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Ma X, Yin J, Qiao L, Wan H, Liu X, Zhou Y, Wu J, Niu L, Wu M, Wang X, Ye H. A programmable targeted protein-degradation platform for versatile applications in mammalian cells and mice. Mol Cell 2024; 84:1585-1600.e7. [PMID: 38479385 DOI: 10.1016/j.molcel.2024.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 04/21/2024]
Abstract
Myriad physiological and pathogenic processes are governed by protein levels and modifications. Controlled protein activity perturbation is essential to studying protein function in cells and animals. Based on Trim-Away technology, we screened for truncation variants of E3 ubiquitinase Trim21 with elevated efficiency (ΔTrim21) and developed multiple ΔTrim21-based targeted protein-degradation systems (ΔTrim-TPD) that can be transfected into host cells. Three ΔTrim-TPD variants are developed to enable chemical and light-triggered programmable activation of TPD in cells and animals. Specifically, we used ΔTrim-TPD for (1) red-light-triggered inhibition of HSV-1 virus proliferation by degrading the packaging protein gD, (2) for chemical-triggered control of the activity of Cas9/dCas9 protein for gene editing, and (3) for blue-light-triggered degradation of two tumor-associated proteins for spatiotemporal inhibition of melanoma tumor growth in mice. Our study demonstrates that multiple ΔTrim21-based controllable TPD systems provide powerful tools for basic biology research and highlight their potential biomedical applications.
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Affiliation(s)
- Xiaoding Ma
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Longliang Qiao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Hang Wan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xingwan Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Wuhu Hospital, Health Science Center, East China Normal University, Wuhu City 241001, China
| | - Jiali Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Lingxue Niu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Min Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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Mason NJ. Immunotherapy with genetically engineered T cells holds promise for the treatment of nonmalignant diseases in the dog. J Am Vet Med Assoc 2024:1-10. [PMID: 38621412 DOI: 10.2460/javma.24.02.0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
The ability to genetically redirect the antigenic specificity of T cells using chimeric antigen receptors (CAR) has led to unprecedented durable clinical remissions in human patients with relapsed/refractory hematological malignancies. This remarkable advance in successful immune cell engineering has now led to investigations into the application of CAR-T-cell technology to treat nonmalignant diseases. The use of CAR-T cells to target and eliminate specific cell subsets involved in the pathogenesis of autoimmunity, fibrosis, senescence, and infectious disease represents a new direction for adoptive cell therapies. While the use of CAR-T cells for nonmalignant disease is still in its infancy, early reports of dramatic clinical responses to CAR-T cells targeting CD19+ B cells in patients with severe autoimmune disease raise the possibility that this approach could lead to durable remissions, eliminating the need for ongoing conventional immunosuppressive therapies. Excitingly, nonmalignant disease processes that may be addressed by CAR-T-cell therapy in humans also occur in our canine populations. Given that technologies for developing canine CAR constructs are now available, robust protocols have been described for generating canine CAR-T cells, and experience is being gathered with their clinical use in oncology, it is anticipated that CAR-T cells will soon enter the veterinary clinics for the treatment of debilitating nonmalignant diseases. Here, we provide a broad overview of CAR-T-cell therapies for nonmalignant diseases and extrapolate these advances into the veterinary space, highlighting areas in which canine CAR-T cells are poised to enter the clinics for the treatment of nonmalignant disease.
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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. J Exp Bot 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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Ma Z, Chang R, Zhu L, Zhu D, Deng Y, Guo X, Cheng Z, Chen X. Metabolic Engineering of Corynebacterium glutamicum for Highly Efficient Production of Ectoine. ACS Synth Biol 2024. [PMID: 38607270 DOI: 10.1021/acssynbio.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Ectoine is a compatible solute that functions as a cell protector from various stresses, protecting cells and stabilizing biomolecules, and is widely used in medicine, cosmetics, and biotechnology. Microbial fermentation has been widely used for the large-scale production of ectoine, and a number of fermentation strategies have been developed to increase the ectoine yield, reduce production costs, and simplify the production process. Here, Corynebacterium glutamicum was engineered for ectoine production by heterologous expression of the ectoine biosynthesis operon ectBAC gene from Halomonas elongata, and a series of genetic modifications were implemented. This included introducing the de3 gene from Escherichia coli BL21 (DE3) to express the T7 promoter, eliminating the lysine transporter protein lysE to limit lysine production, and performing a targeted mutation lysCS301Y on aspartate kinase to alleviate feedback inhibition of lysine. The new engineered strain Ect10 obtained an ectoine titer of 115.87 g/L in an optimized fed-batch fermentation, representing the highest ectoine production level in C. glutamicum and achieving the efficient production of ectoine in a low-salt environment.
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Affiliation(s)
- Zhi Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Renjie Chang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linjiang Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Dianhao Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yanfeng Deng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xinying Guo
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ziyi Cheng
- Department of Mechanical & Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario M5S 3G8, Canada
| | - Xiaolong Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
- Quzhou Eco-Industrial Innovation Institute, Zhejiang University of Technology, Quzhou 324003, PR China
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Homanics GE, Park JE, Bailey L, Schaeffer DJ, Schaeffer L, He J, Li S, Zhang T, Haber A, Spruce C, Greenwood A, Murai T, Schultz L, Mongeau L, Ha SK, Oluoch J, Stein B, Choi SH, Huhe H, Thathiah A, Strick PL, Carter GW, Silva AC, Sukoff Rizzo SJ. Early molecular events of autosomal-dominant Alzheimer's disease in marmosets with PSEN1 mutations. Alzheimers Dement 2024. [PMID: 38574388 DOI: 10.1002/alz.13806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
INTRODUCTION Fundamental questions remain about the key mechanisms that initiate Alzheimer's disease (AD) and the factors that promote its progression. Here we report the successful generation of the first genetically engineered marmosets that carry knock-in (KI) point mutations in the presenilin 1 (PSEN1) gene that can be studied from birth throughout lifespan. METHODS CRISPR/Cas9 was used to generate marmosets with C410Y or A426P point mutations in PSEN1. Founders and their germline offspring are comprehensively studied longitudinally using non-invasive measures including behavior, biomarkers, neuroimaging, and multiomics signatures. RESULTS Prior to adulthood, increases in plasma amyloid beta were observed in PSEN1 mutation carriers relative to non-carriers. Analysis of brain revealed alterations in several enzyme-substrate interactions within the gamma secretase complex prior to adulthood. DISCUSSION Marmosets carrying KI point mutations in PSEN1 provide the opportunity to study the earliest primate-specific mechanisms that contribute to the molecular and cellular root causes of AD onset and progression. HIGHLIGHTS We report the successful generation of genetically engineered marmosets harboring knock-in point mutations in the PSEN1 gene. PSEN1 marmosets and their germline offspring recapitulate the early emergence of AD-related biomarkers. Studies as early in life as possible in PSEN1 marmosets will enable the identification of primate-specific mechanisms that drive disease progression.
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Affiliation(s)
- Gregg E Homanics
- Department of Anesthesiology & Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jung Eun Park
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lauren Bailey
- Department of Medicine, University of Pittsburgh Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David J Schaeffer
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lauren Schaeffer
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jie He
- Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Shuoran Li
- Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tingting Zhang
- Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Annat Haber
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | | | | | - Takeshi Murai
- Department of Medicine, University of Pittsburgh Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Laura Schultz
- Department of Medicine, University of Pittsburgh Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lauren Mongeau
- Department of Medicine, University of Pittsburgh Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Seung-Kwon Ha
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Julia Oluoch
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brianne Stein
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sang Ho Choi
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hasi Huhe
- Department of Medicine, University of Pittsburgh Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amantha Thathiah
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Peter L Strick
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Afonso C Silva
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Stacey J Sukoff Rizzo
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Woudstra C, Sørensen AN, Sørensen MCH, Brøndsted L. Strategies for developing phages into novel antimicrobial tailocins. Trends Microbiol 2024:S0966-842X(24)00069-6. [PMID: 38580606 DOI: 10.1016/j.tim.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
Tailocins are high-molecular-weight bacteriocins produced by bacteria to kill related environmental competitors by binding and puncturing their target. Tailocins are promising alternative antimicrobials, yet the diversity of naturally occurring tailocins is limited. The structural similarities between phage tails and tailocins advocate using phages as scaffolds for developing new tailocins. This article reviews three strategies for producing tailocins: disrupting the capsid-tail junction of phage particles, blocking capsid assembly during phage propagation, and creating headless phage particles synthetically. Particularly appealing is the production of tailocins through synthetic biology using phages with contractile tails as scaffolds to unlock the antimicrobial potential of tailocins.
