1
|
Leclerc D, Siroky MD, Miller SM. Next-generation biological vector platforms for in vivo delivery of genome editing agents. Curr Opin Biotechnol 2024; 85:103040. [PMID: 38103518 DOI: 10.1016/j.copbio.2023.103040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023]
Abstract
CRISPR-based genome editing holds promise for addressing genetic disease, infectious disease, and cancer and has rapidly advanced from primary research to clinical trials in recent years. However, the lack of safe and potent in vivo delivery methods for CRISPR components has limited most ongoing clinical trials to ex vivo gene therapy. Effective CRISPR in vivo genome editing necessitates an effective vehicle ensuring target cell transduction while minimizing off-target effects, toxicity, and immune reactions. In this review, we examine promising biological-derived platforms to deliver DNA editing agents in vivo and the engineering thereof, encompassing potent viral-based vehicles, flexible protein nanocages, and mammalian-derived particles.
Collapse
Affiliation(s)
- Delphine Leclerc
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael D Siroky
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shannon M Miller
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
2
|
Pekrun K, De Alencastro G, Luo QJ, Liu J, Kim Y, Nygaard S, Galivo F, Zhang F, Song R, Tiffany MR, Xu J, Hebrok M, Grompe M, Kay MA. Using a barcoded AAV capsid library to select for clinically relevant gene therapy vectors. JCI Insight 2019; 4:131610. [PMID: 31723052 PMCID: PMC6948855 DOI: 10.1172/jci.insight.131610] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
While gene transfer using recombinant adeno-associated viral (rAAV) vectors has shown success in some clinical trials, there remain many tissues that are not well transduced. Because of the recent success in reprogramming islet-derived cells into functional β cells in animal models, we constructed 2 highly complex barcoded replication competent capsid shuffled libraries and selected for high-transducing variants on primary human islets. We describe the generation of a chimeric AAV capsid (AAV-KP1) that facilitates transduction of primary human islet cells and human embryonic stem cell-derived β cells with up to 10-fold higher efficiency compared with previously studied best-in-class AAV vectors. Remarkably, this chimeric capsid also enabled transduction of both mouse and human hepatocytes at very high levels in a humanized chimeric mouse model, thus providing a versatile vector that has the potential to be used in both preclinical testing and human clinical trials for liver-based diseases and diabetes.
Collapse
Affiliation(s)
- Katja Pekrun
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Gustavo De Alencastro
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Qing-Jun Luo
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Jun Liu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Youngjin Kim
- UCSF Diabetes Center, UCSF, San Francisco, California, USA
| | - Sean Nygaard
- Oregon Stem Cell Center, Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Feorillo Galivo
- Oregon Stem Cell Center, Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Ren Song
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Matthew R. Tiffany
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Jianpeng Xu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | | | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Mark A. Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| |
Collapse
|
3
|
Medrano M, Valbuena A, Rodríguez-Huete A, Mateu MG. Structural determinants of mechanical resistance against breakage of a virus-based protein nanoparticle at a resolution of single amino acids. NANOSCALE 2019; 11:9369-9383. [PMID: 31041970 DOI: 10.1039/c9nr01935a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Virus particles and other protein-based supramolecular complexes have a vast nanotechnological potential. However, protein nanostructures are "soft" materials prone to disruption by force. Whereas some non-biological nanoparticles (NPs) may be stronger, for certain applications protein- and virus-based NPs have potential advantages related to their structure, self-assembly, production, engineering, and/or inbuilt functions. Thus, it may be desirable to acquire the knowledge needed to engineer protein-based nanomaterials with a higher strength against mechanical breakage. Here we have used the capsid of the minute virus of mice to experimentally identify individual chemical groups that determine breakage-related properties of a virus particle. Individual amino acid side chains that establish interactions between building blocks in the viral particle were truncated using protein engineering. Indentation experiments using atomic force microscopy were carried out to investigate the role of each targeted side chain in determining capsid strength and brittleness, by comparing the maximum force and deformation each modified capsid withstood before breaking apart. Side chains with major roles in determining capsid strength against breakage included polar groups located in solvent-exposed positions, and did not generally correspond with those previously identified as determinants of mechanical stiffness. In contrast, apolar side chains buried along the intersubunit interfaces that generally determined capsid stiffness had, at most, a minor influence on strength against disruption. Whereas no correlated variations between strength and either stiffness or brittleness were found, brittleness and stiffness were quantitatively correlated. Implications for developing robust protein-based NPs and for acquiring a deeper physics-based perspective of viruses are discussed.
