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Jagadeeswaran I, Oh J, Sinnett SE. Preclinical Milestones in MECP2 Gene Transfer for Treating Rett Syndrome. Dev Neurosci 2024:1-10. [PMID: 38723617 DOI: 10.1159/000539267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/06/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the transcriptional regulator methyl-CpG-binding protein 2 (MeCP2). After gene transfer in mice, exogenous MeCP2 expression must be regulated to avoid dose-dependent toxicity. SUMMARY The preclinical gene therapy literature for treating RTT illustrates a duly diligent progression that begins with proof-of-concept studies and advances toward the development of safer, regulated MECP2 viral genome designs. This design progression was partly achieved through international collaborative studies. In 2023, clinicians administered investigational gene therapies for RTT to patients a decade after the first preclinical gene therapy publications for RTT (clinical trial numbers NCT05606614 and NCT05898620). As clinicians take on a more prominent role in MECP2 gene therapy research, preclinical researchers may continue to test more nuanced hypotheses regarding the safety, efficacy, and mechanism of MECP2 gene transfer. KEY MESSAGE This review summarizes the history of preclinical MECP2 gene transfer for treating RTT and acknowledges major contributions among colleagues in the field. The first clinical injections are a shared milestone.
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Affiliation(s)
- Indumathy Jagadeeswaran
- Department of Pediatrics, The University of Texas Southwestern Medical Center (UTSWMC), Dallas, Texas, USA,
| | - Jiyoung Oh
- Department of Pediatrics, The University of Texas Southwestern Medical Center (UTSWMC), Dallas, Texas, USA
| | - Sarah E Sinnett
- Department of Pediatrics, The University of Texas Southwestern Medical Center (UTSWMC), Dallas, Texas, USA
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center (UTSWMC), Dallas, Texas, USA
- Peter O'Donnell Jr. Brain Institute, The University of Texas Southwestern Medical Center (UTSWMC), Dallas, Texas, USA
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2
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Unda SR, Pomeranz LE, Marongiu R, Yu X, Kelly L, Hassanzadeh G, Molina H, Vaisey G, Wang P, Dyke JP, Fung EK, Grosenick L, Zirkel R, Antoniazzi AM, Norman S, Liston CM, Schaffer C, Nishimura N, Stanley SA, Friedman JM, Kaplitt MG. Bidirectional Regulation of Motor Circuits Using Magnetogenetic Gene Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.13.548699. [PMID: 37503198 PMCID: PMC10369996 DOI: 10.1101/2023.07.13.548699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here we report a novel suite of magnetogenetic tools, based on a single anti-ferritin nanobody-TRPV1 receptor fusion protein, which regulated neuronal activity when exposed to magnetic fields. AAV-mediated delivery of a floxed nanobody-TRPV1 into the striatum of adenosine 2a receptor-cre driver mice resulted in motor freezing when placed in an MRI or adjacent to a transcranial magnetic stimulation (TMS) device. Functional imaging and fiber photometry both confirmed activation of the target region in response to the magnetic fields. Expression of the same construct in the striatum of wild-type mice along with a second injection of an AAVretro expressing cre into the globus pallidus led to similar circuit specificity and motor responses. Finally, a mutation was generated to gate chloride and inhibit neuronal activity. Expression of this variant in subthalamic nucleus in PitX2-cre parkinsonian mice resulted in reduced local c-fos expression and motor rotational behavior. These data demonstrate that magnetogenetic constructs can bidirectionally regulate activity of specific neuronal circuits non-invasively in-vivo using clinically available devices. Teaser A novel magnetogenetics toolbox to regulate neural circuits in-vivo .
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3
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De Carluccio G, Fusco V, di Bernardo D. Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems. Nat Commun 2024; 15:3311. [PMID: 38632224 PMCID: PMC11024104 DOI: 10.1038/s41467-024-47592-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: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Inducible gene expression systems can be used to control the expression of a gene of interest by means of a small-molecule. One of the most common designs involves engineering a small-molecule responsive transcription factor (TF) and its cognate promoter, which often results in a compromise between minimal uninduced background expression (leakiness) and maximal induced expression. Here, we focus on an alternative strategy using quantitative synthetic biology to mitigate leakiness while maintaining high expression, without modifying neither the TF nor the promoter. Through mathematical modelling and experimental validations, we design the CASwitch, a mammalian synthetic gene circuit based on combining two well-known network motifs: the Coherent Feed-Forward Loop (CFFL) and the Mutual Inhibition (MI). The CASwitch combines the CRISPR-Cas endoribonuclease CasRx with the state-of-the-art Tet-On3G inducible gene system to achieve high performances. To demonstrate the potentialities of the CASwitch, we apply it to three different scenarios: enhancing a whole-cell biosensor, controlling expression of a toxic gene and inducible production of Adeno-Associated Virus (AAV) vectors.
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Affiliation(s)
- Giuliano De Carluccio
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
| | - Virginia Fusco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Naples, Italy.
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy.
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4
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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5
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Umaña JD, Wasserman SR, Song L, Goel AA, Yu X, Jin J, Hathaway NA. Chemical Epigenetic Regulation of Adeno-Associated Virus Delivered Transgenes. Hum Gene Ther 2023; 34:947-957. [PMID: 37624737 PMCID: PMC10517330 DOI: 10.1089/hum.2023.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Adeno-associated virus (AAV) is a powerful gene therapy vector that has been used in several FDA-approved therapies as well as in multiple clinical trials. This vector has high therapeutic versatility with the ability to deliver genetic payloads to a variety of human tissue types, yet there is currently a lack of transgene expression control once the virus is administered. There are also times when transgene expression is too low for the desired therapeutic outcome, necessitating high viral dose administration resulting in possible immunological complications. Herein, we validate a chemically controllable AAV transgene expression technology in vitro that utilizes bifunctional molecules known as chemical epigenetic modifiers (CEMs). These compounds employ endogenous epigenetic machinery to specifically enhance transgene expression of episomal DNA. A recombinant AAV (rAAV) was designed to both deliver the reporter transgene as well as deliver a synthetic zinc finger (ZFs) protein fused to FK506 binding protein (FKBP). These synthetic ZFs target a DNA-binding array sequence upstream of the promoter expressing the AAV transgene to specifically enhance AAV transgene expression in the presence of a CEM. The transcriptional activating compound CEM87 functions by recruiting the epigenetic transcription activator bromodomain-containing protein 4 (BRD4), increasing AAV transgene activity up to fivefold in a dose-dependent manner in HEK293T cells. The highest levels of transgene product activity are seen 24 h following CEM87 treatment. Additionally, the CEM87-mediated enhancement of different transgene products with either Luciferase or green fluorescent protein (GFP) was observed in multiple cell lines and enhancement of transgene expression was capsid serotype independent. The impact of CEM87 activity can be disrupted through drug removal or chemical recruitment site competition with FK506, thus demonstrating the reversibility of the impact of CEM87 on transgene expression. Collectively, this chemically controllable rAAV transgene technology provides temporal gene expression control that could increase the safety and efficiency of AAV-based research and therapies.
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Affiliation(s)
- Jessica D. Umaña
- Division of Chemical Biology and Medicinal Chemistry,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sara R. Wasserman
- Division of Chemical Biology and Medicinal Chemistry,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Liujiang Song
- Gene Therapy Center, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Arushi A. Goel
- Division of Chemical Biology and Medicinal Chemistry,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nathaniel A. Hathaway
- Division of Chemical Biology and Medicinal Chemistry,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Chen X, Dong T, Hu Y, De Pace R, Mattera R, Eberhardt K, Ziegler M, Pirovolakis T, Sahin M, Bonifacino JS, Ebrahimi-Fakhari D, Gray SJ. Intrathecal AAV9/AP4M1 gene therapy for hereditary spastic paraplegia 50 shows safety and efficacy in preclinical studies. J Clin Invest 2023; 133:e164575. [PMID: 36951961 PMCID: PMC10178841 DOI: 10.1172/jci164575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
Spastic paraplegia 50 (SPG50) is an ultrarare childhood-onset neurological disorder caused by biallelic loss-of-function variants in the AP4M1 gene. SPG50 is characterized by progressive spastic paraplegia, global developmental delay, and subsequent intellectual disability, secondary microcephaly, and epilepsy. We preformed preclinical studies evaluating an adeno-associated virus (AAV)/AP4M1 gene therapy for SPG50 and describe in vitro studies that demonstrate transduction of patient-derived fibroblasts with AAV2/AP4M1, resulting in phenotypic rescue. To evaluate efficacy in vivo, Ap4m1-KO mice were intrathecally (i.t.) injected with 5 × 1011, 2.5 × 1011, or 1.25 × 1011 vector genome (vg) doses of AAV9/AP4M1 at P7-P10 or P90. Age- and dose-dependent effects were observed, with early intervention and higher doses achieving the best therapeutic benefits. In parallel, three toxicology studies in WT mice, rats, and nonhuman primates (NHPs) demonstrated that AAV9/AP4M1 had an acceptable safety profile up to a target human dose of 1 × 1015 vg. Of note, similar degrees of minimal-to-mild dorsal root ganglia (DRG) toxicity were observed in both rats and NHPs, supporting the use of rats to monitor DRG toxicity in future i.t. AAV studies. These preclinical results identify an acceptably safe and efficacious dose of i.t.-administered AAV9/AP4M1, supporting an investigational gene transfer clinical trial to treat SPG50.