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Affiliation(s)
- Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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Li J, Agathos SN, Gao Z. Editorial: Emerging trends in genetic engineering of microalgae. Front Bioeng Biotechnol 2024; 12:1403711. [PMID: 38638319 PMCID: PMC11024417 DOI: 10.3389/fbioe.2024.1403711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Affiliation(s)
- Jian Li
- Qingdao Innovation and Development Base, Harbin Engineering University, Qingdao, China
| | - Spiros N. Agathos
- Qingdao Innovation and Development Base, Harbin Engineering University, Qingdao, China
- Earth & Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, Yantai, China
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Wu R, Nahm M, Yang J, Bush CA, Wu H. Identification and genetic engineering of pneumococcal capsule-like polysaccharides in commensal oral streptococci. Microbiol Spectr 2024; 12:e0188523. [PMID: 38488366 DOI: 10.1128/spectrum.01885-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/28/2023] [Indexed: 04/06/2024] Open
Abstract
Capsular polysaccharides (CPS) in Streptococcus pneumoniae are pivotal for bacterial virulence and present extensive diversity. While oral streptococci show pronounced antigenicity toward pneumococcal capsule-specific sera, insights into evolution of capsule diversity remain limited. This study reports a pneumococcal CPS-like genetic locus in Streptococcus parasanguinis, a predominant oral Streptococcus. The discovered locus comprises 15 genes, mirroring high similarity to those from the Wzy-dependent CPS locus of S. pneumoniae. Notably, S. parasanguinis elicited a reaction with pneumococcal 19B antiserum. Through nuclear magnetic resonance analysis, we ascertained that its CPS structure matches the chemical composition of the pneumococcal 19B capsule. By introducing the glucosyltransferase gene cps19cS from a pneumococcal serotype 19C, we successfully transformed S. parasanguinis antigenicity from 19B to 19C. Furthermore, substituting serotype-specific genes, cpsI and cpsJ, with their counterparts from pneumococcal serotype 19A and 19F enabled S. parasanguinis to generate 19A- and 19F-specific CPS, respectively. These findings underscore that S. parasanguinis harbors a versatile 19B-like CPS adaptable to other serotypes. Remarkably, after deleting the locus's initial gene, cpsE, responsible for sugar transfer, we noted halted CPS production, elongated bacterial chains, and diminished biofilm formation. A similar phenotype emerged with the removal of the distinct gene cpsZ, which encodes a putative autolysin. These data highlight the importance of S. parasanguinis CPS for biofilm formation and propose a potential shared ancestry of its CPS locus with S. pneumoniae. IMPORTANCE Diverse capsules from Streptococcus pneumoniae are vital for bacterial virulence and pathogenesis. Oral streptococci show strong responses to a wide range of pneumococcal capsule-specific sera. Yet, the evolution of this capsule diversity in relation to microbe-host interactions remains underexplored. Our research delves into the connection between commensal oral streptococcal and pneumococcal capsules, highlighting the potential for gene transfer and evolution of various capsule types. Understanding the genetic and evolutionary factors that drive capsule diversity in S. pneumoniae and its related oral species is essential for the development of effective pneumococcal vaccines. The present findings provide fresh perspectives on the cross-reactivity between commensal streptococci and S. pneumoniae, its influence on bacteria-host interactions, and the development of new strategies to manage and prevent pneumococcal illnesses by targeting and modulating commensal streptococci.
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Affiliation(s)
- Ren Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, Alabama, USA
| | - Moon Nahm
- Department of Medicine, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Jinghua Yang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - C Allen Bush
- Department of Chemistry and Biochemistry, University of Maryland at Baltimore, Baltimore, Maryland, USA
| | - Hui Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, Alabama, USA
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University School of Dentistry, Portland, Oregon, USA
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Korkmaz N, Himawan S, Usman M, Baik S, Kim M. Bacteriophage Engineering for Improved Copper Ion Binding. Macromol Biosci 2024; 24:e2300354. [PMID: 37985183 DOI: 10.1002/mabi.202300354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/13/2023] [Indexed: 11/22/2023]
Abstract
In this study, fd viruses are genetically modified to display seven cropped versions (H, HG, HGF, HGFA, HGFAN, HGFANV and HGFANVA) of the previously identified Cu(II) specific peptide (HGFANVA). Atomic force microscopy (AFM) imaging reveals the typical filamentous structures of recombinant phages with thicknesses of ≈2-5 nm in dry state. Scanning electron microscopy (SEM) imaging shows that HGFANVA viruses form larger elongated assemblies than H viruses that are deposited with a mineral layer after Cu(II) treatment. C and N peaks are detected for virus samples through Energy dispersive X-ray spectroscopy (EDX) analyses confirming the presence of phage organic material. Cu peak is only detected for engineered viruses after Cu(II) exposure. Enzyme-linked immunosorbent assay (ELISA) analyses show the selective Cu(II) binding of engineered phages. Agarose gel electrophoresis (AGE) and zeta potential analyses reveal negative surface charges of engineered viral constructs. Positively charged Cytopore beads are coated with bacteriophages and used for Cu(II) ion sorption studies. ICP-MS analyses clearly show the improved Cu(II) binding of engineered viruses with respect to wild-type fd phages. Such bottom-up constructed, genetically engineered virus-based biomaterials may be applied in bioremediation studies targeting metal species from environmental samples.
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Affiliation(s)
- Nuriye Korkmaz
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Sandiego Himawan
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
- Bioprogrammable Materials Group, INM - Leibniz Institute for New Materials, Campus D 2.2, D-66123, Saarbrücken, Germany
| | - Muhammed Usman
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Seungyun Baik
- Environmental Safety Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Minyoung Kim
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
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Hussian CHAC, Rahman RNZRA, Leow ATC, Salleh AB, Ali MSM, Latip W. Enhancement in T1 lipase purification recovery using the novel construct pGEX4T1/His-T1. Prep Biochem Biotechnol 2024; 54:526-534. [PMID: 37647127 DOI: 10.1080/10826068.2023.2252052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The Geobacillus zalihae strain T1 produces a thermostable T1 lipase that could be used for industrial purposes. Previously, the GST-T1 lipase was purified through two chromatographic steps: affinity and ion exchange (IEX) but the recovery yield was only 33%. To improve the recovery yield to over 80%, the GST tag from the pGEX system was replaced with a poly-histidine at the N-terminal of the T1 lipase sequence. The novel construct of pGEX/His-T1 lipase was developed by site-directed mutagenesis, where the XbaI restriction site was introduced upstream of the GST tag, allowing the removal of tag via double digestion using XbaI and EcoRI (existing cutting site in the pGEX system). Fragment of 6 × His-T1 lipase fusion was synthesized, cloned into the pGEX4T1 system, and expressed in Escherichia coli BL21 (DE3) pLysS, resulting in lipase-specific activity at 236 U/mg. The single purification step of His-T1 lipase was successfully achieved using nickel Sepharose 6FF with an optimized concentration of 5 mM imidazole for binding, yielding the recovery of 98%, 1,353 U/mg lipase activity, and a 5.7-fold increase in purification fold. His-T1 lipase was characterized and was found to be stable at pH 5-9, active at 70 °C, and optimal at pH 9.
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Affiliation(s)
- Che Haznie Ayu Che Hussian
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Adam Thean Chor Leow
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
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11
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Erana-Perez Z, Igartua M, Santos-Vizcaino E, Hernandez RM. Genetically engineered loaded extracellular vesicles for drug delivery. Trends Pharmacol Sci 2024; 45:350-365. [PMID: 38508958 DOI: 10.1016/j.tips.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
The use of extracellular vesicles (EVs) for drug delivery is being widely explored by scientists from several research fields. To fully exploit their therapeutic potential, multiple methods for loading EVs have been developed. Although exogenous methods have been extensively utilized, in recent years the endogenous method has gained significant attention. This approach, based on parental cell genetic engineering, is suitable for loading large therapeutic biomolecules such as proteins and nucleic acids. We review the most commonly used EV loading methods and emphasize the inherent advantages of the endogenous method over the others. We also examine the most recent advances and applications of this innovative approach to inform on the diverse therapeutic opportunities that lie ahead in the field of EV-based therapies.
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Affiliation(s)
- Zuriñe Erana-Perez
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, 01006 Vitoria-Gasteiz, Spain
| | - Manoli Igartua
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, 01006 Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 01006 Vitoria-Gasteiz, Spain
| | - Edorta Santos-Vizcaino
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, 01006 Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 01006 Vitoria-Gasteiz, Spain.
| | - Rosa Maria Hernandez
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, 01006 Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 01006 Vitoria-Gasteiz, Spain.
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12
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Hu J, Yang F, Liu C, Wang N, Xiao Y, Zhai Y, Wang X, Zhang R, Gao L, Xu M, Wang J, Liu Z, Huang S, Liu W, Hu Y, Liu F, Guo Y, Wang L, Yuan J, Zhang Z, Chu J. UFObow: A single-wavelength excitable Brainbow for simultaneous multicolor ex-vivo and in-vivo imaging of mammalian cells. Commun Biol 2024; 7:394. [PMID: 38561421 PMCID: PMC10984974 DOI: 10.1038/s42003-024-06062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Brainbow is a genetic cell-labeling technique that allows random colorization of multiple cells and real-time visualization of cell fate within a tissue, providing valuable insights into understanding complex biological processes. However, fluorescent proteins (FPs) in Brainbow have distinct excitation spectra with peak difference greater than 35 nm, which requires sequential imaging under multiple excitations and thus leads to long acquisition times. In addition, they are not easily used together with other fluorophores due to severe spectral bleed-through. Here, we report the development of a single-wavelength excitable Brainbow, UFObow, incorporating three newly developed blue-excitable FPs. We have demonstrated that UFObow enables not only tracking the growth dynamics of tumor cells in vivo but also mapping spatial distribution of immune cells within a sub-cubic centimeter tissue, revealing cell heterogeneity. This provides a powerful means to explore complex biology in a simultaneous imaging manner at a single-cell resolution in organs or in vivo.