Collapse
Affiliation(s)
- María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | | | | | | |
Collapse
|
4
|
Milligan JN, Garry DJ. Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering. Methods Mol Biol 2018; 1472:35-45. [PMID: 27671930 DOI: 10.1007/978-1-4939-6343-0_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA shuffling is a powerful tool to develop libraries of variants for protein engineering. Here, we present a protocol to use our freely available and easy-to-use computer program, Shuffle Optimizer. Shuffle Optimizer is written in the Python computer language and increases the nucleotide homology between two pieces of DNA desired to be shuffled together without changing the amino acid sequence. In addition we also include sections on optimal primer design for DNA shuffling and library construction, a small-volume ultrasonicator method to create sheared DNA, and finally a method to reassemble the sheared fragments and recover and clone the library. The Shuffle Optimizer program and these protocols will be useful to anyone desiring to perform any of the nucleotide homology-dependent shuffling methods.
Collapse
Affiliation(s)
- John N Milligan
- The Department of Molecular Biosciences, The University of Texas at Austin, 2506 Speedway STOP A5000, Austin, TX, 78712, USA.
| | - Daniel J Garry
- The Department of Molecular Biosciences, The University of Texas at Austin, 2506 Speedway STOP A5000, Austin, TX, 78712, USA.
| |
Collapse
|
5
|
Tian D, Cao D, Lynn Heffron C, Yugo DM, Rogers AJ, Overend C, Matzinger SR, Subramaniam S, Opriessnig T, LeRoith T, Meng XJ. Enhancing heterologous protection in pigs vaccinated with chimeric porcine reproductive and respiratory syndrome virus containing the full-length sequences of shuffled structural genes of multiple heterologous strains. Vaccine 2017; 35:2427-2434. [PMID: 28343773 DOI: 10.1016/j.vaccine.2017.03.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/08/2017] [Accepted: 03/11/2017] [Indexed: 10/19/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of arguably the most economically important global swine disease. The extensive genetic variation of PRRSV strains is a major obstacle for heterologous protection of current vaccines. Previously, we constructed a panel of chimeric viruses containing only the ectodomain sequences of DNA-shuffled structural genes of different PRRSV strains in the backbone of a commercial vaccine, and found that one chimeric virus had an improved cross-protection efficacy. In this present study, to further enhance the cross-protective efficacy against heterologous strains, we constructed a novel chimeric virus VR2385-S3456 containing the full-length sequences of shuffled structural genes (ORFs 3-6) from 6 heterologous PRRSV strains in the backbone of PRRSV strain VR2385. We showed that the chimeric virus VR2385-S3456 induced a high level of neutralizing antibodies in pigs against two heterologous strains. A subsequent vaccination and challenge study in 48 pigs revealed that the chimeric virus VR2385-S3456 conferred an enhanced cross-protection when challenged with heterologous virus strain NADC20 or a contemporary heterologous strain RFLP 1-7-4. The results suggest that the chimera VR2385-S3456 may be a good PRRSV vaccine candidate for further development to confer heterologous protection.
Collapse
Affiliation(s)
- Debin Tian
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Dianjun Cao
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - C Lynn Heffron
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Danielle M Yugo
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Adam J Rogers
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Christopher Overend
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shannon R Matzinger
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sakthivel Subramaniam
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Tanja Opriessnig
- Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| |
Collapse
|
6
|
Carrillo PJP, Medrano M, Valbuena A, Rodríguez-Huete A, Castellanos M, Pérez R, Mateu MG. Amino Acid Side Chains Buried along Intersubunit Interfaces in a Viral Capsid Preserve Low Mechanical Stiffness Associated with Virus Infectivity. ACS NANO 2017; 11:2194-2208. [PMID: 28117975 DOI: 10.1021/acsnano.6b08549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule experimental techniques and theoretical approaches reveal that important aspects of virus biology can be understood in biomechanical terms at the nanoscale. A detailed knowledge of the relationship in virus capsids between small structural changes caused by single-point mutations and changes in mechanical properties may provide further physics-based insights into virus function; it may also facilitate the engineering of viral nanoparticles with improved mechanical behavior. Here, we used the minute virus of mice to undertake a systematic experimental study on the contribution to capsid stiffness of amino acid side chains at interprotein interfaces and the specific noncovalent interactions they establish. Selected side chains were individually truncated by introducing point mutations to alanine, and the effects on local and global capsid stiffness were determined using atomic force microscopy. The results revealed that, in the natural virus capsid, multiple, mostly hydrophobic, side chains buried along the interfaces between subunits preserve a comparatively low stiffness of most (S2 and S3) regions. Virtually no point mutation tested substantially reduced stiffness, whereas most mutations increased stiffness of the S2/S3 regions. This stiffening was invariably associated with reduced virus yields during cell infection. The experimental evidence suggests that a comparatively low stiffness at S3/S2 capsid regions may have been biologically selected because it facilitates capsid assembly, increasing infectious virus yields. This study demonstrated also that knowledge of individual amino acid side chains and biological pressures that determine the physical behavior of a protein nanoparticle may be used for engineering its mechanical properties.
