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Miah R, Johannessen M, Kjos M, Lentz CS. Development of an inducer-free, virulence gene promoter-controlled, and fluorescent reporter-labeled CRISPR interference system in Staphylococcus aureus. Microbiol Spectr 2024; 12:e0060224. [PMID: 39162514 PMCID: PMC11448056 DOI: 10.1128/spectrum.00602-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/11/2024] [Indexed: 08/21/2024] Open
Abstract
The dCas9-based Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi) gene regulation technique requires two components: a catalytically inactive Cas9 protein (dCas9) and a single-guide RNA that targets the gene of interest. This system is commonly activated by expressing dCas9 through an inducible gene promoter, but these inducers may affect cellular physiology, and accessibility and permeability of the inducer are limited in relevant model systems. Here, we have developed an alternative approach for CRISPRi activation in the clinical isolate Staphylococcus aureus USA300 LAC, where dCas9 was expressed through endogenous virulence gene promoters (vgp); coagulase, autolysin, or fibronectin-binding protein A. Additionally, we integrated a fluorescent reporter gene into the vgp-CRISPRi system to monitor the activity of the dcas9-controlling promoter. Testing the efficacy of vgp-CRISPRi by inducing growth arrest (when targeting penicillin-binding protein 1), downregulating target gene expression, or blocking coagulase-dependent coagulation of blood plasma, we provide a proof-of-concept demonstration that the virulence gene promoter-driven CRISPRi system is functional in S. aureus.IMPORTANCEThe presented inducer-free, endogenous virulence gene promoter-induced, dCas9-based Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi system addresses several shortcomings related to the use of inducer-dependent systems such as effects on cell physiology or limitations in permeability, and it avoids the high, putatively toxic levels of dCas9 in CRISPRi systems controlled by strong, constitutive promoters.
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Affiliation(s)
- Roni Miah
- Department of Medical Biology and Center for New Antibacterial Strategies (CANS), UT- The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Department of Medical Biology and Center for New Antibacterial Strategies (CANS), UT- The Arctic University of Norway, Tromsø, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Christian S Lentz
- Department of Medical Biology and Center for New Antibacterial Strategies (CANS), UT- The Arctic University of Norway, Tromsø, Norway
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Tridgett M, Mulet M, Johny SP, Ababi M, Raghunath M, Fustinoni C, Galabova B, Fernández-Díaz C, Mikalajūnaitė I, Tomás HA, Kucej M, Dunajová L, Zgrundo Z, Page E, McCall L, Parker-Manuel R, Payne T, Peckett M, Kent J, Holland L, Asatryan R, Montgomery L, Chow TL, Beveridge R, Salkauskaite I, Alam MT, Hollard D, Dowding S, Gabriel HB, Branciaroli C, Cawood R, Valenti W, Chang D, Patrício MI, Liu Q. Lentiviral vector packaging and producer cell lines yield titers equivalent to the industry-standard four-plasmid process. Mol Ther Methods Clin Dev 2024; 32:101315. [PMID: 39282073 PMCID: PMC11401174 DOI: 10.1016/j.omtm.2024.101315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/05/2024] [Indexed: 09/18/2024]
Abstract
Lentiviral vector (LVV)-mediated cell and gene therapies have the potential to cure diseases that currently require lifelong intervention. However, the requirement for plasmid transfection hinders large-scale LVV manufacture. Moreover, large-scale plasmid production, testing, and transfection contribute to operational risk and the high cost associated with this therapeutic modality. Thus, we developed LVV packaging and producer cell lines, which reduce or eliminate the need for plasmid transfection during LVV manufacture. To develop a packaging cell line, lentiviral packaging genes were stably integrated by random integration of linearized plasmid DNA. Then, to develop EGFP- and anti-CD19 chimeric antigen receptor-encoding producer cell lines, transfer plasmids were integrated by transposase-mediated integration. Single-cell isolation and testing were performed to isolate the top-performing clonal packaging and producer cell lines. Production of LVVs that encode various cargo genes revealed consistency in the production performance of the packaging and producer cell lines compared to the industry-standard four-plasmid transfection method. By reducing or eliminating the requirement for plasmid transfection, while achieving production performance consistent with the current industry standard, the packaging and producer cell lines developed here can reduce costs and operational risks of LVV manufacture, thus increasing patient access to LVV-mediated cell and gene therapies.