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Affiliation(s)
- Jiahong Hu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fangfang Yang
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chong Liu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Nengzhi Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yinghan Xiao
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yujie Zhai
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xinru Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ren Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Lulu Gao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Mengli Xu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Jialu Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zheng Liu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Songlin Huang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Wenfeng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yajing Hu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Feng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yuqi Guo
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Liang Wang
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jing Yuan
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Zhihong Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China.
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen, 518055, China.
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13
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Santos‐Beneit F. What is the role of microbial biotechnology and genetic engineering in medicine? Microbiologyopen 2024; 13:e1406. [PMID: 38556942 PMCID: PMC10982607 DOI: 10.1002/mbo3.1406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Microbial products are essential for developing various therapeutic agents, including antibiotics, anticancer drugs, vaccines, and therapeutic enzymes. Genetic engineering techniques, functional genomics, and synthetic biology unlock previously uncharacterized natural products. This review highlights major advances in microbial biotechnology, focusing on gene-based technologies for medical applications.
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Affiliation(s)
- Fernando Santos‐Beneit
- Institute of Sustainable ProcessesValladolidSpain
- Department of Chemical Engineering and Environmental Technology, School of Industrial EngineeringUniversity of ValladolidValladolidSpain
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14
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Ishibashi R, Maki R, Toyoshima F. Gene targeting in adult organs using in vivo cleavable donor plasmids for CRISPR-Cas9 and CRISPR-Cas12a. Sci Rep 2024; 14:7615. [PMID: 38556532 PMCID: PMC10982285 DOI: 10.1038/s41598-024-57551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
The CRISPR-Cas system for in vivo genome editing is a powerful tool for gene therapy against several diseases. We have previously developed the pCriMGET_9-12a system, an in vivo cleavable donor plasmid for precise targeted knock-in of exogenous DNA by both Cas9 and Cas12a. Here, we show that the pCriMGET_9-12a system can be applied for in vivo in-frame knock-in of exogenous DNA in adult mouse liver by hydrodynamic delivery of the targeting plasmids. The in vivo cleavable pCriMGET_9-12a donor plasmids significantly increased the knock-in efficiency of both CRISPR-Cas9 and CRISPR-Cas12a in the adult mouse liver compared to uncleavable donor plasmids. This strategy also achieved in-frame reporter gene knock-in without indel mutations. Therefore, in vivo gene targeting using the pCriMGET_9-12a system may contribute to the establishment of safer, more precise, versatile and efficient gene therapy methods in adult organs.
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Affiliation(s)
- Riki Ishibashi
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8507, Japan.
- Department of Mammalian Regulatory Networks, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Ritsuko Maki
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Fumiko Toyoshima
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8507, Japan
- Department of Mammalian Regulatory Networks, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Homeostatic Medicine, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
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15
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Huang BD, Kim D, Yu Y, Wilson CJ. Engineering intelligent chassis cells via recombinase-based MEMORY circuits. Nat Commun 2024; 15:2418. [PMID: 38499601 PMCID: PMC10948884 DOI: 10.1038/s41467-024-46755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Synthetic biologists seek to engineer intelligent living systems capable of decision-making, communication, and memory. Separate technologies exist for each tenet of intelligence; however, the unification of all three properties in a living system has not been achieved. Here, we engineer completely intelligent Escherichia coli strains that harbor six orthogonal and inducible genome-integrated recombinases, forming Molecularly Encoded Memory via an Orthogonal Recombinase arraY (MEMORY). MEMORY chassis cells facilitate intelligence via the discrete multi-input regulation of recombinase functions enabling inheritable DNA inversions, deletions, and genomic insertions. MEMORY cells can achieve programmable and permanent gain (or loss) of functions extrachromosomally or from a specific genomic locus, without the loss or modification of the MEMORY platform - enabling the sequential programming and reprogramming of DNA circuits within the cell. We demonstrate all three tenets of intelligence via a probiotic (Nissle 1917) MEMORY strain capable of information exchange with the gastrointestinal commensal Bacteroides thetaiotaomicron.
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Affiliation(s)
- Brian D Huang
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia
| | - Dowan Kim
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia
| | - Yongjoon Yu
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia
| | - Corey J Wilson
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia.
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16
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Maini Rekdal V, van der Luijt CRB, Chen Y, Kakumanu R, Baidoo EEK, Petzold CJ, Cruz-Morales P, Keasling JD. Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit. Nat Commun 2024; 15:2099. [PMID: 38485948 PMCID: PMC10940619 DOI: 10.1038/s41467-024-46314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Casper R B van der Luijt
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA.
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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17
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Levrier A, Karpathakis I, Nash B, Bowden SD, Lindner AB, Noireaux V. PHEIGES: all-cell-free phage synthesis and selection from engineered genomes. Nat Commun 2024; 15:2223. [PMID: 38472230 PMCID: PMC10933291 DOI: 10.1038/s41467-024-46585-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.
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Affiliation(s)
- Antoine Levrier
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
- Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006, Paris, France
| | - Ioannis Karpathakis
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
- Facultatea de Biotehnologii, USAMV Bucuresti, Sector 1, Cod 011464, Bucureşti, Romania
| | - Bruce Nash
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Steven D Bowden
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Ariel B Lindner
- Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006, Paris, France.
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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18
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Apostolopoulos A, Kawamoto N, Chow SYA, Tsuiji H, Ikeuchi Y, Shichino Y, Iwasaki S. dCas13-mediated translational repression for accurate gene silencing in mammalian cells. Nat Commun 2024; 15:2205. [PMID: 38467613 PMCID: PMC10928199 DOI: 10.1038/s41467-024-46412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Current gene silencing tools based on RNA interference (RNAi) or, more recently, clustered regularly interspaced short palindromic repeats (CRISPR)‒Cas13 systems have critical drawbacks, such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR‒Cas13). Thus, a more specific method of gene knockdown is needed. Here, we develop CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13). Owing to its tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes during translation initiation and does not affect mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy regardless of the translation initiation mechanism: cap-dependent, internal ribosome entry site (IRES)-dependent, or repeat-associated non-AUG (RAN) translation. Strikingly, genome-wide ribosome profiling reveals the ultrahigh gene silencing specificity of CRISPRδ. Moreover, the fusion of a translational repressor to dCas13 further improves the performance. Our method provides a framework for translational repression-based gene silencing in eukaryotes.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05278 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K07016 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005h0001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- Pioneering Projects MEXT | RIKEN
- Pioneering Projects MEXT | RIKEN
- Exploratory Research Center on Life and Living Systems (ExCELLS), 23EX601
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hitomi Tsuiji
- Education and Research Division of Pharmacy, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi, 464-8650, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
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19
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Umene K, Kawahara M. Synthetic receptor scaffolds significantly affect the efficiency of cell fate signals. Sci Rep 2024; 14:5801. [PMID: 38461201 PMCID: PMC10925030 DOI: 10.1038/s41598-024-56612-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 03/11/2024] Open
Abstract
Mimicry of receptor functions by designing synthetic receptors would be one of the recently hot research trends in cell engineering. While several types of synthetic receptors have been designed to induce desired cell fates in response to external stimuli, little is known about which receptor type signals more efficiently for inducing a certain cell fate. In this study, we compared the performance of three types of synthetic receptor scaffolds, i.e. myristoylated, cytosolic, and transmembrane types that signal through JAK-dependent phosphorylation of tyrosine motifs to transduce growth signaling. As a result, the phosphorylation levels of JAK and subsequent downstream signaling molecules were significantly maintained in the cytosolic type receptors, leading to more efficient cell growth than the other types. In contrast, the phosphorylation levels of JAK decreased in a motif-dependent manner in the transmembrane type receptors. Although various studies on receptor engineering based on domain or motif engineering have been reported, to our knowledge this study is the first to demonstrate that synthetic receptor scaffolds significantly affect the efficiency of cell fate signals. These findings are important for both receptor biology and receptor engineering, providing guidelines for rationally designing synthetic receptors that can transduce as efficient signaling as possible.
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Affiliation(s)
- Kirato Umene
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan.
- Laboratory of Cell Vaccine, Microbial Research Center for Health and Medicine (MRCHM), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-Shi, Osaka, 567-0085, Japan.
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20
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Hayashi N, Lai Y, Fuerte-Stone J, Mimee M, Lu TK. Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements. Nat Commun 2024; 15:2096. [PMID: 38453913 PMCID: PMC10920895 DOI: 10.1038/s41467-024-45893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.
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Affiliation(s)
- Naoki Hayashi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Yong Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Research Laboratory of Electronics, MIT, Cambridge, MA, 02139, USA
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Jay Fuerte-Stone
- Department of Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Mark Mimee
- Department of Microbiology, The University of Chicago, Chicago, IL, 60637, USA.
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.
| | - Timothy K Lu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Research Laboratory of Electronics, MIT, Cambridge, MA, 02139, USA.
- Broad Institute, Cambridge, MA, 02139, USA.
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA.