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Affiliation(s)
- Xin Chen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Dong
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Yuhui Hu
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Kathrin Eberhardt
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marvin Ziegler
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mustafa Sahin
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven J. Gray
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
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7
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Mohr M, Damas N, Gudmand-Høyer J, Zeeberg K, Jedrzejczyk D, Vlassis A, Morera-Gómez M, Pereira-Schoning S, Puš U, Oliver-Almirall A, Lyholm Jensen T, Baumgartner R, Tate Weinert B, Gill RT, Warnecke T. The CRISPR-Cas12a Platform for Accurate Genome Editing, Gene Disruption, and Efficient Transgene Integration in Human Immune Cells. ACS Synth Biol 2023; 12:375-389. [PMID: 36750230 PMCID: PMC9942205 DOI: 10.1021/acssynbio.2c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
CRISPR-Cas12a nucleases have expanded the toolbox for targeted genome engineering in a broad range of organisms. Here, using a high-throughput engineering approach, we explored the potential of a novel CRISPR-MAD7 system for genome editing in human cells. We evaluated several thousand optimization conditions and demonstrated accurate genome reprogramming with modified MAD7. We identified crRNAs that allow for ≤95% non-homologous end joining (NHEJ) and 66% frameshift mutations in various genes and observed the high-cleavage fidelity of MAD7 resulting in undetectable off-target activity. We explored the dsDNA delivery efficiency of CRISPR-MAD7, and by using our optimized transfection protocol, we obtained ≤85% chimeric antigen receptor (CAR) insertions in primary T cells, thus exceeding the baseline integration efficiencies of therapeutically relevant transgenes using currently available virus-free technologies. Finally, we evaluated multiplex editing efficiency with CRISPR-MAD7 and demonstrated simultaneous ≤35% CAR transgene insertions and ≤80% gene disruption efficiencies. Both the platform and our transfection procedure are easily adaptable for further preclinical studies and could potentially be used for clinical manufacturing of CAR T cells.
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Affiliation(s)
- Marina Mohr
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Nkerorema Damas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Johanne Gudmand-Høyer
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Katrine Zeeberg
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika Jedrzejczyk
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Arsenios Vlassis
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Sara Pereira-Schoning
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Urška Puš
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Anna Oliver-Almirall
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja Lyholm Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland Baumgartner
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Brian Tate Weinert
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Ryan T. Gill
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark,Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States,
| | - Tanya Warnecke
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States,
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8
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Jimenez-Gonzalez M, Li R, Pomeranz LE, Alvarsson A, Marongiu R, Hampton RF, Kaplitt MG, Vasavada RC, Schwartz GJ, Stanley SA. Mapping and targeted viral activation of pancreatic nerves in mice reveal their roles in the regulation of glucose metabolism. Nat Biomed Eng 2022; 6:1298-1316. [PMID: 35835995 PMCID: PMC9669304 DOI: 10.1038/s41551-022-00909-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
A lack of comprehensive mapping of ganglionic inputs into the pancreas and of technology for the modulation of the activity of specific pancreatic nerves has hindered the study of how they regulate metabolic processes. Here we show that the pancreas-innervating neurons in sympathetic, parasympathetic and sensory ganglia can be mapped in detail by using tissue clearing and retrograde tracing (the tracing of neural connections from the synapse to the cell body), and that genetic payloads can be delivered via intrapancreatic injection to target sites in efferent pancreatic nerves in live mice through optimized adeno-associated viruses and neural-tissue-specific promoters. We also show that, in male mice, the targeted activation of parasympathetic cholinergic intrapancreatic ganglia and neurons doubled plasma-insulin levels and improved glucose tolerance, and that tolerance was impaired by stimulating pancreas-projecting sympathetic neurons. The ability to map the peripheral ganglia innervating the pancreas and to deliver transgenes to specific pancreas-projecting neurons will facilitate the examination of ganglionic inputs and the study of the roles of pancreatic efferent innervation in glucose metabolism.
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Affiliation(s)
- M Jimenez-Gonzalez
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Li
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - L E Pomeranz
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY, USA
| | - A Alvarsson
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Marongiu
- Laboratory of Molecular Neurosurgery, Department of Neurological Surgery, Weill Cornell Medical College, New York, NY, USA
| | - R F Hampton
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M G Kaplitt
- Laboratory of Molecular Neurosurgery, Department of Neurological Surgery, Weill Cornell Medical College, New York, NY, USA
| | - R C Vasavada
- Department of Translational Research and Cellular Therapeutics, City of Hope, Duarte, CA, USA
| | - G J Schwartz
- Departments of Medicine and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - S A Stanley
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens. Cell Syst 2022; 13:376-387.e8. [PMID: 35316656 DOI: 10.1016/j.cels.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/27/2021] [Accepted: 02/25/2022] [Indexed: 12/16/2022]
Abstract
Pooled genetic libraries have improved screening throughput for mapping genotypes to phenotypes. However, selectable phenotypes are limited, restricting screening to outcomes with a low spatiotemporal resolution. Here, we integrated live-cell imaging with pooled library-based screening. To enable intracellular multiplexing, we developed a method called EPICode that uses a combination of short epitopes, which can also appear in various subcellular locations. EPICode thus enables the use of live-cell microscopy to characterize a phenotype of interest over time, including after sequential stimulatory/inhibitory manipulations, and directly connects behavior to the cellular genotype. To test EPICode's capacity against an important milestone-engineering and optimizing dynamic, live-cell reporters-we developed a live-cell PKA kinase translocation reporter with improved sensitivity and specificity. The use of epitopes as fluorescent barcodes introduces a scalable strategy for high-throughput screening broadly applicable to protein engineering and drug discovery settings where image-based phenotyping is desired.
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10
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Brudvig JJ, Weimer JM. CLN7 gene therapy: hope for an ultra-rare condition. J Clin Invest 2022; 132:157820. [PMID: 35229731 PMCID: PMC8884894 DOI: 10.1172/jci157820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
CLN7 Batten disease, also known as variant late infantile neuronal ceroid lipofuscinosis type 7 (vLINCL7), is an ultra-rare form of Batten disease that presents early in life with severe neurological symptoms, including visual deficits, motor problems, and frequent seizures. There is high unmet need for disease-modifying therapies, as no existing treatment can halt progression or prevent premature death. In this issue of the JCI, Chen et al. present an AAV gene therapy for CLN7 that shows marked benefit in a mouse model of CLN7 Batten disease, paving the way for a phase I trial. The candidate gene therapy shows benefit for histopathology, behavioral abnormalities, and survival in mice and offers an acceptable safety profile in both mice and rats. Questions remain regarding dose, scaling, and timing of administration for patients, but this work is a substantial step forward for a very challenging disease.
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11
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Chen X, Dong T, Hu Y, Shaffo FC, Belur NR, Mazzulli JR, Gray SJ. AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 disease. J Clin Invest 2022; 132:146286. [PMID: 35025759 PMCID: PMC8884910 DOI: 10.1172/jci146286] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
Neuronal ceroid lipofuscinosis type 7 (CLN7) disease is a lysosomal storage disease caused by mutations in the facilitator superfamily domain containing 8 (MFSD8) gene, which encodes a membrane-bound lysosomal protein, MFSD8. To test the effectiveness and safety of adeno-associated viral (AAV) gene therapy, an in vitro study demonstrated that AAV2/MFSD8 dose dependently rescued lysosomal function in fibroblasts from a CLN7 patient. An in vivo efficacy study using intrathecal administration of AAV9/MFSD8 to Mfsd8- /- mice at P7-P10 or P120 with high or low dose led to clear age- and dose-dependent effects. A high dose of AAV9/MFSD8 at P7-P10 resulted in widespread MFSD8 mRNA expression, tendency of amelioration of subunit c of mitochondrial ATP synthase accumulation and glial fibrillary acidic protein immunoreactivity, normalization of impaired behaviors, doubled median life span, and extended normal body weight gain. In vivo safety studies in rodents concluded that intrathecal administration of AAV9/MFSD8 was safe and well tolerated. In summary, these results demonstrated that the AAV9/MFSD8 vector is both effective and safe in preclinical models.
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Affiliation(s)
- Xin Chen
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Thomas Dong
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Yuhui Hu
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Frances C Shaffo
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Nandkishore R Belur
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Steven J Gray
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
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12
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Taylor GM, Hitchcock A, Heap JT. Combinatorial assembly platform enabling engineering of genetically stable metabolic pathways in cyanobacteria. Nucleic Acids Res 2021; 49:e123. [PMID: 34554258 PMCID: PMC8643660 DOI: 10.1093/nar/gkab791] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are simple, efficient, genetically-tractable photosynthetic microorganisms which in principle represent ideal biocatalysts for CO2 capture and conversion. However, in practice, genetic instability and low productivity are key, linked problems in engineered cyanobacteria. We took a massively parallel approach, generating and characterising libraries of synthetic promoters and RBSs for the cyanobacterium Synechocystis sp. PCC 6803, and assembling a sparse combinatorial library of millions of metabolic pathway-encoding construct variants. Genetic instability was observed for some variants, which is expected when variants cause metabolic burden. Surprisingly however, in a single combinatorial round without iterative optimisation, 80% of variants chosen at random and cultured photoautotrophically over many generations accumulated the target terpenoid lycopene from atmospheric CO2, apparently overcoming genetic instability. This large-scale parallel metabolic engineering of cyanobacteria provides a new platform for development of genetically stable cyanobacterial biocatalysts for sustainable light-driven production of valuable products directly from CO2, avoiding fossil carbon or competition with food production.