Collapse
Affiliation(s)
- Pablo José P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rebeca Pérez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
7
|
Rana AK, Ankri S. Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases. Front Genet 2016; 7:99. [PMID: 27375676 PMCID: PMC4893491 DOI: 10.3389/fgene.2016.00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
RNA, the earliest genetic and catalytic molecule, has a relatively delicate and labile chemical structure, when compared to DNA. It is prone to be damaged by alkali, heat, nucleases, or stress conditions. One mechanism to protect RNA or DNA from damage is through site-specific methylation. Here, we propose that RNA methylation began prior to DNA methylation in the early forms of life evolving on Earth. In this article, the biochemical properties of some RNA methyltransferases (MTases), such as 2′-O-MTases (Rlml/RlmN), spOUT MTases and the NSun2 MTases are dissected for the insight they provide on the transition from an RNA world to our present RNA/DNA/protein world.
Collapse
Affiliation(s)
- Ajay K Rana
- Division of Biology, State Forensic Science Laboratory, Ministry of Home Affairs, Government of Jharkhand Ranchi, India
| | - Serge Ankri
- Department of Molecular Microbiology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology Haifa, Israel
| |
Collapse
|
8
|
Tian D, Ni YY, Zhou L, Opriessnig T, Cao D, Piñeyro P, Yugo DM, Overend C, Cao Q, Lynn Heffron C, Halbur PG, Pearce DS, Calvert JG, Meng XJ. Chimeric porcine reproductive and respiratory syndrome virus containing shuffled multiple envelope genes confers cross-protection in pigs. Virology 2015; 485:402-13. [DOI: 10.1016/j.virol.2015.08.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/14/2015] [Accepted: 08/19/2015] [Indexed: 11/26/2022]
|
9
|
Guenther CM, Kuypers BE, Lam MT, Robinson TM, Zhao J, Suh J. Synthetic virology: engineering viruses for gene delivery. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:548-58. [PMID: 25195922 PMCID: PMC4227300 DOI: 10.1002/wnan.1287] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/16/2014] [Accepted: 07/20/2014] [Indexed: 12/13/2022]
Abstract
The success of gene therapy relies heavily on the performance of vectors that can effectively deliver transgenes to desired cell populations. As viruses have evolved to deliver genetic material into cells, a prolific area of research has emerged over the last several decades to leverage the innate properties of viruses as well as to engineer new features into them. Specifically, the field of synthetic virology aims to capitalize on knowledge accrued from fundamental virology research in order to design functionally enhanced gene delivery vectors. The enhanced viral vectors, or 'bionic' viruses, feature engineered components, or 'parts', that are natural (intrinsic to viruses or from other organisms) and synthetic (such as man-made polymers or inorganic nanoparticles). Various design strategies--rational, combinatorial, and pseudo-rational--have been pursued to create the hybrid viruses. The gene delivery vectors of the future will likely criss-cross the boundaries between natural and synthetic domains to harness the unique strengths afforded by the various functional parts that can be grafted onto virus capsids. Such research endeavors will further expand and enable enhanced control over the functional capacity of these nanoscale devices for biomedicine.