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Affiliation(s)
- Matthew Tridgett
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Marie Mulet
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Sherin Parokkaran Johny
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Maria Ababi
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Meenakshi Raghunath
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Chloé Fustinoni
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Boryana Galabova
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Cristina Fernández-Díaz
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Iveta Mikalajūnaitė
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Hélio A Tomás
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Marek Kucej
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Lucia Dunajová
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Zofia Zgrundo
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Emma Page
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Lorna McCall
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Richard Parker-Manuel
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Tom Payne
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Matthew Peckett
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Jade Kent
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Louise Holland
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Robert Asatryan
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Louise Montgomery
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Tsz Lung Chow
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Ryan Beveridge
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Ieva Salkauskaite
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Mohine T Alam
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Daniel Hollard
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Sarah Dowding
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Heloísa Berti Gabriel
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Corinne Branciaroli
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Ryan Cawood
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Weimin Valenti
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
- WuXi Advanced Therapies, 4701 League Island Blvd, Philadelphia, PA 19112, USA
| | - David Chang
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
- WuXi Advanced Therapies, 4701 League Island Blvd, Philadelphia, PA 19112, USA
| | - Maria I Patrício
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
| | - Qian Liu
- OXGENE, A WuXi Advanced Therapies Company, Medawar Centre, Robert Robinson Avenue, Oxford, Oxfordshire OX4 4HG, UK
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3
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Leandro K, Rufino-Ramos D, Breyne K, Di Ianni E, Lopes SM, Jorge Nobre R, Kleinstiver BP, Perdigão PRL, Breakefield XO, Pereira de Almeida L. Exploring the potential of cell-derived vesicles for transient delivery of gene editing payloads. Adv Drug Deliv Rev 2024; 211:115346. [PMID: 38849005 PMCID: PMC11366383 DOI: 10.1016/j.addr.2024.115346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024]
Abstract
Gene editing technologies have the potential to correct genetic disorders by modifying, inserting, or deleting specific DNA sequences or genes, paving the way for a new class of genetic therapies. While gene editing tools continue to be improved to increase their precision and efficiency, the limited efficacy of in vivo delivery remains a major hurdle for clinical use. An ideal delivery vehicle should be able to target a sufficient number of diseased cells in a transient time window to maximize on-target editing and mitigate off-target events and immunogenicity. Here, we review major advances in novel delivery platforms based on cell-derived vesicles - extracellular vesicles and virus-like particles - for transient delivery of gene editing payloads. We discuss major findings regarding packaging, in vivo biodistribution, therapeutic efficacy, and safety concerns of cell-derived vesicles delivery of gene editing cargos and their potential for clinical translation.
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Affiliation(s)
- Kevin Leandro
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal
| | - David Rufino-Ramos
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Emilio Di Ianni
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Sara M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; ViraVector - Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra 3004-504, Portugal
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Pedro R L Perdigão
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; ViraVector - Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra 3004-504, Portugal.
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4
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Mseis-Jackson N, Sharma M, Li H. Controlling the Expression Level of the Neuronal Reprogramming Factors for a Successful Reprogramming Outcome. Cells 2024; 13:1223. [PMID: 39056804 PMCID: PMC11274869 DOI: 10.3390/cells13141223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Neuronal reprogramming is a promising approach for making major advancement in regenerative medicine. Distinct from the approach of induced pluripotent stem cells, neuronal reprogramming converts non-neuronal cells to neurons without going through a primitive stem cell stage. In vivo neuronal reprogramming brings this approach to a higher level by changing the cell fate of glial cells to neurons in neural tissue through overexpressing reprogramming factors. Despite the ongoing debate over the validation and interpretation of newly generated neurons, in vivo neuronal reprogramming is still a feasible approach and has the potential to become clinical treatment with further optimization and refinement. Here, we discuss the major neuronal reprogramming factors (mostly pro-neurogenic transcription factors during development), especially the significance of their expression levels during neurogenesis and the reprogramming process focusing on NeuroD1. In the developing central nervous system, these pro-neurogenic transcription factors usually elicit distinct spatiotemporal expression patterns that are critical to their function in generating mature neurons. We argue that these dynamic expression patterns may be similarly needed in the process of reprogramming adult cells into neurons and further into mature neurons with subtype identities. We also summarize the existing approaches and propose new ones that control gene expression levels for a successful reprogramming outcome.