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Affiliation(s)
- George M Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.,School of Life Sciences, The University of Nottingham, Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK
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13
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Kot S, Karumuthil-Melethil S, Woodley E, Zaric V, Thompson P, Chen Z, Lykken E, Keimel JG, Kaemmerer WF, Gray SJ, Walia JS. Investigating Immune Responses to the scAAV9- HEXM Gene Therapy Treatment in Tay-Sachs Disease and Sandhoff Disease Mouse Models. Int J Mol Sci 2021; 22:ijms22136751. [PMID: 34201771 PMCID: PMC8268035 DOI: 10.3390/ijms22136751] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 12/15/2022] Open
Abstract
GM2 gangliosidosis disorders are a group of neurodegenerative diseases that result from a functional deficiency of the enzyme β-hexosaminidase A (HexA). HexA consists of an α- and β-subunit; a deficiency in either subunit results in Tay–Sachs Disease (TSD) or Sandhoff Disease (SD), respectively. Viral vector gene transfer is viewed as a potential method of treating these diseases. A recently constructed isoenzyme to HexA, called HexM, has the ability to effectively catabolize GM2 gangliosides in vivo. Previous gene transfer studies have revealed that the scAAV9-HEXM treatment can improve survival in the murine SD model. However, it is speculated that this treatment could elicit an immune response to the carrier capsid and “non-self”-expressed transgene. This study was designed to assess the immunocompetence of TSD and SD mice, and test the immune response to the scAAV9-HEXM gene transfer. HexM vector-treated mice developed a significant anti-HexM T cell response and antibody response. This study confirms that TSD and SD mouse models are immunocompetent, and that gene transfer expression can create an immune response in these mice. These mouse models could be utilized for investigating methods of mitigating immune responses to gene transfer-expressed “non-self” proteins, and potentially improve treatment efficacy.
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Affiliation(s)
- Shalini Kot
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (S.K.); (E.W.)
| | - Subha Karumuthil-Melethil
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.-M.); (V.Z.); (E.L.); (S.J.G.)
| | - Evan Woodley
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (S.K.); (E.W.)
| | - Violeta Zaric
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.-M.); (V.Z.); (E.L.); (S.J.G.)
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Patrick Thompson
- Medical Genetics, Department of Pediatrics, Queen’s University, Kingston, ON K7L 2V7, Canada; (P.T.); (Z.C.)
| | - Zhilin Chen
- Medical Genetics, Department of Pediatrics, Queen’s University, Kingston, ON K7L 2V7, Canada; (P.T.); (Z.C.)
| | - Erik Lykken
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.-M.); (V.Z.); (E.L.); (S.J.G.)
| | - John G. Keimel
- New Hope Research Foundation, North Oaks, MN 55127, USA; (J.G.K.); (W.F.K.)
| | | | - Steven J. Gray
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.-M.); (V.Z.); (E.L.); (S.J.G.)
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jagdeep S. Walia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (S.K.); (E.W.)
- Medical Genetics, Department of Pediatrics, Queen’s University, Kingston, ON K7L 2V7, Canada; (P.T.); (Z.C.)
- Correspondence:
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14
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von Jonquieres G, Rae CD, Housley GD. Emerging Concepts in Vector Development for Glial Gene Therapy: Implications for Leukodystrophies. Front Cell Neurosci 2021; 15:661857. [PMID: 34239416 PMCID: PMC8258421 DOI: 10.3389/fncel.2021.661857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Central Nervous System (CNS) homeostasis and function rely on intercellular synchronization of metabolic pathways. Developmental and neurochemical imbalances arising from mutations are frequently associated with devastating and often intractable neurological dysfunction. In the absence of pharmacological treatment options, but with knowledge of the genetic cause underlying the pathophysiology, gene therapy holds promise for disease control. Consideration of leukodystrophies provide a case in point; we review cell type – specific expression pattern of the disease – causing genes and reflect on genetic and cellular treatment approaches including ex vivo hematopoietic stem cell gene therapies and in vivo approaches using adeno-associated virus (AAV) vectors. We link recent advances in vectorology to glial targeting directed towards gene therapies for specific leukodystrophies and related developmental or neurometabolic disorders affecting the CNS white matter and frame strategies for therapy development in future.
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Affiliation(s)
- Georg von Jonquieres
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Caroline D Rae
- Neuroscience Research Australia, Randwick, NSW, Australia
| | - Gary D Housley
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
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15
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DeRosa S, Salani M, Smith S, Sangster M, Miller-Browne V, Wassmer S, Xiao R, Vandenberghe L, Slaugenhaupt S, Misko A, Grishchuk Y. MCOLN1 gene therapy corrects neurologic dysfunction in the mouse model of mucolipidosis IV. Hum Mol Genet 2021; 30:908-922. [PMID: 33822942 DOI: 10.1093/hmg/ddab093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Mucolipidosis IV (MLIV) is an orphan disease leading to debilitating psychomotor deficits and vision loss. It is caused by loss-of-function mutations in the MCOLN1 gene that encodes the lysosomal transient receptor potential channel mucolipin1, or TRPML1. With no existing therapy, the unmet need in this disease is very high. Here, we showed that AAV-mediated CNS-targeted gene transfer of the human MCOLN1 gene rescued motor function and alleviated brain pathology in the MLIV mouse model. Using the AAV-PHP.b vector in symptomatic mice, we showed long-term reversal of declined motor function and significant delay of paralysis. Next, using self-complementary AAV9 clinical candidate vector, we showed that its intracerebroventricular administration in post-natal day 1 mice significantly improved motor function, myelination and reduced lysosomal storage load in the MLIV mouse brain. Based on our data and general advancements in the gene therapy field, we propose scAAV9-mediated CSF-targeted MCOLN1 gene transfer as a therapeutic strategy in MLIV.
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Affiliation(s)
- Samantha DeRosa
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Monica Salani
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Sierra Smith
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Madison Sangster
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Victoria Miller-Browne
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Sarah Wassmer
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA 02114, USA
| | - Ru Xiao
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA 02114, USA
| | - Luk Vandenberghe
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA 02114, USA
| | - Susan Slaugenhaupt
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Albert Misko
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
| | - Yulia Grishchuk
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02114, USA
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16
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Gumusgoz E, Guisso DR, Kasiri S, Wu J, Dear M, Verhalen B, Nitschke S, Mitra S, Nitschke F, Minassian BA. Targeting Gys1 with AAV-SaCas9 Decreases Pathogenic Polyglucosan Bodies and Neuroinflammation in Adult Polyglucosan Body and Lafora Disease Mouse Models. Neurotherapeutics 2021; 18:1414-1425. [PMID: 33830476 PMCID: PMC8423949 DOI: 10.1007/s13311-021-01040-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
Many adult and most childhood neurological diseases have a genetic basis. CRISPR/Cas9 biotechnology holds great promise in neurological therapy, pending the clearance of major delivery, efficiency, and specificity hurdles. We applied CRISPR/Cas9 genome editing in its simplest modality, namely inducing gene sequence disruption, to one adult and one pediatric disease. Adult polyglucosan body disease is a neurodegenerative disease resembling amyotrophic lateral sclerosis. Lafora disease is a severe late childhood onset progressive myoclonus epilepsy. The pathogenic insult in both is formation in the brain of glycogen with overlong branches, which precipitates and accumulates into polyglucosan bodies that drive neuroinflammation and neurodegeneration. We packaged Staphylococcus aureus Cas9 and a guide RNA targeting the glycogen synthase gene, Gys1, responsible for brain glycogen branch elongation in AAV9 virus, which we delivered by neonatal intracerebroventricular injection to one mouse model of adult polyglucosan body disease and two mouse models of Lafora disease. This resulted, in all three models, in editing of approximately 17% of Gys1 alleles and a similar extent of reduction of Gys1 mRNA across the brain. The latter led to approximately 50% reductions of GYS1 protein, abnormal glycogen accumulation, and polyglucosan bodies, as well as ameliorations of neuroinflammatory markers in all three models. Our work represents proof of principle for virally delivered CRISPR/Cas9 neurotherapeutics in an adult-onset (adult polyglucosan body) and a childhood-onset (Lafora) neurological diseases.