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21
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Li D, Song F, Mengiste T. Editorial: Molecular biology of plant-fungal interactions. Front Plant Sci 2024; 15:1392149. [PMID: 38504904 PMCID: PMC10949945 DOI: 10.3389/fpls.2024.1392149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024]
Affiliation(s)
- Dayong Li
- Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
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22
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Barzi M, Chen T, Gonzalez TJ, Pankowicz FP, Oh SH, Streff HL, Rosales A, Ma Y, Collias S, Woodfield SE, Diehl AM, Vasudevan SA, Galvan TN, Goss J, Gersbach CA, Bissig-Choisat B, Asokan A, Bissig KD. A humanized mouse model for adeno-associated viral gene therapy. Nat Commun 2024; 15:1955. [PMID: 38438373 PMCID: PMC10912671 DOI: 10.1038/s41467-024-46017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Clinical translation of AAV-mediated gene therapy requires preclinical development across different experimental models, often confounded by variable transduction efficiency. Here, we describe a human liver chimeric transgene-free Il2rg-/-/Rag2-/-/Fah-/-/Aavr-/- (TIRFA) mouse model overcoming this translational roadblock, by combining liver humanization with AAV receptor (AAVR) ablation, rendering murine cells impermissive to AAV transduction. Using human liver chimeric TIRFA mice, we demonstrate increased transduction of clinically used AAV serotypes in primary human hepatocytes compared to humanized mice with wild-type AAVR. Further, we demonstrate AAV transduction in human teratoma-derived primary cells and liver cancer tissue, displaying the versatility of the humanized TIRFA mouse. From a mechanistic perspective, our results support the notion that AAVR functions as both an entry receptor and an intracellular receptor essential for transduction. The TIRFA mouse should allow prediction of AAV gene transfer efficiency and the study of AAV vector biology in a preclinical human setting.
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Affiliation(s)
- Mercedes Barzi
- Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA
| | - Tong Chen
- Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Francis P Pankowicz
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seh Hoon Oh
- Department of Medicine, Division of Gastroenterology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Helen L Streff
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Alan Rosales
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Yunhan Ma
- Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA
| | - Sabrina Collias
- Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA
| | - Sarah E Woodfield
- Michael E. DeBakey Department of Surgery, Divisions of Pediatric Surgery and Surgical Research, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Surgery, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Anna Mae Diehl
- Department of Medicine, Division of Gastroenterology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Sanjeev A Vasudevan
- Michael E. DeBakey Department of Surgery, Divisions of Pediatric Surgery and Surgical Research, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Surgery, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Thao N Galvan
- Department of Surgery, Texas Children's Hospital, Houston, TX, 77030, USA
- Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation and Division of Hepatobiliary Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John Goss
- Department of Surgery, Texas Children's Hospital, Houston, TX, 77030, USA
- Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation and Division of Hepatobiliary Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Duke University, Durham, NC, USA
- Duke Cancer Center, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, School of Medicine, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Beatrice Bissig-Choisat
- Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, School of Medicine, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Karl-Dimiter Bissig
- Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Medicine, Division of Gastroenterology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Cancer Center, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Regeneration Center, School of Medicine, Duke University, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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23
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Mullins E, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Naegeli H, Nogué F, Rostoks N, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Ardizzone M, Camargo AM, De Sanctis G, Federici S, Fernandez A, Gennaro A, Gómez Ruiz JÁ, Goumperis T, Grammatikou P, Kagkli DM, Lenzi P, Neri FM, Papadopoulou N, Raffaello T. Assessment of genetically modified maize DP202216 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2019-159). EFSA J 2024; 22:e8655. [PMID: 38510324 PMCID: PMC10952026 DOI: 10.2903/j.efsa.2024.8655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Genetically modified maize DP202216 was developed to confer tolerance to glufosinate-ammonium-containing herbicides and to provide an opportunity for yield enhancement under field conditions. These properties were achieved by introducing the mo-pat and zmm28 expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize DP202216 and its comparator needs further assessment, except for the levels of stearic acid (C18:0), which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the PAT and ZMM28 proteins as expressed in maize DP202216, and finds no evidence that the genetic modification would change the overall allergenicity of maize DP202216. In the context of this application, the consumption of food and feed from maize DP202216 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize DP202216 is as safe as the comparator and non-GM reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize DP202216 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize DP202216. The GMO Panel concludes that maize DP202216 is as safe as its comparator and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment.
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24
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Yi Z, Zhang X, Tang W, Yu Y, Wei X, Zhang X, Wei W. Strand-selective base editing of human mitochondrial DNA using mitoBEs. Nat Biotechnol 2024; 42:498-509. [PMID: 37217751 PMCID: PMC10940147 DOI: 10.1038/s41587-023-01791-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
A number of mitochondrial diseases in humans are caused by point mutations that could be corrected by base editors, but delivery of CRISPR guide RNAs into the mitochondria is difficult. In this study, we present mitochondrial DNA base editors (mitoBEs), which combine a transcription activator-like effector (TALE)-fused nickase and a deaminase for precise base editing in mitochondrial DNA. Combining mitochondria-localized, programmable TALE binding proteins with the nickase MutH or Nt.BspD6I(C) and either the single-stranded DNA-specific adenine deaminase TadA8e or the cytosine deaminase ABOBEC1 and UGI, we achieve A-to-G or C-to-T base editing with up to 77% efficiency and high specificity. We find that mitoBEs are DNA strand-selective mitochondrial base editors, with editing results more likely to be retained on the nonnicked DNA strand. Furthermore, we correct pathogenic mitochondrial DNA mutations in patient-derived cells by delivering mitoBEs encoded in circular RNAs. mitoBEs offer a precise, efficient DNA editing tool with broad applicability for therapy in mitochondrial genetic diseases.
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Affiliation(s)
- Zongyi Yi
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Changping Laboratory, Beijing, P.R. China
| | - Xiaoxue Zhang
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Wei Tang
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Ying Yu
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
| | - Xiaoxu Wei
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Xue Zhang
- Changping Laboratory, Beijing, P.R. China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China.
- Changping Laboratory, Beijing, P.R. China.
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25
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Li M, Jia W. Formation and hazard of ethyl carbamate and construction of genetically engineered Saccharomyces cerevisiae strains in Huangjiu (Chinese grain wine). Compr Rev Food Sci Food Saf 2024; 23:e13321. [PMID: 38517033 DOI: 10.1111/1541-4337.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/18/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Huangjiu, a well-known conventional fermented Chinese grain wine, is widely consumed in Asia for its distinct flavor. Trace amounts of ethyl carbamate (EC) may be generated during the fermentation or storage process. The International Agency for Research on Cancer elevated EC to a Class 2A carcinogen, so it is necessary to regulate EC content in Huangjiu. The risk of intake of dietary EC is mainly assessed through the margin of exposure (MOE) recommended by the European Food Safety Authority, with a smaller MOE indicating a higher risk. Interventions are necessary to reduce EC formation. As urea, one of the main precursors of EC formation in Huangjiu, is primarily produced by Saccharomyces cerevisiae through the catabolism of arginine, the construction of dominant engineered fermentation strains is a favorable trend for the future production and application of Huangjiu. This review summarized the formation and carcinogenic mechanism of EC from the perspectives of precursor substances, metabolic pathways after ingestion, and risk assessment. The methods of constructing dominant S. cerevisiae strains in Huangjiu by genetic engineering technology were reviewed, which provided an important theoretical basis for reducing EC content and strengthening practical control of Huangjiu safety, and the future research direction was prospected.
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Affiliation(s)
- Mi Li
- School of Food Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | - Wei Jia
- School of Food Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China
- Shaanxi Research Institute of Agricultural Products Processing Technology, Xi'an, China
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26
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Shakhova ES, Karataeva TA, Markina NM, Mitiouchkina T, Palkina KA, Perfilov MM, Wood MG, Hoang TT, Hall MP, Fakhranurova LI, Alekberova AE, Malyshevskaia AK, Gorbachev DA, Bugaeva EN, Pletneva LK, Babenko VV, Boldyreva DI, Gorokhovatsky AY, Balakireva AV, Gao F, Choob VV, Encell LP, Wood KV, Yampolsky IV, Sarkisyan KS, Mishin AS. An improved pathway for autonomous bioluminescence imaging in eukaryotes. Nat Methods 2024; 21:406-410. [PMID: 38253843 PMCID: PMC10927554 DOI: 10.1038/s41592-023-02152-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]
Abstract
The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.