Collapse
Affiliation(s)
| | - Brianna E. Kuypers
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, 77005
| | - Michael T. Lam
- Department of Bioengineering, Rice University, Houston, TX, 77005
| | | | - Julia Zhao
- Department of Chemistry, Rice University, Houston, TX, 77005
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, TX, 77005
| |
Collapse
|
10
|
Maguire CA, Ramirez SH, Merkel SF, Sena-Esteves M, Breakefield XO. Gene therapy for the nervous system: challenges and new strategies. Neurotherapeutics 2014; 11:817-39. [PMID: 25159276 PMCID: PMC4391389 DOI: 10.1007/s13311-014-0299-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Current clinical treatments for central nervous system (CNS) diseases, such as Parkinson's disease and glioblastoma do not halt disease progression and have significant treatment morbidities. Gene therapy has the potential to "permanently" correct disease by bringing in a normal gene to correct a mutant gene deficiency, knocking down mRNA of mutant alleles, and inducing cell-death in cancer cells using transgenes encoding apoptosis-inducing proteins. Promising results in clinical trials of eye disease (Leber's congenital aumorosis) and Parkinson's disease have shown that gene-based neurotherapeutics have great potential. The recent development of genome editing technology, such as zinc finger nucleases, TALENS, and CRISPR, has made the ultimate goal of gene correction a step closer. This review summarizes the challenges faced by gene-based neurotherapeutics and the current and recent strategies designed to overcome these barriers. We have chosen the following challenges to focus on in this review: (1) delivery vehicles (both virus and nonviral), (2) use of promoters for vector-mediated gene expression in CNS, and (3) delivery across the blood-brain barrier. The final section (4) focuses on promising pre-clinical/clinical studies of neurotherapeutics.
Collapse
Affiliation(s)
- Casey A Maguire
- Department of Neurology, Massachusetts General Hospital, and Neuroscience Program, Harvard Medical School, Molecular Neurogenetics Unit, 13th Street, Building 149, Charlestown, MA, 02129, USA,
| | | | | | | | | |
Collapse
|
11
|
Ho ML, Adler BA, Torre ML, Silberg JJ, Suh J. SCHEMA computational design of virus capsid chimeras: calibrating how genome packaging, protection, and transduction correlate with calculated structural disruption. ACS Synth Biol 2013; 2:724-33. [PMID: 23899192 DOI: 10.1021/sb400076r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adeno-associated virus (AAV) recombination can result in chimeric capsid protein subunits whose ability to assemble into an oligomeric capsid, package a genome, and transduce cells depends on the inheritance of sequence from different AAV parents. To develop quantitative design principles for guiding site-directed recombination of AAV capsids, we have examined how capsid structural perturbations predicted by the SCHEMA algorithm correlate with experimental measurements of disruption in seventeen chimeric capsid proteins. In our small chimera population, created by recombining AAV serotypes 2 and 4, we found that protection of viral genomes and cellular transduction were inversely related to calculated disruption of the capsid structure. Interestingly, however, we did not observe a correlation between genome packaging and calculated structural disruption; a majority of the chimeric capsid proteins formed at least partially assembled capsids and more than half packaged genomes, including those with the highest SCHEMA disruption. These results suggest that the sequence space accessed by recombination of divergent AAV serotypes is rich in capsid chimeras that assemble into 60-mer capsids and package viral genomes. Overall, the SCHEMA algorithm may be useful for delineating quantitative design principles to guide the creation of libraries enriched in genome-protecting virus nanoparticles that can effectively transduce cells. Such improvements to the virus design process may help advance not only gene therapy applications but also other bionanotechnologies dependent upon the development of viruses with new sequences and functions.
Collapse
Affiliation(s)
- Michelle L. Ho
- Department
of Bioengineering and ‡Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005,
United States
| | - Benjamin A. Adler
- Department
of Bioengineering and ‡Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005,
United States
| | - Michael L. Torre
- Department
of Bioengineering and ‡Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005,
United States
| | - Jonathan J. Silberg
- Department
of Bioengineering and ‡Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005,
United States
| | - Junghae Suh
- Department
of Bioengineering and ‡Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005,
United States
| |
Collapse
|
12
|
Nielsen TT, Nielsen JE. Antisense gene silencing: therapy for neurodegenerative disorders? Genes (Basel) 2013; 4:457-84. [PMID: 24705213 PMCID: PMC3924827 DOI: 10.3390/genes4030457] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/11/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023] Open
Abstract
Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied to mammalian cells, the technology of RNAi expanded from being a valuable experimental tool to being an applicable method for gene-specific therapeutic regulation, and much effort has been put into further refinement of the technique. This review will focus on how RNAi has developed over the years and how the technique is exploited in a pre-clinical and clinical perspective in relation to neurodegenerative disorders.