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Affiliation(s)
- Emrah Gumusgoz
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Dikran R Guisso
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sahba Kasiri
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jun Wu
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Matthew Dear
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Brandy Verhalen
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Present address: Corteva Agriscience, IA, 50131, Johnston, USA
| | - Silvia Nitschke
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sharmistha Mitra
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Felix Nitschke
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Berge A Minassian
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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17
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Mol AA, Groher F, Schreiber B, Rühmkorff C, Suess B. Robust gene expression control in human cells with a novel universal TetR aptamer splicing module. Nucleic Acids Res 2020; 47:e132. [PMID: 31504742 PMCID: PMC6846422 DOI: 10.1093/nar/gkz753] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/12/2023] Open
Abstract
Fine-tuning of gene expression is desirable for a wide range of applications in synthetic biology. In this context, RNA regulatory devices provide a powerful and highly functional tool. We developed a versatile, robust and reversible device to control gene expression by splicing regulation in human cells using an aptamer that is recognized by the Tet repressor TetR. Upon insertion in proximity to the 5′ splice site, intron retention can be controlled via the binding of TetR to the aptamer. Although we were able to demonstrate regulation for different introns, the genomic context had a major impact on regulation. In consequence, we advanced the aptamer to develop a splice device. Our novel device contains the aptamer integrated into a context of exonic and intronic sequences that create and maintain an environment allowing a reliable and robust splicing event. The exon-born, additional amino acids will then be cleaved off by a self-cleaving peptide. This design allows portability of the splicing device, which we confirmed by demonstrating its functionality in different gene contexts. Intriguingly, our splicing device shows a high dynamic range and low basal activity, i.e. desirable features that often prove a major challenge when implementing synthetic biology in mammalian cell lines.
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Affiliation(s)
- Adam A Mol
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Britta Schreiber
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Ciaran Rühmkorff
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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18
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Crabtree E, Song L, Llanga T, Bower JJ, Cullen M, Salmon JH, Hirsch ML, Gilger BC. AAV-mediated expression of HLA-G1/5 reduces severity of experimental autoimmune uveitis. Sci Rep 2019; 9:19864. [PMID: 31882729 PMCID: PMC6934797 DOI: 10.1038/s41598-019-56462-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022] Open
Abstract
Non-infectious uveitis (NIU) is an intractable, recurrent, and painful disease that is a common cause of vision loss. Available treatments of NIU, such as the use of topical corticosteroids, are non-specific and have serious side effects which limits them to short-term use; however, NIU requires long-term treatment to prevent vision loss. Therefore, a single dose therapeutic that mediates long-term immunosuppression with minimal side effects is desirable. In order to develop an effective long-term therapy for NIU, an adeno-associated virus (AAV) gene therapy approach was used to exploit a natural immune tolerance mechanism induced by the human leukocyte antigen G (HLA-G). To mimic the prevention of NIU, naïve Lewis rats received a single intravitreal injection of AAV particles harboring codon-optimized cDNAs encoding HLA-G1 and HLA-G5 isoforms one week prior to the induction of experimental autoimmune uveitis (EAU). AAV-mediated expression of the HLA-G-1 and -5 transgenes in the targeted ocular tissues following a single intravitreal injection of AAV-HLA-G1/5 significantly decreased clinical and histopathological inflammation scores compared to untreated EAU eyes (p < 0.04). Thus, localized ocular gene delivery of AAV-HLA-G1/5 may reduce the off-target risks and establish a long-term immunosuppressive effect that would serve as an effective and novel therapeutic strategy for NIU, with the potential for applications to additional ocular immune-mediated diseases.
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Affiliation(s)
- Elizabeth Crabtree
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Liujiang Song
- Department of Pediatrics, Hunan Normal University Medical College, Changsha, Hunan, China
- Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC, USA
| | - Telmo Llanga
- Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jacquelyn J Bower
- Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Megan Cullen
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jacklyn H Salmon
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Matthew L Hirsch
- Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC, USA
| | - Brian C Gilger
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
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19
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Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nat Commun 2019; 10:2013. [PMID: 31043592 PMCID: PMC6494899 DOI: 10.1038/s41467-019-09974-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 04/04/2019] [Indexed: 01/26/2023] Open
Abstract
Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells.
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Affiliation(s)
- Hélène Chassin
- 0000 0001 2156 2780grid.5801.cDepartment of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marius Müller
- Cilag AG, Hochstrasse 201, CH-8200 Schaffhausen, Switzerland
| | - Marcel Tigges
- Cilag AG, Hochstrasse 201, CH-8200 Schaffhausen, Switzerland
| | - Leo Scheller
- 0000 0001 2156 2780grid.5801.cDepartment of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Moritz Lang
- 0000000404312247grid.33565.36Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
| | - Martin Fussenegger
- 0000 0001 2156 2780grid.5801.cDepartment of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland ,0000 0004 1937 0642grid.6612.3Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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20
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Deverman BE, Ravina BM, Bankiewicz KS, Paul SM, Sah DWY. Gene therapy for neurological disorders: progress and prospects. Nat Rev Drug Discov 2018; 17:641-659. [DOI: 10.1038/nrd.2018.110] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Sustained AAV9-mediated expression of a non-self protein in the CNS of non-human primates after immunomodulation. PLoS One 2018; 13:e0198154. [PMID: 29874260 PMCID: PMC5991358 DOI: 10.1371/journal.pone.0198154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
A critical issue in transgene delivery studies is immune reactivity to the transgene- encoded protein and its impact on sustained gene expression. Here, we test the hypothesis that immunomodulation by rapamycin can decrease immune reactivity after intrathecal AAV9 delivery of a transgene (GFP) in non-human primates, resulting in sustained GFP expression in the CNS. We show that rapamycin treatment clearly reduced the overall immunogenicity of the AAV9/GFP vector by lowering GFP- and AAV9-specific antibody responses, and decreasing T cell responses including cytokine and cytolytic effector responses. Spinal cord GFP protein expression was sustained for twelve weeks, with no toxicity. Immune correlates of robust transgene expression include negligible GFP-specific CD4 and CD8 T cell responses, absence of GFP-specific IFN-γ producing T cells, and absence of GFP-specific cytotoxic T cells, which support the hypothesis that decreased T cell reactivity results in sustained transgene expression. These data strongly support the use of modest doses of rapamycin to modulate immune responses for intrathecal gene therapies, and potentially a much wider range of viral vector-based therapeutics.
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22
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Lykken EA, Shyng C, Edwards RJ, Rozenberg A, Gray SJ. Recent progress and considerations for AAV gene therapies targeting the central nervous system. J Neurodev Disord 2018; 10:16. [PMID: 29776328 PMCID: PMC5960126 DOI: 10.1186/s11689-018-9234-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/01/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders, as a class of diseases, have been particularly difficult to treat even when the underlying cause(s), such as genetic alterations, are understood. What treatments do exist are generally not curative and instead seek to improve quality of life for affected individuals. The advent of gene therapy via gene replacement offers the potential for transformative therapies to slow or even stop disease progression for current patients and perhaps minimize or prevent the appearance of symptoms in future patients. MAIN BODY This review focuses on adeno-associated virus (AAV) gene therapies for diseases of the central nervous system. An overview of advances in AAV vector design for therapy is provided, along with a description of current strategies to develop AAV vectors with tailored tropism. Next, progress towards treatment of neurodegenerative diseases is presented at both the pre-clinical and clinical stages, focusing on a few select diseases to highlight broad categories of therapeutic parameters. Special considerations for more challenging cases are then discussed in addition to the immunological aspects of gene therapy. CONCLUSION With the promising clinical trial results that have been observed for the latest AAV gene therapies and continued pre-clinical successes, the question is no longer whether a therapy can be developed for certain neurodevelopmental disorders, but rather, how quickly.
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Affiliation(s)
- Erik Allen Lykken
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Charles Shyng
- University of North Carolina at Chapel Hill, Gene Therapy Center, Chapel Hill, NC 27599 USA
| | - Reginald James Edwards
- University of North Carolina at Chapel Hill, Gene Therapy Center, Chapel Hill, NC 27599 USA
| | - Alejandra Rozenberg
- University of North Carolina at Chapel Hill, Gene Therapy Center, Chapel Hill, NC 27599 USA
| | - Steven James Gray
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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23
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Kobori S, Yokobayashi Y. Analyzing and Tuning Ribozyme Activity by Deep Sequencing To Modulate Gene Expression Level in Mammalian Cells. ACS Synth Biol 2018; 7:371-376. [PMID: 29343061 DOI: 10.1021/acssynbio.7b00367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-cleaving ribozymes, in combination with aptamers and various classes of RNAs, have been heavily engineered to create RNA devices to control gene expression. Although understanding of sequence-function relationships of ribozymes is critical for such efforts, our current knowledge of self-cleaving ribozymes is mostly limited to the results from small scale mutational studies performed under different conditions, or qualitative results of mutate-and-select experiments that may contain experimental biases. Here, we applied our strategy based on deep sequencing to comprehensively assay a large number of mutants to systematically examine the effect of the P4 stem sequence on the activity of an HDV-like ribozyme. We discovered that the ribozyme activity is highly sensitive to the sequence and the apparent stability of the varied positions. Furthermore, we demonstrated that the collection of the ribozyme variants with different activities can be used as a convenient device to fine-tune the level of gene expression in mammalian cells.