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Affiliation(s)
- Ekaterina S Shakhova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Karataeva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda M Markina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kseniia A Palkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maxim M Perfilov
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - Anna E Alekberova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena K Malyshevskaia
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Gorbachev
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Vladislav V Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria I Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey Y Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia V Balakireva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Feng Gao
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Vladimir V Choob
- Planta LLC, Moscow, Russia
- Botanical Garden of Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Ilia V Yampolsky
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Light Bio Inc, Ketchum, ID, USA
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Karen S Sarkisyan
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Light Bio Inc, Ketchum, ID, USA.
| | - Alexander S Mishin
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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27
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Truong DJJ, Geilenkeuser J, Wendel SV, Wilming JCH, Armbrust N, Binder EMH, Santl TH, Siebenhaar A, Gruber C, Phlairaharn T, Živanić M, Westmeyer GG. Exonuclease-enhanced prime editors. Nat Methods 2024; 21:455-464. [PMID: 38302659 PMCID: PMC10927552 DOI: 10.1038/s41592-023-02162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
Prime editing (PE) is a powerful gene-editing technique based on targeted gRNA-templated reverse transcription and integration of the de novo synthesized single-stranded DNA. To circumvent one of the main bottlenecks of the method, the competition of the reverse-transcribed 3' flap with the original 5' flap DNA, we generated an enhanced fluorescence-activated cell sorting reporter cell line to develop an exonuclease-enhanced PE strategy ('Exo-PE') composed of an improved PE complex and an aptamer-recruited DNA-exonuclease to remove the 5' original DNA flap. Exo-PE achieved better overall editing efficacy than the reference PE2 strategy for insertions ≥30 base pairs in several endogenous loci and cell lines while maintaining the high editing precision of PE2. By enabling the precise incorporation of larger insertions, Exo-PE complements the growing palette of different PE tools and spurs additional refinements of the PE machinery.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Julian Geilenkeuser
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Stephanie Victoria Wendel
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Julius Clemens Heinrich Wilming
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Niklas Armbrust
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Eva Maria Hildegard Binder
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Tobias Heinrich Santl
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Annika Siebenhaar
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Christoph Gruber
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany
| | - Teeradon Phlairaharn
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Milica Živanić
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Gil Gregor Westmeyer
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany.
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany.
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28
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Schmitt DS, Siegel SD, Selle K. Applications of designer phage encoding recombinant gene payloads. Trends Biotechnol 2024; 42:326-338. [PMID: 37833198 DOI: 10.1016/j.tibtech.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Advances in genetic engineering, synthetic biology, and DNA sequencing have transformed the re-emergent therapeutic bacteriophage field. The increasing rate of multidrug resistant (MDR) infections and the speed at which new bacteriophages can be isolated, sequenced, characterized, and engineered has reinvigorated phage therapy and unlocked new applications of phages for modulating bacteria. The methods used to genetically engineer bacteriophages are undergoing significant development, but identification of heterologous gene payloads with desirable activity and determination of their impact on bacteria or human cells in translationally relevant applications remain underexplored areas. Here, we discuss and categorize recombinant gene payloads for their potential outcome on phage-bacteria interactions when genetically engineered into phage genomes for expression in their bacterial hosts.
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Affiliation(s)
- Daniel S Schmitt
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, USA
| | - Sara D Siegel
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, USA
| | - Kurt Selle
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, USA.
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Krishnan N, Jiang Y, Zhou J, Mohapatra A, Peng FX, Duan Y, Holay M, Chekuri S, Guo Z, Gao W, Fang RH, Zhang L. A modular approach to enhancing cell membrane-coated nanoparticle functionality using genetic engineering. Nat Nanotechnol 2024; 19:345-353. [PMID: 37903891 PMCID: PMC10954421 DOI: 10.1038/s41565-023-01533-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Since their initial development, cell membrane-coated nanoparticles (CNPs) have become increasingly popular in the biomedical field. Despite their inherent versatility and ability to enable complex biological applications, there is considerable interest in augmenting the performance of CNPs through the introduction of additional functionalities. Here we demonstrate a genetic-engineering-based modular approach to CNP functionalization that can encompass a wide range of ligands onto the nanoparticle surface. The cell membrane coating is engineered to express a SpyCatcher membrane anchor that can readily form a covalent bond with any moiety modified with SpyTag. To demonstrate the broad utility of this technique, three unique targeted CNP formulations are generated using different classes of targeting ligands, including a designed ankyrin repeat protein, an affibody and a single-chain variable fragment. In vitro, the modified nanoparticles exhibit enhanced affinity towards cell lines overexpressing the cognate receptors for each ligand. When formulated with a chemotherapeutic payload, the modularly functionalized nanoparticles display strong targeting ability and growth suppression in a murine tumour xenograft model of ovarian cancer. Our data suggest genetic engineering offers a feasible approach for accelerating the development of multifunctional CNPs for a broad range of biomedical applications.
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Affiliation(s)
- Nishta Krishnan
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yao Jiang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jiarong Zhou
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Animesh Mohapatra
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Fei-Xing Peng
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yaou Duan
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Maya Holay
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Sanam Chekuri
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Zhongyuan Guo
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Weiwei Gao
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ronnie H Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
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Liang Z, Zheng K, Xie G, Luo X, Li H. Sugar Utilization-Associated Food-Grade Selection Markers in Lactic Acid Bacteria and Yeast. Pol J Microbiol 2024; 73:3-10. [PMID: 38437472 PMCID: PMC10911659 DOI: 10.33073/pjm-2024-011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/27/2024] [Indexed: 03/06/2024] Open
Abstract
This comprehensive review explores the development of food-grade selection markers in lactic acid bacteria and yeast; some of their strains are precisely defined as safe microorganisms and are crucial in the food industry. Lactic acid bacteria, known for their ability to ferment carbohydrates into lactic acid, provide essential nutrients and contribute to immune responses. With its strong fermentation capabilities and rich nutritional profile, yeast finds use in various food products. Genetic engineering in these microorganisms has grown rapidly, enabling the expression of enzymes and secondary products for food production. However, the focus is on ensuring safety, necessitating food-grade selection markers. Traditional antibiotic and heavy metal resistance selection markers pose environmental and health risks, prompting the search for safer alternatives. Complementary selection markers, such as sugar utilization markers, offer a promising solution. These markers use carbohydrates as carbon sources for growth and are associated with the natural metabolism of lactic acid bacteria and yeast. This review discusses the use of specific sugars, such as lactose, melibiose, sucrose, D-xylose, glucosamine, and N-acetylglucosamine, as selection markers, highlighting their advantages and limitations. In summary, this review underscores the importance of food-grade selection markers in genetic engineering and offers insights into their applications, benefits, and challenges, providing valuable information for researchers in the field of food microbiology and biotechnology.
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Affiliation(s)
- Zhiwen Liang
- School of Life and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ke Zheng
- School of Life and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Guifeng Xie
- Guangzhou MEIZHONG Biotechnology Co., Ltd, Guangzhou, China
| | - Xiongsheng Luo
- Guangzhou MEIZHONG Biotechnology Co., Ltd, Guangzhou, China
| | - Huangjin Li
- School of Life and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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31
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Shi W, Feng Y, Tang J, Xu Y, Wang W, Zhang L, Jiang X, Ding Z, Xi K, Chen L, Gu Y. A Genetically Engineered "Reinforced Concrete" Scaffold Regulates the N2 Neutrophil Innate Immune Cascade to Repair Bone Defects. Adv Healthc Mater 2024:e2304585. [PMID: 38411324 DOI: 10.1002/adhm.202304585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/17/2024] [Indexed: 02/28/2024]
Abstract
The innate immune response is crucial to inflammation, but how neutrophils and macrophages act in bone repair and tissue engineering treatment strategies await clarification. In this study, it is found that N2 neutrophils release stronger "eat me" signals to induce macrophage phagocytosis and polarize into the M2 anti-inflammatory phenotype. Guided by this biological mechanism, a mesoporous bioactive glass scaffold (MBG) is filled with hyaluronic acid methacryloyl (HAMA) hydrogel loaded with Transforming growth factor-β1 (TGFβ1) adenovirus (Ad@H), constructing a genetically engineered composite scaffold (Ad@H/M). The scaffold not only has good hydrophilicity and biocompatibility, but also provides mechanical stress support for bone repair. Adenovirus infection quickly induces N2 neutrophils, upregulating NF-κB and MAPK signaling pathways through Toll-like receptor 4 (TLR4) to promote the inflammatory response and macrophage phagocytosis. Macrophages perform phagocytosis and polarize towards the M2 phenotype, mediating the inflammatory response by inhibiting the PI3K-AKT-NF-κB pathway, maintaining homeostasis of the osteogenic microenvironment. The role of the Ad@H/M scaffold in regulating early inflammation and promoting long-term bone regeneration is further validated in vivo. In brief, this study focuses on the cascade of reactions between neutrophils and macrophage subtypes, and reports a composite scaffold that coordinates the innate immune response to promote bone repair.
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Affiliation(s)
- Wenxiao Shi
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Yu Feng
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Jincheng Tang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Yichang Xu
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Wei Wang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Lichen Zhang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Xinzhao Jiang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Zhouye Ding
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Kun Xi
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Liang Chen
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
| | - Yong Gu
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, P. R. China
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32
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Chen K, Stahl EC, Kang MH, Xu B, Allen R, Trinidad M, Doudna JA. Engineering self-deliverable ribonucleoproteins for genome editing in the brain. Nat Commun 2024; 15:1727. [PMID: 38409124 PMCID: PMC10897210 DOI: 10.1038/s41467-024-45998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
The delivery of CRISPR ribonucleoproteins (RNPs) for genome editing in vitro and in vivo has important advantages over other delivery methods, including reduced off-target and immunogenic effects. However, effective delivery of RNPs remains challenging in certain cell types due to low efficiency and cell toxicity. To address these issues, we engineer self-deliverable RNPs that can promote efficient cellular uptake and carry out robust genome editing without the need for helper materials or biomolecules. Screening of cell-penetrating peptides (CPPs) fused to CRISPR-Cas9 protein identifies potent constructs capable of efficient genome editing of neural progenitor cells. Further engineering of these fusion proteins establishes a C-terminal Cas9 fusion with three copies of A22p, a peptide derived from human semaphorin-3a, that exhibits substantially improved editing efficacy compared to other constructs. We find that self-deliverable Cas9 RNPs generate robust genome edits in clinically relevant genes when injected directly into the mouse striatum. Overall, self-deliverable Cas9 proteins provide a facile and effective platform for genome editing in vitro and in vivo.
