the study of disease pathogenesis and the development of effective therapies.
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Affiliation(s)
| | - Sandra G. Obwar
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Maria Ericsson
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Aisha Saldanha
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Elena V. Ivanova
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - Dilshad H. Khan
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
| | - Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
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50
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Godbout K, Rousseau J, Tremblay JP. Successful Correction by Prime Editing of a Mutation in the RYR1 Gene Responsible for a Myopathy. Cells 2023; 13:31. [PMID: 38201236 PMCID: PMC10777931 DOI: 10.3390/cells13010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
We report the first correction from prime editing a mutation in the RYR1 gene, paving the way to gene therapies for RYR1-related myopathies. The RYR1 gene codes for a calcium channel named Ryanodine receptor 1, which is expressed in skeletal muscle fibers. The failure of this channel causes muscle weakness in patients, which leads to motor disabilities. Currently, there are no effective treatments for these diseases, which are mainly caused by point mutations. Prime editing allows for the modification of precise nucleotides in the DNA. Our results showed a 59% correction rate of the T4709M mutation in the RYR1 gene in human myoblasts by RNA delivery of the prime editing components. It is to be noted that T4709M is recessive and, thus, persons having a heterozygous mutation are healthy. These results are the first demonstration that correcting mutations in the RYR1 gene is possible.
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Affiliation(s)
- Kelly Godbout
- Molecular Biology Department, Laval University, Quebec, QC G1V 0A6, Canada;
- CHU de Québec Research Center, Laval University, Quebec, QC G1V 4G2, Canada;
| | - Joël Rousseau
- CHU de Québec Research Center, Laval University, Quebec, QC G1V 4G2, Canada;
| | - Jacques P. Tremblay
- Molecular Biology Department, Laval University, Quebec, QC G1V 0A6, Canada;
- CHU de Québec Research Center, Laval University, Quebec, QC G1V 4G2, Canada;
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