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Affiliation(s)
- Shungo Kobori
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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24
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Bailey RM, Armao D, Nagabhushan Kalburgi S, Gray SJ. Development of Intrathecal AAV9 Gene Therapy for Giant Axonal Neuropathy. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 9:160-171. [PMID: 29766026 PMCID: PMC5948230 DOI: 10.1016/j.omtm.2018.02.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/09/2018] [Indexed: 12/30/2022]
Abstract
An NIH-sponsored phase I clinical trial is underway to test a potential treatment for giant axonal neuropathy (GAN) using viral-mediated GAN gene replacement (https://clinicaltrials.gov/ct2/show/NCT02362438). This trial marks the first instance of intrathecal (IT) adeno-associated viral (AAV) gene transfer in humans. GAN is a rare pediatric neurodegenerative disorder caused by autosomal recessive loss-of-function mutations in the GAN gene, which encodes the gigaxonin protein. Gigaxonin is involved in the regulation, turnover, and degradation of intermediate filaments (IFs). The pathologic signature of GAN is giant axonal swellings filled with disorganized accumulations of IFs. Herein, we describe the development and characterization of the AAV vector carrying a normal copy of the human GAN transgene (AAV9/JeT-GAN) currently employed in the clinical trial. Treatment with AAV/JeT-GAN restored the normal configuration of IFs in patient fibroblasts within days in cell culture and by 4 weeks in GAN KO mice. IT delivery of AAV9/JeT-GAN in aged GAN KO mice preserved sciatic nerve ultrastructure, reduced neuronal IF accumulations and attenuated rotarod dysfunction. This strategy conferred sustained wild-type gigaxonin expression across the PNS and CNS for at least 1 year in mice. These results support the clinical evaluation of AAV9/JeT-GAN for potential therapeutic outcomes and treatment for GAN patients.
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Affiliation(s)
- Rachel M Bailey
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Diane Armao
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Steven J Gray
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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25
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Varman AM, Follenfant R, Liu F, Davis RW, Lin YK, Singh S. Hybrid phenolic-inducible promoters towards construction of self-inducible systems for microbial lignin valorization. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:182. [PMID: 29988329 PMCID: PMC6022352 DOI: 10.1186/s13068-018-1179-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/19/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Engineering strategies to create promoters that are both higher strength and tunable in the presence of inexpensive compounds are of high importance to develop metabolic engineering technologies that can be commercialized. Lignocellulosic biomass stands out as the most abundant renewable feedstock for the production of biofuels and chemicals. However, lignin a major polymeric component of the biomass is made up of aromatic units and remains as an untapped resource. Novel synthetic biology tools for the expression of heterologous proteins are critical for the effective engineering of a microbe to valorize lignin. This study demonstrates the first successful attempt in the creation of engineered promoters that can be induced by aromatics present in lignocellulosic hydrolysates to increase heterologous protein production. RESULTS A hybrid promoter engineering approach was utilized for the construction of phenolic-inducible promoters of higher strength. The hybrid promoters were constructed by replacing the spacer region of an endogenous promoter, PemrR present in E. coli that was naturally inducible by phenolics. In the presence of vanillin, the engineered promoters Pvtac, Pvtrc, and Pvtic increased protein expression by 4.6-, 3.0-, and 1.5-fold, respectively, in comparison with a native promoter, PemrR. In the presence of vanillic acid, Pvtac, Pvtrc, and Pvtic improved protein expression by 9.5-, 6.8-, and 2.1-fold, respectively, in comparison with PemrR. Among the cells induced with vanillin, the emergence of a sub-population constituting the healthy and dividing cells using flow cytometry was observed. The analysis also revealed this smaller sub-population to be the primary contributor for the increased expression that was observed with the engineered promoters. CONCLUSIONS This study demonstrates the first successful attempt in the creation of engineered promoters that can be induced by aromatics to increase heterologous protein production. Employing promoters inducible by phenolics will provide the following advantages: (1) develop substrate inducible systems; (2) lower operating costs by replacing expensive IPTG currently used for induction; (3) develop dynamic regulatory systems; and (4) provide flexibility in operating conditions. The flow cytometry findings strongly suggest the need for novel approaches to maintain a healthy cell population in the presence of phenolics to achieve increased heterologous protein expression and, thereby, valorize lignin efficiently.
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Affiliation(s)
- Arul M. Varman
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA USA 94550
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287 USA
| | - Rhiannon Follenfant
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA USA 94550
| | - Fang Liu
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA USA 94550
| | - Ryan W. Davis
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA USA 94550
| | - Yone K. Lin
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA USA 94550
| | - Seema Singh
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA USA 94550
- Joint Bioenergy Institute, Emeryville, CA USA 94608
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN 55108 USA
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26
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Hirsch ML, Conatser LM, Smith SM, Salmon JH, Wu J, Buglak NE, Davis R, Gilger BC. AAV vector-meditated expression of HLA-G reduces injury-induced corneal vascularization, immune cell infiltration, and fibrosis. Sci Rep 2017; 7:17840. [PMID: 29259248 PMCID: PMC5736662 DOI: 10.1038/s41598-017-18002-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/05/2017] [Indexed: 01/11/2023] Open
Abstract
Over 1.5 million individuals suffer from cornea vascularization due to genetic and/or environmental factors, compromising visual acuity and often resulting in blindness. Current treatments of corneal vascularization are limited in efficacy and elicit undesirable effects including, ironically, vision loss. To develop a safe and effective therapy for corneal vascularization, adeno-associated virus (AAV) gene therapy, exploiting a natural immune tolerance mechanism induced by human leukocyte antigen G (HLA-G), was investigated. Self-complementary AAV cassettes containing codon optimized HLA-G1 (transmembrane) or HLA-G5 (soluble) isoforms were validated in vitro. Then, following a corneal intrastromal injection, AAV vector transduction kinetics, using a chimeric AAV capsid, were determined in rabbits. One week following corneal trauma, a single intrastromal injection of scAAV8G9-optHLA-G1 + G5 prevented corneal vascularization, inhibited trauma-induced T-lymphocyte infiltration (some of which were CD8+), and dramatically reduced myofibroblast formation compared to control treated eyes. Biodistribution analyses suggested AAV vectors persisted only in the trauma-induced corneas; however, a neutralizing antibody response to the vector capsid was observed inconsistently. The collective data demonstrate the clinical potential of scAAV8G9-optHLA-G to safely and effectively treat corneal vascularization and inhibit fibrosis while alluding to broader roles in ocular surface immunity and allogenic organ transplantation.
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Affiliation(s)
- Matthew L Hirsch
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Laura M Conatser
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Sara M Smith
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jacklyn H Salmon
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jerry Wu
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nicholas E Buglak
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Rich Davis
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Brian C Gilger
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA.
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27
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Karumuthil-Melethil S, Marshall MS, Heindel C, Jakubauskas B, Bongarzone ER, Gray SJ. Intrathecal administration of AAV/GALC vectors in 10-11-day-old twitcher mice improves survival and is enhanced by bone marrow transplant. J Neurosci Res 2017; 94:1138-51. [PMID: 27638599 DOI: 10.1002/jnr.23882] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/11/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022]
Abstract
Globoid cell leukodystrophy (GLD), or Krabbe disease, is an autosomal recessive neurodegenerative disease caused by the deficiency of the lysosomal enzyme galactocerebrosidase (GALC). Hematopoietic stem cell transplantation (HSCT) provides modest benefit in presymptomatic patients but is well short of a cure. Gene transfer experiments using viral vectors have shown some success in extending the survival in the mouse model of GLD, twitcher mice. The present study compares three single-stranded (ss) AAV serotypes, two natural and one engineered (with oligodendrocyte tropism), and a self-complementary (sc) AAV vector, all packaged with a codon-optimized murine GALC gene. The vectors were delivered via a lumbar intrathecal route for global CNS distribution on PND10-11 at a dose of 2 × 10(11) vector genomes (vg) per mouse. The results showed a similar significant extension of life span of the twitcher mice for all three serotypes (AAV9, AAVrh10, and AAV-Olig001) as well as the scAAV9 vector, compared to control cohorts. The rAAV gene transfer facilitated GALC biodistribution and detectable enzymatic activity throughout the CNS as well as in sciatic nerve and liver. When combined with BMT from syngeneic wild-type mice, there was significant improvement in survival for ssAAV9. Histopathological analysis of brain, spinal cord, and sciatic nerve showed significant improvement in preservation of myelin, with ssAAV9 providing the greatest benefit. In summary, we demonstrate that lumbar intrathecal delivery of rAAV/mGALCopt can significantly enhance the life span of twitcher mice treated at PND10-11 and that BMT synergizes with this treatment to improve the survival further. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Michael S Marshall
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois
| | - Clifford Heindel
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Benas Jakubauskas
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois
| | - Ernesto R Bongarzone
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois
| | - Steven J Gray
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. .,Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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28
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Brown AJ, Gibson SJ, Hatton D, James DC. In silico design of context-responsive mammalian promoters with user-defined functionality. Nucleic Acids Res 2017; 45:10906-10919. [PMID: 28977454 PMCID: PMC5737543 DOI: 10.1093/nar/gkx768] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Comprehensive de novo-design of complex mammalian promoters is restricted by unpredictable combinatorial interactions between constituent transcription factor regulatory elements (TFREs). In this study, we show that modular binding sites that do not function cooperatively can be identified by analyzing host cell transcription factor expression profiles, and subsequently testing cognate TFRE activities in varying homotypic and heterotypic promoter architectures. TFREs that displayed position-insensitive, additive function within a specific expression context could be rationally combined together in silico to create promoters with highly predictable activities. As TFRE order and spacing did not affect the performance of these TFRE-combinations, compositions could be specifically arranged to preclude the formation of undesirable sequence features. This facilitated simple in silico-design of promoters with context-required, user-defined functionalities. To demonstrate this, we de novo-created promoters for biopharmaceutical production in CHO cells that exhibited precisely designed activity dynamics and long-term expression-stability, without causing observable retroactive effects on cellular performance. The design process described can be utilized for applications requiring context-responsive, customizable promoter function, particularly where co-expression of synthetic TFs is not suitable. Although the synthetic promoter structure utilized does not closely resemble native mammalian architectures, our findings also provide additional support for a flexible billboard model of promoter regulation.