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Affiliation(s)
- Natalie Mseis-Jackson
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Mehek Sharma
- Department of Biological Sciences, College of Science & Mathematics, Augusta University, Augusta, GA 30912, USA;
| | - Hedong Li
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
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5
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Lelyte I, Rao VR, Kalesnykas G, Ragauskas S, Kaja S, Ahmed Z. Prospects and limitations of cumate-inducible lentivirus as a tool for investigating VEGF-A-mediated pathology in diabetic retinopathy. Sci Rep 2024; 14:14325. [PMID: 38906906 PMCID: PMC11192717 DOI: 10.1038/s41598-024-63590-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/30/2024] [Indexed: 06/23/2024] Open
Abstract
Diabetic retinopathy (DR) is a multifactorial disease displaying vascular-associated pathologies, including vascular leakage and neovascularization, ultimately leading to visual impairment. However, animal models accurately reflecting these pathologies are lacking. Vascular endothelial growth factor A (VEGF-A) is an important factor in the development of micro- and macro-vascular pathology in DR. In this study, we evaluated the feasibility of using a cumate-inducible lentivirus (LV) mediated expression of vegf-a to understand DR pathology in vitro and in vivo. Retinal pigment epithelial cells (ARPE-19) were transduced with cumate-inducible LV expressing vegf-a, with subsequent analysis of vegf-a expression and its impact on cell proliferation, viability, motility, and permeability. Cumate tolerability in adult Wistar rat eyes was assessed as an initial step towards a potential DR animal model development, by administering cumate via intravitreal injections (IVT) and evaluating consequent effects by spectral domain optical coherence tomography (SD-OCT), flash electroretinography (fERG), ophthalmic examination (OE), and immunohistochemistry. Transduction of ARPE-19 cells with cumate-inducible LV resulted in ~ 2.5-fold increase in vegf-a mRNA and ~ threefold increase in VEGF-A protein secretion. Transduced cells displayed enhanced cell proliferation, viability, permeability, and migration in tube-like structures. However, IVT cumate injections led to apparent retinal toxicity, manifesting as retinal layer abnormalities, haemorrhage, vitreous opacities, and significant reductions in a- and b-wave amplitudes, along with increased microglial activation and reactive gliosis. In summary, while cumate-inducible LV-mediated vegf-a expression is valuable for in vitro mechanistic studies in cellular drug discovery, its use is not a feasible approach to model DR in in vivo studies due to cumate-induced retinal toxicity.
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Affiliation(s)
- Inesa Lelyte
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- R&D Division, Experimentica Ltd., 10243, Vilnius, Lithuania.
- Department of Ophthalmology, Loyola University Chicago, Maywood, IL, 60153, USA.
| | - Vidhya R Rao
- Department of Ophthalmology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Giedrius Kalesnykas
- R&D Division, Experimentica Ltd., 10243, Vilnius, Lithuania
- R&D Division, Experimentica Ltd., Kuopio, Finland
- Experimentica Inc., Fort Worth, TX, USA
| | | | - Simon Kaja
- Department of Ophthalmology, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Zubair Ahmed
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Centre for Trauma Sciences Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Davis-Anderson K, Micheva-Viteva S, Solomon E, Hovde B, Cirigliano E, Harris J, Twary S, Iyer R. CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function. Int J Mol Sci 2023; 24:16161. [PMID: 38003351 PMCID: PMC10671572 DOI: 10.3390/ijms242216161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Neurodegeneration causes a significant disease burden and there are few therapeutic interventions available for reversing or slowing the disease progression. Induced pluripotent stem cells (iPSCs) hold significant potential since they are sourced from adult tissue and have the capacity to be differentiated into numerous cell lineages, including motor neurons. This differentiation process traditionally relies on cell lineage patterning factors to be supplied in the differentiation media. Genetic engineering of iPSC with the introduction of recombinant master regulators of motor neuron (MN) differentiation has the potential to shorten and streamline cell developmental programs. We have established stable iPSC cell lines with transient induction of exogenous LHX3 and ISL1 from the Tet-activator regulatory region and have demonstrated that induction of the transgenes is not sufficient for the development of mature MNs in the absence of neuron patterning factors. Comparative global transcriptome analysis of MN development from native and Lhx-ISL1 modified iPSC cultures demonstrated that the genetic manipulation helped to streamline the neuronal patterning process. However, leaky gene expression of the exogenous MN master regulators in iPSC resulted in the premature activation of genetic pathways characteristic of the mature MN function. Dysregulation of metabolic and regulatory pathways within the developmental process affected the MN electrophysiological responses.