Collapse
Affiliation(s)
- Troels T Nielsen
- Danish Dementia Research Centre, Neurogenetics Clinic, Department of Neurology, Section 6702, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark.
| | - Jørgen E Nielsen
- Danish Dementia Research Centre, Neurogenetics Clinic, Department of Neurology, Section 6702, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| |
Collapse
|
13
|
Engineering a serum-resistant and thermostable vesicular stomatitis virus G glycoprotein for pseudotyping retroviral and lentiviral vectors. Gene Ther 2013; 20:807-15. [PMID: 23364315 PMCID: PMC3735647 DOI: 10.1038/gt.2013.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 11/13/2012] [Accepted: 12/17/2012] [Indexed: 01/19/2023]
Abstract
Vesicular stomatitis virus G glycoprotein (VSV-G) is the most widely used envelope protein for retroviral and lentiviral vector pseudotyping; however, serum inactivation of VSV-G pseudotyped vectors is a significant challenge for in vivo gene delivery. To address this problem, we conducted directed evolution of VSV-G to increase its resistance to human serum neutralization. After six selection cycles, numerous common mutations were present. Based on their location within VSV-G, we analyzed whether substitutions in several surface exposed residues could endow viral vectors with higher resistance to serum. S162T, T230N, and T368A mutations enhanced serum resistance, and additionally K66T, T368A, and E380K substitutions increased the thermostability of VSV-G pseudotyped retroviral vectors, an advantageous byproduct of the selection strategy. Analysis of a number of combined mutants revealed that VSV-G harboring T230N + T368A or K66T + S162T + T230N + T368A mutations exhibited both higher in vitro resistance to human serum and higher thermostability, as well as enhanced resistance to rabbit and mouse serum. Finally, lentiviral vectors pseudotyped with these variants were more resistant to human serum in a murine model. These serum-resistant and thermostable VSV-G variants may aid the application of retroviral and lentiviral vectors to gene therapy.
Collapse
|
14
|
Zhou L, Ni YY, Piñeyro P, Sanford BJ, Cossaboom CM, Dryman BA, Huang YW, Cao DJ, Meng XJ. DNA shuffling of the GP3 genes of porcine reproductive and respiratory syndrome virus (PRRSV) produces a chimeric virus with an improved cross-neutralizing ability against a heterologous PRRSV strain. Virology 2012; 434:96-109. [PMID: 23051709 DOI: 10.1016/j.virol.2012.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/30/2012] [Accepted: 09/10/2012] [Indexed: 11/19/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen. Here we applied the DNA shuffling approaches to molecularly breed the PRRSV GP3 gene, a neutralizing antibodies inducer, in an attempt to improve its heterologous cross-neutralizing ability. The GP3 genes of six different PRRSV strains were bred by traditional DNA shuffling. Additionally, synthetic DNA shuffling of the GP3 gene was also performed using degenerate oligonucleotides. The shuffled-GP3-libraries were cloned into the backbone of a DNA-launched PRRSV infectious clone pIR-VR2385-CA. Four traditional-shuffled chimeras each representing all 6 parental strains and four other synthetic-shuffled chimeras were successfully rescued. These chimeras displayed similar levels of replication both in vitro and in vivo, compared to the backbone parental virus, indicating that the GP3 shuffling did not impair the replication capability of the chimeras. One chimera GP3TS22 induced significantly higher levels of cross-neutralizing antibodies in pigs against a heterologous PRRSV strain FL-12.
Collapse
Affiliation(s)
- Lei Zhou
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061-0913, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Mateu MG. Mechanical properties of viruses analyzed by atomic force microscopy: A virological perspective. Virus Res 2012; 168:1-22. [DOI: 10.1016/j.virusres.2012.06.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/05/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
|
16
|
Wang XF, Li QZ, Bao TW, Cong WR, Song WX, Zhou XW. In vitro rapid evolution of fungal immunomodulatory proteins by DNA family shuffling. Appl Microbiol Biotechnol 2012; 97:2455-65. [PMID: 22615051 DOI: 10.1007/s00253-012-4131-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/19/2012] [Accepted: 04/22/2012] [Indexed: 11/26/2022]
Abstract
Fungal immunomodulatory proteins (FIPs) found in a wide variety of mushrooms hold significant therapeutic potential. Despite much research, the structural determinants for their immunomodulatory functions remain unknown. In this study, a DNA shuffling technique was used to create two shuffled FIP protein libraries: an intrageneric group containing products of shuffling between FIP-glu (FIP gene isolated from Ganoderma lucidum) and FIP-gsi (FIP gene isolated from Ganoderma sinense) genes and an intergeneric group containing the products of shuffling between FIP-glu, FIP-fve (FIP gene isolated from Flammulina velutipes), and FIP-vvo (FIP gene isolated from Volvariella volvacea) genes. The gene shuffling generated 426 and 412 recombinant clones, respectively. Using colony blot analysis, we selected clones that expressed relatively high levels of shuffled gene products recognized by specific polyclonal antibodies. We analyzed the DNA sequences of the selected shuffled genes, and testing of their protein products revealed that they maintained functional abilities to agglutinate blood cells and induce cytokine production by splenocytes from Kunming mice in vitro. Meanwhile, the relationships between protein structure and the hemagglutination activity and between the changed nucleotide sites and expression levels were explored by bioinformatic analysis. These combined analyses identified the nucleotide changes involved in regulating the expression levels and hemagglutination activities of the FIPs. Therefore, we were able to generate recombinant FIPs with improved biological activities and expression levels by using DNA shuffling, a powerful tool for the generation of novel therapeutic proteins and for their structural and functional studies.