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Affiliation(s)
- Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
| | - Suzanne J Gibson
- Biopharmaceutical Development, MedImmune, Cambridge CB21 6GH, UK
| | - Diane Hatton
- Biopharmaceutical Development, MedImmune, Cambridge CB21 6GH, UK
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
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29
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Impact of different promoters, promoter mutation, and an enhancer on recombinant protein expression in CHO cells. Sci Rep 2017; 7:10416. [PMID: 28874794 PMCID: PMC5585415 DOI: 10.1038/s41598-017-10966-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/17/2017] [Indexed: 11/09/2022] Open
Abstract
In the present study, six commonly used promoters, including cytomegalovirus major immediate-early (CMV), the CMV enhancer fused to the chicken beta-actin promoter (CAG), human elongation factor-1α (HEF-1α), mouse cytomegalovirus (mouse CMV), Chinese hamster elongation factor-1α (CHEF-1α), and phosphoglycerate kinase (PGK), a CMV promoter mutant and a CAG enhancer, were evaluated to determine their effects on transgene expression and stability in transfected CHO cells. The promoters and enhancer were cloned or synthesized, and mutation at C-404 in the CMV promoter was generated; then all elements were transfected into CHO cells. Stably transfected CHO cells were identified via screening under the selection pressure of G418. Flow cytometry, qPCR, and qRT-PCR were used to explore eGFP expression levels, gene copy number, and mRNA expression levels, respectively. Furthermore, the erythropoietin (EPO) gene was used to test the selected strong promoter. Of the six promoters, the CHEF-1α promoter yielded the highest transgene expression levels, whereas the CMV promoter maintained transgene expression more stably during long-term culture of cells. We conclude that CHEF-1α promoter conferred higher level of EPO expression in CHO cells, but the CMV promoter with its high levels of stability performs best in this vector system.
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30
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Karumuthil-Melethil S, Nagabhushan Kalburgi S, Thompson P, Tropak M, Kaytor MD, Keimel JG, Mark BL, Mahuran D, Walia JS, Gray SJ. Novel Vector Design and Hexosaminidase Variant Enabling Self-Complementary Adeno-Associated Virus for the Treatment of Tay-Sachs Disease. Hum Gene Ther 2017; 27:509-21. [PMID: 27197548 DOI: 10.1089/hum.2016.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
GM2 gangliosidosis is a family of three genetic neurodegenerative disorders caused by the accumulation of GM2 ganglioside (GM2) in neuronal tissue. Two of these are due to the deficiency of the heterodimeric (α-β), "A" isoenzyme of lysosomal β-hexosaminidase (HexA). Mutations in the α-subunit (encoded by HEXA) lead to Tay-Sachs disease (TSD), whereas mutations in the β-subunit (encoded by HEXB) lead to Sandhoff disease (SD). The third form results from a deficiency of the GM2 activator protein (GM2AP), a substrate-specific cofactor for HexA. In their infantile, acute forms, these diseases rapidly progress with mental and psychomotor deterioration resulting in death by approximately 4 years of age. After gene transfer that overexpresses one of the deficient subunits, the amount of HexA heterodimer formed would empirically be limited by the availability of the other endogenous Hex subunit. The present study used a new variant of the human HexA α-subunit, μ, incorporating critical sequences from the β-subunit that produce a stable homodimer (HexM) and promote functional interactions with the GM2AP- GM2 complex. We report the design of a compact adeno-associated viral (AAV) genome using a synthetic promoter-intron combination to allow self-complementary (sc) packaging of the HEXM gene. Also, a previously published capsid mutant, AAV9.47, was used to deliver the gene to brain and spinal cord while having restricted biodistribution to the liver. The novel capsid and cassette design combination was characterized in vivo in TSD mice for its ability to efficiently transduce cells in the central nervous system when delivered intravenously in both adult and neonatal mice. This study demonstrates that the modified HexM is capable of degrading long-standing GM2 storage in mice, and it further demonstrates the potential of this novel scAAV vector design to facilitate widespread distribution of the HEXM gene or potentially other similar-sized genes to the nervous system.
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Affiliation(s)
| | | | - Patrick Thompson
- 2 Medical Genetics/Departments of Pediatrics, Queen's University , Kingston, Ontario, Canada
| | - Michael Tropak
- 3 Genetics and Genome Biology, SickKids, Toronto, Ontario, Canada
| | | | - John G Keimel
- 4 New Hope Research Foundation , North Oaks, Minnesota
| | - Brian L Mark
- 5 Department of Microbiology, University of Manitoba , Winnipeg, Manitoba, Canada
| | - Don Mahuran
- 3 Genetics and Genome Biology, SickKids, Toronto, Ontario, Canada .,6 Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Jagdeep S Walia
- 2 Medical Genetics/Departments of Pediatrics, Queen's University , Kingston, Ontario, Canada
| | - Steven J Gray
- 1 Gene Therapy Center, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,7 Department of Ophthalmology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
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31
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Gadalla KK, Vudhironarit T, Hector RD, Sinnett S, Bahey NG, Bailey ME, Gray SJ, Cobb SR. Development of a Novel AAV Gene Therapy Cassette with Improved Safety Features and Efficacy in a Mouse Model of Rett Syndrome. Mol Ther Methods Clin Dev 2017; 5:180-190. [PMID: 28497075 PMCID: PMC5423329 DOI: 10.1016/j.omtm.2017.04.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/19/2017] [Indexed: 12/21/2022]
Abstract
Rett syndrome (RTT), caused by loss-of-function mutations in the MECP2 gene, is a neurological disorder characterized by severe impairment of motor and cognitive functions. The aim of this study was to investigate the impact of vector design, dosage, and delivery route on the efficacy and safety of gene augmentation therapy in mouse models of RTT. Our results show that AAV-mediated delivery of MECP2 to Mecp2 null mice by systemic administration, and utilizing a minimal endogenous promoter, was associated with a narrow therapeutic window and resulted in liver toxicity at higher doses. Lower doses of this vector significantly extended the survival of mice lacking MeCP2 or expressing a mutant T158M allele but had no impact on RTT-like neurological phenotypes. Modifying vector design by incorporating an extended Mecp2 promoter and additional regulatory 3' UTR elements significantly reduced hepatic toxicity after systemic administration. Moreover, direct cerebroventricular injection of this vector into neonatal Mecp2-null mice resulted in high brain transduction efficiency, increased survival and body weight, and an amelioration of RTT-like phenotypes. Our results show that controlling levels of MeCP2 expression in the liver is achievable through modification of the expression cassette. However, it also highlights the importance of achieving high brain transduction to impact the RTT-like phenotypes.
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Affiliation(s)
- Kamal K.E. Gadalla
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Pharmacology Department, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Thishnapha Vudhironarit
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ralph D. Hector
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sarah Sinnett
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Noha G. Bahey
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Histology Department, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Mark E.S. Bailey
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Steven J. Gray
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Stuart R. Cobb
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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Abstract
Dysferlinopathy is an autosomal recessive muscular dystrophy characterized by the progressive loss of motility that is caused by mutations throughout the DYSF gene. There are currently no approved therapies that ameliorate or reverse dysferlinopathy. Gene delivery using adeno-associated vectors (AAVs) is a leading therapeutic strategy for genetic diseases; however, the large size of dysferlin cDNA (6.2 kB) precludes packaging into a single AAV capsid. Therefore, using 3D structural modeling and hypothesizing dysferlin C2 domain redundancy, a 30% smaller, dysferlin-like molecule amenable to single AAV vector packaging was engineered (termed Nano-Dysferlin). The intracellular distribution of Nano-Dysferlin was similar to wild-type dysferlin and neither demonstrated toxicity when overexpressed in dysferlin-deficient patient myoblasts. Intramuscular injection of AAV-Nano-Dysferlin in young dysferlin-deficient mice significantly improved muscle integrity and decreased muscle turnover 3 weeks after treatment, as determined by Evans blue dye uptake and central nucleated fibers, respectively. Systemically administered AAV-Nano-Dysferlin to young adult dysferlin-deficient mice restored motor function and improved muscle integrity nearly 8 months after a single injection. These preclinical data are the first report of a smaller dysferlin variant tailored for AAV single particle delivery that restores motor function and, therefore, represents an attractive candidate for the treatment of dysferlinopathy.
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Saxena P, Bojar D, Fussenegger M. Design of Synthetic Promoters for Gene Circuits in Mammalian Cells. Methods Mol Biol 2017; 1651:263-273. [PMID: 28801913 DOI: 10.1007/978-1-4939-7223-4_19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic biology, the synthesis of engineering and biology, has rapidly matured and has dramatically increased the complexity of artificial gene circuits in recent years. The deployment of intricate synthetic gene circuits in mammalian cells requires the establishment of very precise and orthogonal control of transgene expression. In this chapter, we describe methods of modulating the expression of transgenes at the transcriptional level. Using cAMP-response element-binding protein (CREB)-dependent promoters as examples, a tool for the precise tuning of gene expression by using different core promoters and by varying the binding affinity of transcription factor operator sites is described.