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Affiliation(s)
- Katie Davis-Anderson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Sofiya Micheva-Viteva
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Emilia Solomon
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Blake Hovde
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Elisa Cirigliano
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer Harris
- Information Systems and Modeling Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Scott Twary
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Rashi Iyer
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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7
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Kim S, Jo KW, Park JM, Shin A, Kurita R, Nakamura Y, Kweon S, Baek EJ. Irradiation is not sufficient to eradicate residual immortalized erythroid cells in in vitro-generated red blood cell products. Transfusion 2023. [PMID: 37154531 DOI: 10.1111/trf.17394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND The generation of immortalized erythroid progenitor cell lines capable of producing enough red blood cells (RBCs) for blood transfusion typically requires the overexpression of oncogenes in stem cells or progenitor cells to permanently proliferate immature cells. It is essential that any live oncogene-expressing cells are eliminated from the final RBC products for clinical use. STUDY DESIGN AND METHODS It is believed that safety issues may be resolved by using a leukoreduction filter or by irradiating the final products, as is conventionally done in blood banks; however, this has never been proven to be effective. Therefore, to investigate whether immortalized erythroblasts can be completely removed using γ-ray irradiation, we irradiated the erythroblast cell line, HiDEP, and the erythroleukemic cell line, K562 that overexpress HPV16 E6/E7. We then analyzed the extent of cell death using flow cytometry and polymerase chain reaction (PCR). The cells were also subjected to leukoreduction filters. RESULTS Using γ-ray irradiation at 25 Gy, 90.4% of HiDEP cells, 91.6% of K562-HPV16 E6/E7 cells, and 93.5% of non-transduced K562 cells were dead. In addition, 5.58 × 107 HiDEP cells were passed through a leukoreduction filter, and 38 intact cells were harvested, revealing a filter removal efficiency of 99.9999%. However, both intact cells and oncogene DNA were still detected. DISCUSSION Irradiation cannot induce total cell death of oncogene-expressing erythroblasts and leukocyte filter efficiency is not 100%. Therefore, our findings imply that for clinical applications, safer methods should be developed to completely remove residual nucleated cells from cell line-derived RBC products.
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Affiliation(s)
- Suyeon Kim
- Department of Research and Development, ArtBlood Inc., Seoul, Korea
| | - Kyeong Won Jo
- Department of Research and Development, ArtBlood Inc., Seoul, Korea
| | - Ju Mi Park
- Department of Research and Development, ArtBlood Inc., Seoul, Korea
| | - Arim Shin
- Department of Translational Medicine, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Soonho Kweon
- Department of Research and Development, ArtBlood Inc., Seoul, Korea
| | - Eun Jung Baek
- Department of Research and Development, ArtBlood Inc., Seoul, Korea
- Department of Translational Medicine, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
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8
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Gao F, Wang F, Cao H, Chen Y, Diao Y, Kapranov P. Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes. Int J Mol Sci 2023; 24:4163. [PMID: 36835575 PMCID: PMC9959880 DOI: 10.3390/ijms24044163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The human genome encodes a multitude of different noncoding transcripts that have been traditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple functional transcripts that warrant future studies.
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Affiliation(s)
| | | | | | | | | | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
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9
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Freeman AH, Tembiwa K, Brenner JR, Chase MR, Fortune SM, Morita YS, Boutte CC. Arginine methylation sites on SepIVA help balance elongation and septation in Mycobacterium smegmatis. Mol Microbiol 2023; 119:208-223. [PMID: 36416406 PMCID: PMC10023300 DOI: 10.1111/mmi.15006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022]
Abstract
The growth of mycobacterial cells requires successful coordination between elongation and septation. However, it is not clear which factors mediate this coordination. Here, we studied the function and post-translational modification of an essential division factor, SepIVA, in Mycobacterium smegmatis. We find that SepIVA is arginine methylated, and that alteration of its methylation sites affects both septation and polar elongation of Msmeg. Furthermore, we show that SepIVA regulates the localization of MurG and that this regulation may impact polar elongation. Finally, we map SepIVA's two regulatory functions to different ends of the protein: the N-terminus regulates elongation while the C-terminus regulates division. These results establish SepIVA as a regulator of both elongation and division and characterize a physiological role for protein arginine methylation sites for the first time in mycobacteria.
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Affiliation(s)
- Angela H Freeman
- Department of Biology, University of Texas at Arlington,
Arlington, Texas, USA
| | - Karen Tembiwa
- Department of Biology, University of Texas at Arlington,
Arlington, Texas, USA
| | - James R Brenner
- Department of Microbiology, University of Massachusetts,
Amherst, Massachusetts, USA
| | - Michael R Chase
- Department of Immunology and Infectious Disease, Harvard TH
Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Disease, Harvard TH
Chan School of Public Health, Boston, Massachusetts, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts,
Amherst, Massachusetts, USA
| | - Cara C Boutte
- Department of Biology, University of Texas at Arlington,
Arlington, Texas, USA
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10
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Ma D, Yuan Q, Peng F, Paredes V, Zeng H, Yang Q, Peddi A, Patel A, Liu MS, Sun Z, Gao X. Engineered PROTAC-CID Systems for Mammalian Inducible Gene Regulation. J Am Chem Soc 2023; 145:1593-1606. [PMID: 36626587 PMCID: PMC10162582 DOI: 10.1021/jacs.2c09129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Gene regulation via chemically induced dimerization (CID) is useful for biomedical research. However, the number, type, versatility, and in vivo applications of CID tools remain limited. Here, we demonstrate the development of proteolysis-targeting chimera-based scalable CID (PROTAC-CID) platforms by systematically engineering the available PROTAC systems for inducible gene regulation and gene editing. Further, we show orthogonal PROTAC-CIDs that can fine-tune gene expression at gradient levels or multiplex biological signals with different logic gating operations. Coupling the PROTAC-CID platform with genetic circuits, we achieve digitally inducible expression of DNA recombinases, base- and prime-editors for transient genome manipulation. Finally, we package a compact PROTAC-CID system into adeno-associated viral vectors for inducible and reversible gene activation in vivo. This work provides a versatile molecular toolbox that expands the scope of chemically inducible gene regulation in human cells and mice.