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Affiliation(s)
- Kai Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Min Hyung Kang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bryant Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Ryan Allen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marena Trinidad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institutes, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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33
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Zhang E, Neugebauer ME, Krasnow NA, Liu DR. Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference. Nat Commun 2024; 15:1697. [PMID: 38402281 PMCID: PMC10894238 DOI: 10.1038/s41467-024-45969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
TadA-derived cytosine base editors (TadCBEs) enable programmable C•G-to-T•A editing while retaining the small size, high on-target activity, and low off-target activity of TadA deaminases. Existing TadCBEs, however, exhibit residual A•T-to-G•C editing at certain positions and lower editing efficiencies at some sequence contexts and with non-SpCas9 targeting domains. To address these limitations, we use phage-assisted evolution to evolve CBE6s from a TadA-mediated dual cytosine and adenine base editor, discovering mutations at N46 and Y73 in TadA that prevent A•T-to-G•C editing and improve C•G-to-T•A editing with expanded sequence-context compatibility, respectively. In E. coli, CBE6 variants offer high C•G-to-T•A editing and no detected A•T-to-G•C editing in any sequence context. In human cells, CBE6 variants exhibit broad Cas domain compatibility and retain low off-target editing despite exceeding BE4max and previous TadCBEs in on-target editing efficiency. Finally, we show that the high selectivity of CBE6 variants is well-suited for therapeutically relevant stop codon installation without creating unwanted missense mutations from residual A•T-to-G•C editing.
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Affiliation(s)
- Emily Zhang
- 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
| | - Monica E Neugebauer
- 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
| | - Nicholas A Krasnow
- 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
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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34
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Ding D, Shaw AY, Sinai S, Rollins N, Prywes N, Savage DF, Laub MT, Marks DS. Protein design using structure-based residue preferences. Nat Commun 2024; 15:1639. [PMID: 38388493 PMCID: PMC10884402 DOI: 10.1038/s41467-024-45621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at individual residues-without accounting for mutation interactions-explain much and sometimes virtually all of the combinatorial mutation effects across 8 datasets (R2 ~ 78-98%). Hence, few observations (~100 times the number of mutated residues) enable accurate prediction of held-out variant effects (Pearson r > 0.80). We hypothesized that the local structural contexts around a residue could be sufficient to predict mutation preferences, and develop an unsupervised approach termed CoVES (Combinatorial Variant Effects from Structure). Our results suggest that CoVES outperforms not just model-free methods but also similarly to complex models for creating functional and diverse protein variants. CoVES offers an effective alternative to complicated models for identifying functional protein mutations.
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Affiliation(s)
- David Ding
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
| | - Ada Y Shaw
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sam Sinai
- Dyno Therapeutics, Watertown, MA, 02472, USA
| | - Nathan Rollins
- Seismic Therapeutics, Lab Central, Cambridge, MA, 02142, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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35
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Qiao P, Ning L, Chen J, Tang Y, Zhao R, Chen G, Ye Q, Zhou T, Chen J, Zhong W. The critical roles of propanethiol oxidoreductase and sulfide-quinone oxidoreductase in the propanethiol catabolism pathway in Pseudomonas putida S-1. Appl Environ Microbiol 2024; 90:e0195923. [PMID: 38193681 PMCID: PMC10880595 DOI: 10.1128/aem.01959-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024] Open
Abstract
Propanethiol (PT) is a hazardous pollutant that poses risks to both the environment and human well-being. Pseudomonas putida S-1 has been identified as a microorganism capable of utilizing PT as its sole carbon source. However, the metabolic pathway responsible for PT degradation in P. putida S-1 has remained poorly understood, impeding its optimization and practical application. In this study, we investigated the catabolic network involved in PT desulfurization with P. putida S-1 and identified key gene modules crucial to this process. Notably, propanethiol oxidoreductase (PTO) catalyzes the initial degradation of PT, a pivotal step for P. putida S-1's survival on PT. PTO facilitates the oxidation of PT, resulting H2S, H2O2, and propionaldehyde (PA). Catalase-peroxidase catalyzes the conversion of H2O2 to oxygen and water, while PA undergoes gradual conversion to Succinyl-CoA, which is subsequently utilized in the tricarboxylic acid cycle. H2S is digested in a comprehensive desulfurization network where sulfide-quinone oxidoreductase (SQOR) predominantly converts it to sulfane sulfur. The transcriptome analysis suggests that sulfur can be finally converted to sulfite or sulfate and exported out of the cell. The PT degradation capacity of P. putida S-1 was enhanced by increasing the transcription level of PTO and SQOR genes in vivo.IMPORTANCEThis work investigated the PT catabolism pathway in Pseudomonas putida S-1, a microorganism capable of utilizing PT as the sole carbon source. Critical genes that control the initiation of PT degradation were identified and characterized, such as pto and sqor. By increasing the transcription level of pto and sqor genes in vivo, we have successfully enhanced the PT degradation efficiency and growth rate of P. putida S-1. This work does not only reveal a unique PT degradation pathway but also highlights the potential of enhancing the microbial desulfurization process in the bioremediation of thiol-contaminated environment.
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Affiliation(s)
- Pei Qiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Lixiao Ning
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jinhui Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuhang Tang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Rui Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Guoqing Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qun Ye
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tong Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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36
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Smidler AL, Marrogi E, Kauffman J, Paton DG, Westervelt KA, Church GM, Esvelt KM, Shaw WR, Catteruccia F. CRISPR-mediated germline mutagenesis for genetic sterilization of Anopheles gambiae males. Sci Rep 2024; 14:4057. [PMID: 38374393 PMCID: PMC10876656 DOI: 10.1038/s41598-024-54498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
Rapid spread of insecticide resistance among anopheline mosquitoes threatens malaria elimination efforts, necessitating development of alternative vector control technologies. Sterile insect technique (SIT) has been successfully implemented in multiple insect pests to suppress field populations by the release of large numbers of sterile males, yet it has proven difficult to adapt to Anopheles vectors. Here we outline adaptation of a CRISPR-based genetic sterilization system to selectively ablate male sperm cells in the malaria mosquito Anopheles gambiae. We achieve robust mosaic biallelic mutagenesis of zero population growth (zpg, a gene essential for differentiation of germ cells) in F1 individuals after intercrossing a germline-expressing Cas9 transgenic line to a line expressing zpg-targeting gRNAs. Approximately 95% of mutagenized males display complete genetic sterilization, and cause similarly high levels of infertility in their female mates. Using a fluorescence reporter that allows detection of the germline leads to a 100% accurate selection of spermless males, improving the system. These males cause a striking reduction in mosquito population size when released at field-like frequencies in competition cages against wild type males. These findings demonstrate that such a genetic system could be adopted for SIT against important malaria vectors.
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Affiliation(s)
- Andrea L Smidler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biology, University of California - San Diego, San Diego, CA, 92093, USA
| | - Eryney Marrogi
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jamie Kauffman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Douglas G Paton
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Kathleen A Westervelt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin M Esvelt
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - W Robert Shaw
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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37
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Gao Y, Solberg T, Wang R, Yu Y, Al-Rasheid KAS, Gao F. Application of RNA interference and protein localization to investigate housekeeping and developmentally regulated genes in the emerging model protozoan Paramecium caudatum. Commun Biol 2024; 7:204. [PMID: 38374195 PMCID: PMC10876655 DOI: 10.1038/s42003-024-05906-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/09/2024] [Indexed: 02/21/2024] Open
Abstract
Unicellular eukaryotes represent tremendous evolutionary diversity. However, the molecular mechanisms underlying this diversity remain largely unexplored, partly due to a limitation of genetic tools to only a few model species. Paramecium caudatum is a well-known unicellular eukaryote with an unexpectedly large germline genome, of which only two percent is retained in the somatic genome following sexual processes, revealing extensive DNA elimination. However, further progress in understanding the molecular mechanisms governing this process is hampered by a lack of suitable genetic tools. Here, we report the successful application of gene knockdown and protein localization methods to interrogate the function of both housekeeping and developmentally regulated genes in P. caudatum. Using these methods, we achieved the expected phenotypes upon RNAi by feeding, and determined the localization of these proteins by microinjection of fusion constructs containing fluorescent protein or antibody tags. Lastly, we used these methods to reveal that P. caudatum PiggyMac, a domesticated piggyBac transposase, is essential for sexual development, and is likely to be an active transposase directly involved in DNA cleavage. The application of these methods lays the groundwork for future studies of gene function in P. caudatum and can be used to answer important biological questions in the future.
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Affiliation(s)
- Yunyi Gao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Therese Solberg
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, 108-8345, Japan
| | - Rui Wang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yueer Yu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Feng Gao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laoshan Laboratory, Qingdao, 266237, China.