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Affiliation(s)
- Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Daniel Bojar
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland. .,Faculty of Science, University of Basel, Mattenstrasse 26, Basel, CH-4058, Switzerland.
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34
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Cheng JK, Alper HS. Transcriptomics-Guided Design of Synthetic Promoters for a Mammalian System. ACS Synth Biol 2016; 5:1455-1465. [PMID: 27268512 DOI: 10.1021/acssynbio.6b00075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite recent advances in improving titers for therapeutic proteins such as antibodies to the 10 g/L scale, these high yields can only be achieved in select mammalian hosts. Regardless of the host or product, strong promoters are required to obtain high levels of transgene expression. However, the promoters employed to drive this expression are rather limited in variety and are usually either viral-derived or screened empirically during vector design. To begin to move away from viral parts, we employed a more systematic approach to identify and design new synthetic promoters using endogenous elements. To do so, we established a workflow to design these elements by (1) analyzing the transcriptomics profile of a specific cell line under a desired, representative cell culture condition, (2) identifying key genetic motifs using bioinformatics that can be used to rationally construct synthetic promoters, (3) building synthetic promoters using conventional DNA synthesis and molecular biology techniques, and (4) evaluating the performance of these synthetic promoters using model proteins. The resulting promoters perform comparably to the hCMV IE promoter variants tested, but with endogenous components. During this design-build-test cycle we also investigated the underlying design rules for transcription factor binding site arrangement in synthetic promoters. Overall, this approach of using an "omics-guided" workflow for designing synthetic promoters facilitates the construction of high expression vectors for immediate use in current production hosts.
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Affiliation(s)
- Joseph K. Cheng
- Department
of Chemical Engineering, The University of Texas at Austin, 200
E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Hal S. Alper
- Department
of Chemical Engineering, The University of Texas at Austin, 200
E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
- Institute
for Cellular and Molecular Biology The University of Texas at Austin, 2500
Speedway Avenue, Austin, Texas 78712, United States
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35
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Schreiber T, Tissier A. Libraries of Synthetic TALE-Activated Promoters: Methods and Applications. Methods Enzymol 2016; 576:361-78. [PMID: 27480693 DOI: 10.1016/bs.mie.2016.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The discovery of proteins with programmable DNA-binding specificities triggered a whole array of applications in synthetic biology, including genome editing, regulation of transcription, and epigenetic modifications. Among those, transcription activator-like effectors (TALEs) due to their natural function as transcription regulators, are especially well-suited for the development of orthogonal systems for the control of gene expression. We describe here the construction and testing of libraries of synthetic TALE-activated promoters which are under the control of a single TALE with a given DNA-binding specificity. These libraries consist of a fixed DNA-binding element for the TALE, a TATA box, and variable sequences of 19 bases upstream and 43 bases downstream of the DNA-binding element. These libraries were cloned using a Golden Gate cloning strategy making them usable as standard parts in a modular cloning system. The broad range of promoter activities detected and the versatility of these promoter libraries make them valuable tools for applications in the fine-tuning of expression in metabolic engineering projects or in the design and implementation of regulatory circuits.
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Affiliation(s)
- T Schreiber
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - A Tissier
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany.
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36
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Baser B, van den Heuvel J. Assembling Multi-subunit Complexes Using Mammalian Expression. ADVANCED TECHNOLOGIES FOR PROTEIN COMPLEX PRODUCTION AND CHARACTERIZATION 2016; 896:225-38. [DOI: 10.1007/978-3-319-27216-0_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Van Hove B, Love AM, Ajikumar PK, De Mey M. Programming Biology: Expanding the Toolset for the Engineering of Transcription. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Promoter and Terminator Discovery and Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:21-44. [PMID: 27277391 DOI: 10.1007/10_2016_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Control of gene expression is crucial to optimize metabolic pathways and synthetic gene networks. Promoters and terminators are stretches of DNA upstream and downstream (respectively) of genes that control both the rate at which the gene is transcribed and the rate at which mRNA is degraded. As a result, both of these elements control net protein expression from a synthetic construct. Thus, it is highly important to discover and engineer promoters and terminators with desired characteristics. This chapter highlights various approaches taken to catalogue these important synthetic elements. Specifically, early strategies have focused largely on semi-rational techniques such as saturation mutagenesis to diversify native promoters and terminators. Next, in an effort to reduce the length of the synthetic biology design cycle, efforts in the field have turned towards the rational design of synthetic promoters and terminators. In this vein, we cover recently developed methods such as hybrid engineering, high throughput characterization, and thermodynamic modeling which allow finer control in the rational design of novel promoters and terminators. Emphasis is placed on the methodologies used and this chapter showcases the utility of these methods across multiple host organisms.
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Zhang C, Tsoi R, You L. Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb) 2015; 8:456-64. [PMID: 26674800 DOI: 10.1039/c5ib00275c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic biology has grown tremendously over the past fifteen years. It represents a new strategy to develop biological understanding and holds great promise for diverse practical applications. Engineering of a gene circuit typically involves computational design of the circuit, selection of circuit components, and test and optimization of circuit functions. A fundamental challenge in this process is the predictable control of circuit function due to multiple layers of biological uncertainties. These uncertainties can arise from different sources. We categorize these uncertainties into incomplete quantification of parts, interactions between heterologous components and the host, or stochastic dynamics of chemical reactions and outline potential design strategies to minimize or exploit them.
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Affiliation(s)
- Carolyn Zhang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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Lu M, Williamson N, Boschetti C, Ellis T, Yoshimi T, Tunnacliffe A. Expression-level dependent perturbation of cell proteostasis and nuclear morphology by aggregation-prone polyglutamine proteins. Biotechnol Bioeng 2015; 112:1883-92. [PMID: 25854808 DOI: 10.1002/bit.25606] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/18/2015] [Accepted: 03/20/2015] [Indexed: 12/17/2022]
Abstract
We describe a gene expression system for use in mammalian cells that yields reproducible, inducible gene expression that can be modulated within the physiological range. A synthetic promoter library was generated from which representatives were selected that gave weak, intermediate-strength or strong promoter activity. Each promoter resulted in a tight expression range when used to drive single-copy reporter genes integrated at the same genome location in stable cell lines, in contrast to the broad range of expression typical of transiently transfected cells. To test this new expression system in neurodegenerative disease models, we used each promoter type to generate cell lines carrying single-copy genes encoding polyglutamine-containing proteins. Expression over a period of up to three months resulted in a proportion of cells developing juxtanuclear aggresomes whose rate of formation, penetrance, and morphology were expression-level dependent. At the highest expression levels, fibrillar aggregates deposit close to the nuclear envelope, indicating that cell proteostasis is overwhelmed by misfolded protein species. We also observed expression-level dependent, abnormal nuclear morphology in cells containing aggresomes, with up to ∼80% of cells affected. This system constitutes a valuable tool in gene regulation at different levels and allows the quantitative assessment of gene expression effects when developing disease models or investigating cell function through the introduction of gene constructs.
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Affiliation(s)
- Meng Lu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom
| | - Neil Williamson
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom
| | - Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom
| | - Tom Ellis
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom
| | - Tatsuya Yoshimi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom.
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Brown AJ, Sweeney B, Mainwaring DO, James DC. Synthetic promoters for CHO cell engineering. Biotechnol Bioeng 2014; 111:1638-47. [PMID: 24615264 DOI: 10.1002/bit.25227] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 01/15/2023]
Abstract
We describe for the first time the creation of a library of 140 synthetic promoters specifically designed to regulate the expression of recombinant genes in CHO cells. Initially, 10 common viral promoter sequences known to be active in CHO cells were analyzed using bioinformatic sequence analysis programs to determine the identity and relative abundance of transcription factor regulatory elements (TFREs; or transcription factor binding sites) they contained. Based on this, 28 synthetic reporters were constructed that each harbored seven repeats of a discrete TFRE sequence upstream of a minimal CMV core promoter element and secreted alkaline phosphatase (SEAP) reporter gene. After evaluation of the relative activity of TFREs by transient expression in CHO-S cells, we constructed a first generation library of 96 synthetic promoters derived from random ligation of six active TFREs inserted into the same reporter construct backbone. Comparison of the sequence and relative activity of first generation promoters revealed that individual TFRE blocks were either relatively abundant in active promoters (NFκB, E-box), equally distributed across promoters of varying activity (C/EBPα, GC-box) or relatively abundant in low activity promoters (E4F1, CRE). These data were utilized to create a second generation of 44 synthetic promoters based on random ligation of a fixed ratio of 4 TFREs (NFκB 5: E-box 3: C/EBPα 1: GC-box 1). Comparison of the sequence and relative activity of second generation promoters revealed that the most active promoters contained relatively high numbers of both NFκB and E-box TFREs in approximately equal proportion, with a correspondingly low number of GC-box and C/EBPα blocks. The most active second generation promoters achieved approximately twice the activity of a control construct harboring the human cytomegalovirus (CMV) promoter. Lastly, we evaluated the function of a subset of synthetic promoters exhibiting a broad range of activity in different CHO cell host cell lines (CHO-S, CHO-K1, and CHO-DG44) and across extended fed-batch transient expression in CHO-S cells. In general, the different synthetic promoters both maintained their relative activity and the most active promoters consistently and significantly exceeded the activity of the CMV control promoter. For advanced cell engineering strategies our synthetic promoter libraries offer precise control of recombinant transcriptional activity in CHO cells spanning over two orders of magnitude.