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Affiliation(s)
- Dacheng Ma
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Qichen Yuan
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Fei Peng
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Victor Paredes
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Hongzhi Zeng
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Qiaochu Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Advaith Peddi
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Anika Patel
- Department of Computer Sciences, Rice University, Houston, Texas 77005, USA
| | - Megan S. Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Zheng Sun
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
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11
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Sijben HJ, Dall’ Acqua L, Liu R, Jarret A, Christodoulaki E, Onstein S, Wolf G, Verburgt SJ, Le Dévédec SE, Wiedmer T, Superti-Furga G, IJzerman AP, Heitman LH. Impedance-Based Phenotypic Readout of Transporter Function: A Case for Glutamate Transporters. Front Pharmacol 2022; 13:872335. [PMID: 35677430 PMCID: PMC9169222 DOI: 10.3389/fphar.2022.872335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Excitatory amino acid transporters (EAAT/SLC1) mediate Na+-dependent uptake of extracellular glutamate and are potential drug targets for neurological disorders. Conventional methods to assess glutamate transport in vitro are based on radiolabels, fluorescent dyes or electrophysiology, which potentially compromise the cell’s physiology and are generally less suited for primary drug screens. Here, we describe a novel label-free method to assess human EAAT function in living cells, i.e., without the use of chemical modifications to the substrate or cellular environment. In adherent HEK293 cells overexpressing EAAT1, stimulation with glutamate or aspartate induced cell spreading, which was detected in real-time using an impedance-based biosensor. This change in cell morphology was prevented in the presence of the Na+/K+-ATPase inhibitor ouabain and EAAT inhibitors, which suggests the substrate-induced response was ion-dependent and transporter-specific. A mechanistic explanation for the phenotypic response was substantiated by actin cytoskeleton remodeling and changes in the intracellular levels of the osmolyte taurine, which suggests that the response involves cell swelling. In addition, substrate-induced cellular responses were observed for cells expressing other EAAT subtypes, as well as in a breast cancer cell line (MDA-MB-468) with endogenous EAAT1 expression. These findings allowed the development of a label-free high-throughput screening assay, which could be beneficial in early drug discovery for EAATs and holds potential for the study of other transport proteins that modulate cell shape.
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Affiliation(s)
- Hubert J. Sijben
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Laura Dall’ Acqua
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Rongfang Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Abigail Jarret
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Simone J. Verburgt
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Laura H. Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
- Oncode Institute, Leiden, Netherlands
- *Correspondence: Laura H. Heitman,
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12
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In vivo inducible reverse genetics in patients' tumors to identify individual therapeutic targets. Nat Commun 2021; 12:5655. [PMID: 34580292 PMCID: PMC8476619 DOI: 10.1038/s41467-021-25963-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/09/2021] [Indexed: 01/18/2023] Open
Abstract
High-throughput sequencing describes multiple alterations in individual tumors, but their functional relevance is often unclear. Clinic-close, individualized molecular model systems are required for functional validation and to identify therapeutic targets of high significance for each patient. Here, we establish a Cre-ERT2-loxP (causes recombination, estrogen receptor mutant T2, locus of X-over P1) based inducible RNAi- (ribonucleic acid interference) mediated gene silencing system in patient-derived xenograft (PDX) models of acute leukemias in vivo. Mimicking anti-cancer therapy in patients, gene inhibition is initiated in mice harboring orthotopic tumors. In fluorochrome guided, competitive in vivo trials, silencing of the apoptosis regulator MCL1 (myeloid cell leukemia sequence 1) correlates to pharmacological MCL1 inhibition in patients´ tumors, demonstrating the ability of the method to detect therapeutic vulnerabilities. The technique identifies a major tumor-maintaining potency of the MLL-AF4 (mixed lineage leukemia, ALL1-fused gene from chromosome 4) fusion, restricted to samples carrying the translocation. DUX4 (double homeobox 4) plays an essential role in patients’ leukemias carrying the recently described DUX4-IGH (immunoglobulin heavy chain) translocation, while the downstream mediator DDIT4L (DNA-damage-inducible transcript 4 like) is identified as therapeutic vulnerability. By individualizing functional genomics in established tumors in vivo, our technique decisively complements the value chain of precision oncology. Being broadly applicable to tumors of all kinds, it will considerably reinforce personalizing anti-cancer treatment in the future. Preclinical molecular models are useful that mimic a patient´s response to targeted therapy. Here, the authors establish an in vivo inducible RNAi-mediated gene silencing system in patient-derived xenograft models of acute leukemia to identify individual vulnerabilities and therapeutic targets.