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38
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Liang Y, Gao S, Qi X, Valentovich LN, An Y. Progress in Gene Editing and Metabolic Regulation of Saccharomyces cerevisiae with CRISPR/Cas9 Tools. ACS Synth Biol 2024; 13:428-448. [PMID: 38326929 DOI: 10.1021/acssynbio.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The CRISPR/Cas9 systems have been developed as tools for genetic engineering and metabolic engineering in various organisms. In this review, various aspects of CRISPR/Cas9 in Saccharomyces cerevisiae, from basic principles to practical applications, have been summarized. First, a comprehensive review has been conducted on the history of CRISPR/Cas9, successful cases of gene disruptions, and efficiencies of multiple DNA fragment insertions. Such advanced systems have accelerated the development of microbial engineering by reducing time and labor, and have enhanced the understanding of molecular genetics. Furthermore, the research progress of the CRISPR/Cas9-based systems in the production of high-value-added chemicals and the improvement of stress tolerance in S. cerevisiae have been summarized, which should have an important reference value for genetic and synthetic biology studies based on S. cerevisiae.
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Affiliation(s)
- Yaokun Liang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, Guangdong 511370, China
| | - Leonid N Valentovich
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
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Fauser F, Kadam BN, Arangundy-Franklin S, Davis JE, Vaidya V, Schmidt NJ, Lew G, Xia DF, Mureli R, Ng C, Zhou Y, Scarlott NA, Eshleman J, Bendaña YR, Shivak DA, Reik A, Li P, Davis GD, Miller JC. Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells. Nat Commun 2024; 15:1181. [PMID: 38360922 PMCID: PMC10869815 DOI: 10.1038/s41467-024-45100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.
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Affiliation(s)
| | | | | | | | | | | | - Garrett Lew
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | - Danny F Xia
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | - Colman Ng
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
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Martins B, Bister A, Dohmen RGJ, Gouveia MA, Hueber R, Melzener L, Messmer T, Papadopoulos J, Pimenta J, Raina D, Schaeken L, Shirley S, Bouchet BP, Flack JE. Advances and Challenges in Cell Biology for Cultured Meat. Annu Rev Anim Biosci 2024; 12:345-368. [PMID: 37963400 DOI: 10.1146/annurev-animal-021022-055132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Cultured meat is an emerging biotechnology that aims to produce meat from animal cell culture, rather than from the raising and slaughtering of livestock, on environmental and animal welfare grounds. The detailed understanding and accurate manipulation of cell biology are critical to the design of cultured meat bioprocesses. Recent years have seen significant interest in this field, with numerous scientific and commercial breakthroughs. Nevertheless, these technologies remain at a nascent stage, and myriad challenges remain, spanning the entire bioprocess. From a cell biological perspective, these include the identification of suitable starting cell types, tuning of proliferation and differentiation conditions, and optimization of cell-biomaterial interactions to create nutritious, enticing foods. Here, we discuss the key advances and outstanding challenges in cultured meat, with a particular focus on cell biology, and argue that solving the remaining bottlenecks in a cost-effective, scalable fashion will require coordinated, concerted scientific efforts. Success will also require solutions to nonscientific challenges, including regulatory approval, consumer acceptance, and market feasibility. However, if these can be overcome, cultured meat technologies can revolutionize our approach to food.
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Affiliation(s)
- Beatriz Martins
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Arthur Bister
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Richard G J Dohmen
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
- Department of Physiology, Maastricht University, Maastricht, The Netherlands
| | - Maria Ana Gouveia
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Rui Hueber
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Lea Melzener
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
- Department of Physiology, Maastricht University, Maastricht, The Netherlands
| | - Tobias Messmer
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
- Department of Physiology, Maastricht University, Maastricht, The Netherlands
| | - Joanna Papadopoulos
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Joana Pimenta
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Dhruv Raina
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Lieke Schaeken
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Sara Shirley
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
| | - Benjamin P Bouchet
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands;
| | - Joshua E Flack
- Mosa Meat B.V., Maastricht, The Netherlands; , , , , , , , , , , , ,
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41
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Ali A, Kemter E, Wolf E. Advances in Organ and Tissue Xenotransplantation. Annu Rev Anim Biosci 2024; 12:369-390. [PMID: 37906838 DOI: 10.1146/annurev-animal-021122-102606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
End-stage organ failure can result from various preexisting conditions and occurs in patients of all ages, and organ transplantation remains its only treatment. In recent years, extensive research has been done to explore the possibility of transplanting animal organs into humans, a process referred to as xenotransplantation. Due to their matching organ sizes and other anatomical and physiological similarities with humans, pigs are the preferred organ donor species. Organ rejection due to host immune response and possible interspecies infectious pathogen transmission have been the biggest hurdles to xenotransplantation's success. Use of genetically engineered pigs as tissue and organ donors for xenotransplantation has helped to address these hurdles. Although several preclinical trials have been conducted in nonhuman primates, some barriers still exist and demand further efforts. This review focuses on the recent advances and remaining challenges in organ and tissue xenotransplantation.
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Affiliation(s)
- Asghar Ali
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany; , ,
- Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Elisabeth Kemter
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany; , ,
- Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany; , ,
- Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
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Zarka KA, Jagd LM, Douches DS. T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop ® enrichment technology. Front Plant Sci 2024; 15:1330429. [PMID: 38419775 PMCID: PMC10900525 DOI: 10.3389/fpls.2024.1330429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Before the commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, polymerase chain reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole-genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole-genomic sequencing coverage that meets the regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234, and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.
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Affiliation(s)
- Kelly A. Zarka
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - David S. Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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Gecse G, Labunskaite R, Pedersen M, Kilstrup M, Johanson T. Minimizing acetate formation from overflow metabolism in Escherichia coli: comparison of genetic engineering strategies to improve robustness toward sugar gradients in large-scale fermentation processes. Front Bioeng Biotechnol 2024; 12:1339054. [PMID: 38419731 PMCID: PMC10899681 DOI: 10.3389/fbioe.2024.1339054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction: Escherichia coli, a well characterized workhorse in biotechnology, has been used to produce many recombinant proteins and metabolites, but have a major drawback in its tendency to revert to overflow metabolism. This phenomenon occurs when excess sugar triggers the production of mainly acetate under aerobic conditions, a detrimental by-product that reduces carbon efficiency, increases cell maintenance, and ultimately inhibits growth. Although this can be prevented by controlled feeding of the sugar carbon source to limit its availability, gradients in commercial-scale bioreactors can still induce it in otherwise carbon-limited cells. While the underlying mechanisms have been extensively studied, these have mostly used non-limited cultures. In contrast, industrial production typically employs carbon-limited processes, which results in a substantially different cell physiology. Objective: The objective of this study was to evaluate and compare the efficiency of different metabolic engineering strategies with the aim to reduce overflow metabolism and increase the robustness of an industrial 2'-O-fucosyllactose producing strain under industrially relevant conditions. Methods: Three distinct metabolic engineering strategies were compared: i) alterations to pathways leading to and from acetate, ii) increased flux towards the tricarboxylic acid (TCA) cycle, and iii) reduced glucose uptake rate. The engineered strains were evaluated for growth, acetate formation, and product yield under non-limiting batch conditions, carbon limited fed-batch conditions, and after a glucose pulse in fed-batch mode. Results and Discussion: The findings demonstrated that blockage of the major acetate production pathways by deletion of the pta and poxB genes or increased carbon flux into the TCA cycle by overexpression of the gltA and deletion of the iclR genes, were efficient ways to reduce acetate accumulation. Surprisingly, a reduced glucose uptake rate did not reduce acetate formation despite it having previously been shown as a very effective strategy. Interestingly, overexpression of gltA was the most efficient way to reduce acetate accumulation in non-limited cultures, whereas disruption of the poxB and pta genes was more effective for carbon-limited cultures exposed to a sudden glucose shock. Strains from both strategies showed increased tolerance towards a glucose pulse during carbon-limited growth indicating feasible ways to engineer industrial E. coli strains with enhanced robustness.
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Affiliation(s)
| | | | | | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Dennis G, Posewitz MC. Advances in light system engineering across the phototrophic spectrum. Front Plant Sci 2024; 15:1332456. [PMID: 38410727 PMCID: PMC10895028 DOI: 10.3389/fpls.2024.1332456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Current work in photosynthetic engineering is progressing along the lines of cyanobacterial, microalgal, and plant research. These are interconnected through the fundamental mechanisms of photosynthesis and advances in one field can often be leveraged to improve another. It is worthwhile for researchers specializing in one or more of these systems to be aware of the work being done across the entire research space as parallel advances of techniques and experimental approaches can often be applied across the field of photosynthesis research. This review focuses on research published in recent years related to the light reactions of photosynthesis in cyanobacteria, eukaryotic algae, and plants. Highlighted are attempts to improve photosynthetic efficiency, and subsequent biomass production. Also discussed are studies on cross-field heterologous expression, and related work on augmented and novel light capture systems. This is reviewed in the context of translatability in research across diverse photosynthetic organisms.