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Affiliation(s)
- Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, University of Sheffield, Mappin St., Sheffield, S1 3JD, England
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Rytter JV, Helmark S, Chen J, Lezyk MJ, Solem C, Jensen PR. Synthetic promoter libraries for Corynebacterium glutamicum. Appl Microbiol Biotechnol 2014; 98:2617-23. [DOI: 10.1007/s00253-013-5481-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 02/01/2023]
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An internal ribosome entry site (IRES) mutant library for tuning expression level of multiple genes in mammalian cells. PLoS One 2013; 8:e82100. [PMID: 24349195 PMCID: PMC3857217 DOI: 10.1371/journal.pone.0082100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/28/2013] [Indexed: 12/30/2022] Open
Abstract
A set of mutated Encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) elements with varying strengths is generated by mutating the translation initiation codons of 10th, 11th, and 12th AUG to non-AUG triplets. They are able to control the relative expression of multiple genes over a wide range in mammalian cells in both transient and stable transfections. The relative strength of each IRES mutant remains similar in different mammalian cell lines and is not gene specific. The expressed proteins have correct molecular weights. Optimization of light chain over heavy chain expression by these IRES mutants enhances monoclonal antibody expression level and quality in stable transfections. Uses of this set of IRES mutants can be extended to other applications such as synthetic biology, investigating interactions between proteins and its complexes, cell engineering, multi-subunit protein production, gene therapy, and reprogramming of somatic cells into stem cells.
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Roccaro M, Ahmadinejad N, Colby T, Somssich IE. Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library. BMC PLANT BIOLOGY 2013; 13:164. [PMID: 24138055 PMCID: PMC3923269 DOI: 10.1186/1471-2229-13-164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/08/2013] [Indexed: 06/01/2023]
Abstract
BACKGROUND The identification of endogenous cis-regulatory DNA elements (CREs) responsive to endogenous and environmental cues is important for studying gene regulation and for biotechnological applications but is labor and time intensive. Alternatively, by taking a synthetic biology approach small specific DNA binding sites tailored to the needs of the scientist can be generated and rapidly identified. RESULTS Here we report a novel approach to identify stimulus-responsive synthetic CREs (SynCREs) from an unbiased random synthetic element (SynE) library. Functional SynCREs were isolated by screening the SynE libray for elements mediating transcriptional activity in plant protoplasts. Responsive elements were chromatin immunoprecipitated by targeting the active Ser-5 phosphorylated RNA polymerase II CTD (Pol II ChIP). Using sequential enrichment, deep sequencing and a bioinformatics pipeline, candidate responsive SynCREs were identified within a pool of constitutively active DNA elements and further validated. These included bonafide biotic/abiotic stress-responsive motifs along with novel SynCREs. We tested several SynCREs in Arabidopsis and confirmed their response to biotic stimuli. CONCLUSIONS Successful isolation of synthetic stress-responsive elements from our screen illustrates the power of the described methodology. This approach can be applied to any transfectable eukaryotic system since it exploits a universal feature of the eukaryotic Pol II.
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Affiliation(s)
- Mario Roccaro
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
| | - Nahal Ahmadinejad
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
- Current address: INRES - Crop Bioinformatics, Universität Bonn, Katzenburgweg 2, Bonn 53115, Germany
| | - Thomas Colby
- Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
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Endo K, Stapleton JA, Hayashi K, Saito H, Inoue T. Quantitative and simultaneous translational control of distinct mammalian mRNAs. Nucleic Acids Res 2013; 41:e135. [PMID: 23685611 PMCID: PMC3711428 DOI: 10.1093/nar/gkt347] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The introduction of multiple genes into cells is increasingly required for understanding and engineering biological systems. Small-molecule–responsive transcriptional regulation has been widely used to control transgene expression. In contrast, methods for specific and simultaneous regulation of multiple genes with a single regulatory protein remain undeveloped. In this report, we describe a method for quantitatively tuning the expression of multiple transgenes with a translational regulatory protein. A protein that binds a specific RNA motif inserted in the 5′-untranslated region (UTR) of an mRNA modulates the translation of that message in mammalian cells. We provide two independent mechanisms by which to rationally fine-tune the output: the efficiency of translation correlates well with the distance between the inserted motif and the 5′ terminus of the mRNA and is further modulated by the tandem insertion of multiple RNA motifs. The combination of these two approaches allowed us to fine-tune the translational efficiency of target mRNAs over a wide dynamic range. Moreover, we controlled the expression of two transgenes simultaneously and specifically by engineering each cis-regulatory 5′-UTR. The approach provides a useful alternative regulatory layer for controlling gene expression in biological research and engineering.
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Affiliation(s)
- Kei Endo
- International Cooperative Research Project, Japan Science and Technology Agency, 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
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Blazeck J, Alper HS. Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotechnol J 2012; 8:46-58. [DOI: 10.1002/biot.201200120] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/25/2012] [Accepted: 07/17/2012] [Indexed: 12/25/2022]
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Lanza AM, Blazeck JJ, Crook NC, Alper HS. Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach. PLoS One 2012; 7:e36193. [PMID: 22558379 PMCID: PMC3338614 DOI: 10.1371/journal.pone.0036193] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/03/2012] [Indexed: 11/18/2022] Open
Abstract
Establishing causative links between protein functional domains and global gene regulation is critical for advancements in genetics, biotechnology, disease treatment, and systems biology. This task is challenging for multifunctional proteins when relying on traditional approaches such as gene deletions since they remove all domains simultaneously. Here, we describe a novel approach to extract quantitative, causative links by modulating the expression of a dominant mutant allele to create a function-specific competitive inhibition. Using the yeast histone acetyltransferase Gcn5p as a case study, we demonstrate the utility of this approach and (1) find evidence that Gcn5p is more involved in cell-wide gene repression, instead of the accepted gene activation associated with HATs, (2) identify previously unknown gene targets and interactions for Gcn5p-based acetylation, (3) quantify the strength of some Gcn5p-DNA associations, (4) demonstrate that this approach can be used to correctly identify canonical chromatin modifications, (5) establish the role of acetyltransferase activity on synthetic lethal interactions, and (6) identify new functional classes of genes regulated by Gcn5p acetyltransferase activity—all six of these major conclusions were unattainable by using standard gene knockout studies alone. We recommend that a graded dominant mutant approach be utilized in conjunction with a traditional knockout to study multifunctional proteins and generate higher-resolution data that more accurately probes protein domain function and influence.
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Affiliation(s)
- Amanda M. Lanza
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - John J. Blazeck
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Nathan C. Crook
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Hal S. Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Abstract
Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist.
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Affiliation(s)
- Tore Dehli
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301/242, 2800, Lyngby, Denmark,
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Ferreira JP, Lawhorn IEB, Peacock RWS, Wang CL. Quantitative assessment of Ras over-expression via shotgun deployment of vectors utilizing synthetic promoters. Integr Biol (Camb) 2011; 4:108-14. [PMID: 22108821 DOI: 10.1039/c1ib00082a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We sought to characterize and compare wild-type and oncogenic Ras over-expression. Because different levels of Ras over-expression can have different effects on cell phenotype, it was important to evaluate a wide range of expression. Different expression levels were achieved by using retroviral vectors equipped with different strength promoters. Cells were "shotgun" transduced with a mixture of these vectors to generate heterogeneous populations exhibiting a range of expression levels. We used flow cytometry to analyze the populations and generate high-resolution, nearly continuous Ras dose-response curves. These efforts revealed that a single-copy level of oncogenic Ras generated maximal imatinib resistance and activated MAPK pathway signaling as effectively as six-fold amplification of wild-type Ras. Although further increased expression lead to even greater signal transduction, this increased expression had minimal or decreasing effects on the proliferation rate. In addition, this study introduces a general method to quantify genetic dose-response relationships and identify gene expression ranges that produce an optimized phenotypic response.
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Affiliation(s)
- Joshua P Ferreira
- Department of Chemical Engineering, Stanford University, 381 N-S Axis, Rm 113, Stanford, CA 94305, USA
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50
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Ferreira JP, Peacock RWS, Lawhorn IEB, Wang CL. Modulating ectopic gene expression levels by using retroviral vectors equipped with synthetic promoters. SYSTEMS AND SYNTHETIC BIOLOGY 2011. [PMID: 23205156 DOI: 10.1007/s11693-011-9089-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
UNLABELLED The human cytomegalovirus and elongation factor 1α promoters are constitutive promoters commonly employed by mammalian expression vectors. These promoters generally produce high levels of expression in many types of cells and tissues. To generate a library of synthetic promoters capable of generating a range of low, intermediate, and high expression levels, the TATA and CAAT box elements of these promoters were mutated. Other promoter variants were also generated by random mutagenesis. Evaluation using plasmid vectors integrated at a single site in the genome revealed that these various synthetic promoters were capable of expression levels spanning a 40-fold range. Retroviral vectors were equipped with the synthetic promoters and evaluated for their ability to reproduce the graded expression demonstrated by plasmid integration. A vector with a self-inactivating long terminal repeat could neither reproduce the full range of expression levels nor produce stable expression. Using a second vector design, the different synthetic promoters enabled stable expression over a broad range of expression levels in different cell lines. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s11693-011-9089-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua P Ferreira
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305 USA
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