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13
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Love AC, Tran SH, Prescher JA. Caged Cumate Enables Proximity-Dependent Control Over Gene Expression. Chembiochem 2021; 22:2440-2448. [PMID: 34031982 PMCID: PMC9870035 DOI: 10.1002/cbic.202100158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/17/2021] [Indexed: 01/26/2023]
Abstract
Cell-cell interactions underlie diverse physiological processes yet remain challenging to examine with conventional imaging tools. Here we report a novel strategy to illuminate cell proximity using transcriptional activators. We repurposed cumate, a small molecule inducer of gene expression, by caging its key carboxylate group with a nitrile. Nitrilase-expressing activator cells released the cage, liberating cumate for consumption by reporter cells. Reporter cells comprising a cumate-responsive switch expressed a target gene when in close proximity to the activator cells. Overall, this strategy provides a versatile platform to image and potentially manipulate cellular interactions over time.
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Affiliation(s)
- Anna C Love
- Department of Chemistry, University of California, Irvine, 1120 Natural Sciences II, Irvine, CA 92697, USA
| | - Sabrina H Tran
- Department of Biological Sciences, University of California, Irvine, 5120 Natural Sciences II, Irvine, CA, 92627, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, 1120 Natural Sciences II, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, 101 Theory, Ste. 101, Irvine, CA 92697, USA
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14
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Yang J, Lee J, Land MA, Lai S, Igoshin OA, St-Pierre F. A synthetic circuit for buffering gene dosage variation between individual mammalian cells. Nat Commun 2021; 12:4132. [PMID: 34226556 PMCID: PMC8257781 DOI: 10.1038/s41467-021-23889-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits - Equalizers - that buffer copy-number variation at the single-cell level. Equalizers couple a transcriptional negative feedback loop with post-transcriptional incoherent feedforward control. Computational modeling suggests that the combination of these two topologies enables Equalizers to operate over a wide range of plasmid copy numbers. We demonstrate experimentally that Equalizers outperform other gene dosage compensation topologies and produce as low cell-to-cell variation as chromosomally integrated genes. We also show that episome-encoded Equalizers enable the rapid generation of extrachromosomal cell lines with stable and uniform expression. Overall, Equalizers are simple and versatile devices for homogeneous gene expression and can facilitate the engineering of synthetic circuits that function reliably in every cell.
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Affiliation(s)
- Jin Yang
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Michelle A Land
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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15
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Anderson NC, Chen PF, Meganathan K, Afshar Saber W, Petersen AJ, Bhattacharyya A, Kroll KL, Sahin M. Balancing serendipity and reproducibility: Pluripotent stem cells as experimental systems for intellectual and developmental disorders. Stem Cell Reports 2021; 16:1446-1457. [PMID: 33861989 PMCID: PMC8190574 DOI: 10.1016/j.stemcr.2021.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) and their differentiation into neural lineages is a revolutionary experimental system for studying neurological disorders, including intellectual and developmental disabilities (IDDs). However, issues related to variability and reproducibility have hindered translating preclinical findings into drug discovery. Here, we identify areas for improvement by conducting a comprehensive review of 58 research articles that utilized iPSC-derived neural cells to investigate genetically defined IDDs. Based upon these findings, we propose recommendations for best practices that can be adopted by research scientists as well as journal editors.
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Affiliation(s)
- Nickesha C Anderson
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pin-Fang Chen
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kesavan Meganathan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wardiya Afshar Saber
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA.
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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16
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Expression of Secreted Neutrophil Gelatinase-Associated Lipocalin in 293T Cell Using the Inducible Dual-Function System. Processes (Basel) 2021. [DOI: 10.3390/pr9050855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Neutrophil gelatinase-associated lipocalin (NGAL) has emerged as a promising biomarker for the early prediction of acute kidney injury (AKI). The production of recombinant NGAL is considered to be necessary for the development of a detection method. This study intended to express the recombinant NGAL protein in 293T cell under the Tet-On inducible system and human serum albumin signal sequence (HSA-SS). The transfection efficiency and protein modulation were assessed by detecting the expression of the enhanced green fluorescent protein (EGFP) and secreted NGAL protein. Both proteins were detected only in the presence of a doxycycline (Dox) inducer. Cell toxicity was not found under any conditions. Moreover, a higher level of soluble NGAL protein in the supernatant secreted by HSA-SS compared with a native signal peptide (Nat-SS) was observed. In summary, this work successfully optimized the conditions for induction of NGAL expression. This system will provide as an efficient strategy to produce other recombinant proteins secreted from a mammalian cell.