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Affiliation(s)
- Galen Dennis
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States
| | - Matthew C Posewitz
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States
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Gonçalves AF, Lima-Pinheiro A, Teixeira M, Cassiano GC, Cravo P, Ferreira PE. Mutation in the 26S proteasome regulatory subunit rpn2 gene in Plasmodium falciparum confers resistance to artemisinin. Front Cell Infect Microbiol 2024; 14:1342856. [PMID: 38404287 PMCID: PMC10884193 DOI: 10.3389/fcimb.2024.1342856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/22/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Malaria parasites increasingly develop resistance to all drugs available in the market, hampering the goal of reducing malaria burden. Methods Herein, we evaluated the impact of a single-nucleotide variant, E738K, present in the 26S proteasome regulatory subunit rpn2 gene, identified in Plasmodium chabaudi resistant parasites. Plasmids carrying a functional rpn2 interspecies chimeric gene with 5' recombination region from P. falciparum and 3' from P. chabaudi were constructed and transfected into Dd2 P. falciparum parasites. Results and discussion The 738K variant parasite line presented increased parasite survival when subjected to dihydroartemisinin (DHA), as well as increased chymotrypsin-like activity and decreased accumulation of polyubiquitinated proteins. We thus conclude that the ubiquitin-proteasome pathway, including the 738K variant, play an important role in parasite response to DHA, being the first report of a mutation in a potential DHA drug target enhancing parasite survival and contributing to a significant advance in the understanding the biology of artemisinin resistance.
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Affiliation(s)
- Adriana F. Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS)/ Biomaterials, Biodegradables and Biomimetics Research Group (3B's)-PT Government Associate Laboratory, Braga, Portugal
| | - Ana Lima-Pinheiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS)/ Biomaterials, Biodegradables and Biomimetics Research Group (3B's)-PT Government Associate Laboratory, Braga, Portugal
| | - Miguel Teixeira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS)/ Biomaterials, Biodegradables and Biomimetics Research Group (3B's)-PT Government Associate Laboratory, Braga, Portugal
- Department of Protection of Specific Crops, InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
| | - Gustavo Capatti Cassiano
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Pedro Cravo
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Pedro E. Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS)/ Biomaterials, Biodegradables and Biomimetics Research Group (3B's)-PT Government Associate Laboratory, Braga, Portugal
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Nabors LB, Lamb LS, Goswami T, Rochlin K, Youngblood SL. Adoptive cell therapy for high grade gliomas using simultaneous temozolomide and intracranial mgmt-modified γδ t cells following standard post-resection chemotherapy and radiotherapy: current strategy and future directions. Front Immunol 2024; 15:1299044. [PMID: 38384458 PMCID: PMC10880006 DOI: 10.3389/fimmu.2024.1299044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Cellular therapies, including chimeric antigen receptor T cell therapies (CAR-T), while generally successful in hematologic malignancies, face substantial challenges against solid tumors such as glioblastoma (GBM) due to rapid growth, antigen heterogeneity, and inadequate depth of response to cytoreductive and immune therapies, We have previously shown that GBM constitutively express stress associated NKG2D ligands (NKG2DL) recognized by gamma delta (γδ) T cells, a minor lymphocyte subset that innately recognize target molecules via the γδ T cell receptor (TCR), NKG2D, and multiple other mechanisms. Given that NKG2DL expression is often insufficient on GBM cells to elicit a meaningful response to γδ T cell immunotherapy, we then demonstrated that NKG2DL expression can be transiently upregulated by activation of the DNA damage response (DDR) pathway using alkylating agents such as Temozolomide (TMZ). TMZ, however, is also toxic to γδ T cells. Using a p140K/MGMT lentivector, which confers resistance to TMZ by expression of O(6)-methylguanine-DNA-methyltransferase (MGMT), we genetically engineered γδ T cells that maintain full effector function in the presence of therapeutic doses of TMZ. We then validated a therapeutic system that we termed Drug Resistance Immunotherapy (DRI) that combines a standard regimen of TMZ concomitantly with simultaneous intracranial infusion of TMZ-resistant γδ T cells in a first-in-human Phase I clinical trial (NCT04165941). This manuscript will discuss DRI as a rational therapeutic approach to newly diagnosed GBM and the importance of repeated administration of DRI in combination with the standard-of-care Stupp regimen in patients with stable minimal residual disease.
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Affiliation(s)
- L B Nabors
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - L S Lamb
- IN8Bio, Inc., New York, NY, United States
| | - T Goswami
- IN8Bio, Inc., New York, NY, United States
| | - K Rochlin
- IN8Bio, Inc., New York, NY, United States
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Cautereels C, Smets J, De Saeger J, Cool L, Zhu Y, Zimmermann A, Steensels J, Gorkovskiy A, Jacobs TB, Verstrepen KJ. Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts. Nat Commun 2024; 15:1113. [PMID: 38326330 PMCID: PMC10850332 DOI: 10.1038/s41467-024-44996-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Lloyd Cool
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Yanmei Zhu
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium.
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Pan Y, Wu X, Liu L, Zhao C, Zhang J, Yang S, Pan P, Huang Q, Zhao XZ, Tian R, Rao L. Genetically Engineered Cytomembrane Nanovaccines for Cancer Immunotherapy. Adv Healthc Mater 2024:e2400068. [PMID: 38320299 DOI: 10.1002/adhm.202400068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Indexed: 02/08/2024]
Abstract
Cancer nanovaccines have attracted widespread attention by inducing potent cytotoxic T cell responses to improve immune checkpoint blockade (ICB) therapy, while the lack of co-stimulatory molecules limits their clinical applications. Here, a genetically engineered cancer cytomembrane nanovaccine is reported that simultaneously overexpresses co-stimulatory molecule CD40L and immune checkpoint inhibitor PD1 to elicit robust antitumor immunity for cancer immunotherapy. The CD40L and tumor antigens inherited from cancer cytomembranes effectively stimulate dendritic cell (DC)-mediated immune activation of cytotoxic T cells, while the PD1 on cancer cytomembranes significantly blocks PD1/PD-L1 signaling pathway, synergistically stimulating antitumor immune responses. Benefiting from the targeting ability of cancer cytomembranes, this nanovaccines formula shows an enhanced lymph node trafficking and retention. Compared with original cancer cytomembranes, this genetically engineered nanovaccine induces twofold DC maturation and shows satisfactory precaution efficacy in a breast tumor mouse model. This genetically engineered cytomembrane nanovaccine offers a simple, safe, and robust strategy by incorporating cytomembrane components and co-stimulatory molecules for enhanced cancer immunotherapy.
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Affiliation(s)
- Yuanwei Pan
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Xianjia Wu
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Lujie Liu
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Chenchen Zhao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Jing Zhang
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Shengren Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Pan Pan
- The First Affiliated Hospital of Jinan University, Guangzhou, 510632, China
| | - Qinqin Huang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Xing-Zhong Zhao
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Rui Tian
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Lang Rao
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
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49
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Azi F, Wang Z, Chen W, Lin D, Xu P. Developing Ganoderma lucidum as a next-generation cell factory for food and nutraceuticals. Trends Biotechnol 2024; 42:197-211. [PMID: 37659953 DOI: 10.1016/j.tibtech.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/04/2023]
Abstract
Ganoderma lucidum holds a colossal reservoir of hydrolytic enzymes and therapeutic compounds and can be a sustainable source of proteins and bioactive compounds. Its metabolic versatility, propelled by its rich genome content, provides excellent biosynthetic machinery for innovation-driven pathway engineering. However, robust regulatory networks and low frequency of homologous recombination are critical bottlenecks that limit the development of molecular tools and precise genetic markers for biomanufacturing innovations in this organism. Modern synthetic biology provides tools that could help to accelerate precise multiple gene targeting and editing and untangling the biosynthetic machinery of G. lucidum. This review provides insight into molecular strategies to unwind the regulatory bottlenecks and transform G. lucidum into efficient cell factories for food and nutraceuticals.
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Affiliation(s)
- Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel
| | - Zhe Wang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wenhao Chen
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel
| | - Dewei Lin
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, GTIIT, Shantou, Guangdong 515063, China.
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50
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Davis JR, Banskota S, Levy JM, Newby GA, Wang X, Anzalone AV, Nelson AT, Chen PJ, Hennes AD, An M, Roh H, Randolph PB, Musunuru K, Liu DR. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat Biotechnol 2024; 42:253-264. [PMID: 37142705 PMCID: PMC10869272 DOI: 10.1038/s41587-023-01758-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/22/2023] [Indexed: 05/06/2023]
Abstract
Realizing the promise of prime editing for the study and treatment of genetic disorders requires efficient methods for delivering prime editors (PEs) in vivo. Here we describe the identification of bottlenecks limiting adeno-associated virus (AAV)-mediated prime editing in vivo and the development of AAV-PE vectors with increased PE expression, prime editing guide RNA stability and modulation of DNA repair. The resulting dual-AAV systems, v1em and v3em PE-AAV, enable therapeutically relevant prime editing in mouse brain (up to 42% efficiency in cortex), liver (up to 46%) and heart (up to 11%). We apply these systems to install putative protective mutations in vivo for Alzheimer's disease in astrocytes and for coronary artery disease in hepatocytes. In vivo prime editing with v3em PE-AAV caused no detectable off-target effects or significant changes in liver enzymes or histology. Optimized PE-AAV systems support the highest unenriched levels of in vivo prime editing reported to date, facilitating the study and potential treatment of diseases with a genetic component.
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Affiliation(s)
- Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jonathan M 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
| | - 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
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew V Anzalone
- 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
| | - Andrew T Nelson
- 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
| | - Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Andrew D Hennes
- 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
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Heejin Roh
- 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
| | - Peyton B Randolph
- 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
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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