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17
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Kim DH, Park BJ, Ahn HS, Go HJ, Kim DY, Kim JH, Lee JB, Park SY, Song CS, Lee SW, Choi IS. Canine interferon lambda 3 expressed using an adenoviral vector effectively induces antiviral activity against canine influenza virus. Virus Res 2021; 296:198342. [PMID: 33607185 DOI: 10.1016/j.virusres.2021.198342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/23/2022]
Abstract
Interferon-lambda (IFN-λ) is a type-III IFN and is considered a candidate of antiviral therapeutics. Although the antiviral effects of IFN-λ have been investigated in several studies, it has not been clinically approved as an antiviral agent. In this study, an adenoviral vector expression system employing a tetracycline-operator system was developed to control the expression of canine IFN-λ3. The antiviral effects of canine IFN-λ3 were determined in Madin-Darby canine kidney cells and canine tracheal epithelial cells. After transducing each cell line with recombinant adenovirus containing canine interferon lambda3 gene (Ad-caIFNλ3), the mRNA-expression of interferon-stimulated genes Mx1, ISG15, and OAS1 increased significantly (P < 0.05). The replication of canine influenza virus (CIV) was significantly suppressed in Ad-caIFNλ3-infected cells. These results indicate that the newly constructed adenoviral vector system could express canine IFN-λ3, which could subsequently inhibit CIV replication in two canine cell lines. These data imply that the recombinant Ad-caIFNλ3 can potentially be used to treat canine influenza and other viral diseases.
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Affiliation(s)
- Dong-Hwi Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Byung-Joo Park
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hee-Seop Ahn
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hyeon-Jeong Go
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Da-Yoon Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Jae-Hyeong Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Joong-Bok Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Seung-Yong Park
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Chang-Seon Song
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Sang-Won Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - In-Soo Choi
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
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18
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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19
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Garcia-Marques J, Espinosa-Medina I, Ku KY, Yang CP, Koyama M, Yu HH, Lee T. A programmable sequence of reporters for lineage analysis. Nat Neurosci 2020; 23:1618-1628. [PMID: 32719561 DOI: 10.1038/s41593-020-0676-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 06/19/2020] [Indexed: 12/22/2022]
Abstract
We present CLADES (cell lineage access driven by an edition sequence), a technology for cell lineage studies based on CRISPR-Cas9 techniques. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a predetermined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, thereby coupling birth order to reporter expression. This system, which can also be temporally induced by heat shock, enables the temporal resolution of lineage development and can therefore be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, predominantly marking each generation with the corresponding combination of reporters. CLADES therefore offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.
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Affiliation(s)
| | | | - Kai-Yuan Ku
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Po Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Hung-Hsiang Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzumin Lee
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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20
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Liu P, Zhao L, Loos F, Marty C, Xie W, Martins I, Lachkar S, Qu B, Waeckel-Énée E, Plo I, Vainchenker W, Perez F, Rodriguez D, López-Otin C, van Endert P, Zitvogel L, Kepp O, Kroemer G. Immunosuppression by Mutated Calreticulin Released from Malignant Cells. Mol Cell 2019; 77:748-760.e9. [PMID: 31785928 DOI: 10.1016/j.molcel.2019.11.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/23/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022]
Abstract
Mutations affecting exon 9 of the CALR gene lead to the generation of a C-terminally modified calreticulin (CALR) protein that lacks the KDEL endoplasmic reticulum (ER) retention signal and consequently mislocalizes outside of the ER where it activates the thrombopoietin receptor in a cell-autonomous fashion, thus driving myeloproliferative diseases. Here, we used the retention using selective hooks (RUSH) assay to monitor the trafficking of CALR. We found that exon-9-mutated CALR was released from cells in response to the biotin-mediated detachment from its ER-localized hook, in vitro and in vivo. Cellular CALR release was confirmed in suitable mouse models bearing exon-9-mutated hematopoietic systems or tumors. Extracellular CALR mediated immunomodulatory effects and inhibited the phagocytosis of dying cancer cells by dendritic cells (DC), thereby suppressing antineoplastic immune responses elicited by chemotherapeutic agents or by PD-1 blockade. Altogether, our results demonstrate paracrine immunosuppressive effects for exon-9-mutated CALR.
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Affiliation(s)
- Peng Liu
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Liwei Zhao
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France; Université Paris-Saclay, Villejuif, France
| | - Friedemann Loos
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Caroline Marty
- Université Paris-Saclay, Villejuif, France; INSERM, UMR 1170, Villejuif, France; Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Wei Xie
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Isabelle Martins
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Sylvie Lachkar
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Bo Qu
- Gustave Roussy Comprehensive Cancer Center, Villejuif, France; INSERM, U1015, Villejuif, France; Center of Clinical Investigations, CIC1428, Villejuif, France
| | - Emmanuelle Waeckel-Énée
- Université of Paris, Paris, France; INSERM, U1151, Paris, France; CNRS UMR8253, Paris, France
| | - Isabelle Plo
- Université Paris-Saclay, Villejuif, France; INSERM, UMR 1170, Villejuif, France; Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - William Vainchenker
- Université Paris-Saclay, Villejuif, France; INSERM, UMR 1170, Villejuif, France; Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Franck Perez
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS, Paris, France
| | - David Rodriguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carlos López-Otin
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France; Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Peter van Endert
- Université of Paris, Paris, France; INSERM, U1151, Paris, France; CNRS UMR8253, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Center, Villejuif, France; INSERM, U1015, Villejuif, France; Center of Clinical Investigations, CIC1428, Villejuif, France
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France.
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Sciences, Suzhou, China; Karolinska Institutet, Department of Women's and Children's Health, Stockholm, Sweden; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
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Capella Roca B, Alarcón Miguez A, Keenan J, Suda S, Barron N, O’Gorman D, Doolan P, Clynes M. Zinc supplementation increases protein titer of recombinant CHO cells. Cytotechnology 2019; 71:915-924. [PMID: 31396753 PMCID: PMC6787129 DOI: 10.1007/s10616-019-00334-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/01/2019] [Indexed: 12/20/2022] Open
Abstract
In order to study the impact of zinc and copper on the titer levels of mAb and recombinant protein in CHO cells, the IgG-expressing (DP12) and EPO-expressing (SK15) cell lines were cultured in chemically defined media with increasing concentrations of either metal. Supplementation with 25 mg/l in CDM media resulted in a significant increase in EPO (1.7-fold) and IgG (2.6-fold) titers compared to control (no added zinc). Titers at this Zn concentration in CDM containing the insulin replacing agent aurintricarboxylic acid (ATA) (CDM + A) showed a 1.8-fold (EPO) and 1.2-fold (IgG) titers increase compared to control. ATA appeared to also reduce the specific productivity (Qp) enhancement induced by Zn-25, with up to 4.9-fold (DP12) and 1.9-fold (SK15) Qp increase in CDM compared to the 1.6-fold (DP12) and 1.5-fold (SK15) Qp increase observed in CDM + A. A 31% reduced Viable Cell Density (VCD) in DP12 was observed in both Zn-supplemented media (3 × 106 cells/ml vs 4.2 × 106 cells/ml, day 5), whereas SK15 Zn-25 cultures displayed a 24% lower peak only in CDM + A (2.2 × 106 cells/ml vs 3.2 × 106 cells/ml, day 5). Supplementation with copper at 13.7-20 mg/l resulted in less significant cell line/product-type dependent effects on titer, VCD and Viability. Analysis of the energetic phenotype of both cell lines in 25 mg/l Zn-supplemented CDM media revealed a twofold increase in the oxygen consumption rate (OCR) compared to non-supplemented cells. Together, these data suggest that high zinc supplementation may induce an increase in oxidative respiration metabolism that results in increased Qp and titers in suspension CHO cultures.
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Affiliation(s)
- Berta Capella Roca
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
- SSPC-SFI, Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland
| | - Antonio Alarcón Miguez
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Joanne Keenan
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
- SSPC-SFI, Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland
| | - Srinivas Suda
- National Institute for Bioprocessing Research and Training, University College Dublin, Dublin, Ireland
| | - Niall Barron
- SSPC-SFI, Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland
- National Institute for Bioprocessing Research and Training, University College Dublin, Dublin, Ireland
| | - Donal O’Gorman
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Padraig Doolan
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
- SSPC-SFI, Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland
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Costello A, Lao NT, Barron N, Clynes M. Continuous translation of circularized mRNA improves recombinant protein titer. Metab Eng 2019; 52:284-292. [DOI: 10.1016/j.ymben.2019.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 01/16/2023]
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23
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Depletion of endogenous miRNA-378-3p increases peak cell density of CHO DP12 cells and is correlated with elevated levels of ubiquitin carboxyl-terminal hydrolase 14. J Biotechnol 2018; 288:30-40. [DOI: 10.1016/j.jbiotec.2018.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/27/2018] [Accepted: 10/28/2018] [Indexed: 01/01/2023]
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