Collapse
Affiliation(s)
- Xue-Fei Wang
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | | | | | | | | | | |
Collapse
|
17
|
Iyer G, Ramaswamy S, Asher D, Mehta U, Leahy A, Chung F, Cheng KS. Reduced surface area chromatography for flow-through purification of viruses and virus like particles. J Chromatogr A 2011; 1218:3973-81. [DOI: 10.1016/j.chroma.2011.04.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 04/28/2011] [Indexed: 11/26/2022]
|
18
|
Yang L, Li J, Xiao X. Directed evolution of adeno-associated virus (AAV) as vector for muscle gene therapy. Methods Mol Biol 2011; 709:127-39. [PMID: 21194025 DOI: 10.1007/978-1-61737-982-6_8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Adeno-associated virus (AAV) is emerging as a vector of choice for muscle gene therapy because of its effective and stable transduction in striated muscles. AAV naturally evolve into multiple serotypes with diverse capsid gene sequences that are apparently the determinants of their tissue tropism and infectivity. Certain AAV serotypes show robust gene transfer upon direct intramuscular injection, while others are effective in crossing the endothelial barrier to reach muscle when delivered intravenously. Muscular dystrophy gene therapy requires efficient body-wide muscle gene transfer. However, preferential liver transduction by nearly all natural AAV serotypes could be an undesirable feature for muscle-directed applications, especially by means of systemic gene delivery. Here we describe a method of in vitro evolution and in vivo selection of AAV capsids that target striated muscles and detarget the liver. Using DNA shuffling technology, we have generated a capsid gene library by in vitro scrambling and shuffling the capsid genes of natural AAV1 to AAV9. To minimize the bias and limitation of in vitro screening on culture cells, we performed direct in vivo panning in adult mice after intravenous injection of the shuffled capsid library that packaged their own coding sequences. The AAV variants enriched in the heart and muscle are retrieved by capsid gene PCR and subsequently characterized for their tissue tropisms. This directed evolution and in vivo selection method should be useful in generating novel gene therapy vectors for muscle and heart and other tissues.
Collapse
Affiliation(s)
- Lin Yang
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | |
Collapse
|
19
|
Mateu MG. Virus engineering: functionalization and stabilization. Protein Eng Des Sel 2010; 24:53-63. [PMID: 20923881 DOI: 10.1093/protein/gzq069] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chemically and/or genetically engineered viruses, viral capsids and viral-like particles carry the promise of important and diverse applications in biomedicine, biotechnology and nanotechnology. Potential uses include new vaccines, vectors for gene therapy and targeted drug delivery, contrast agents for molecular imaging and building blocks for the construction of nanostructured materials and electronic nanodevices. For many of the contemplated applications, the improvement of the physical stability of viral particles may be critical to adequately meet the demanding physicochemical conditions they may encounter during production, storage and/or medical or industrial use. The first part of this review attempts to provide an updated general overview of the fast-moving, interdisciplinary virus engineering field; the second part focuses specifically on the modification of the physical stability of viral particles by protein engineering, an emerging subject that has not been reviewed before.
Collapse
Affiliation(s)
- Mauricio G Mateu
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
| |
Collapse
|
20
|
Abstract
Gene therapy for the correction of inherited or acquired disease has gained increasing importance in recent years. Successful treatment of children suffering from severe combined immunodeficiency (SCID) was achieved using retrovirus vectors for gene transfer. Encouraging improvements of vision were reported in a genetic eye disorder (LCA) leading to early childhood blindness. Adeno-associated virus (AAV) vectors were used for gene transfer in these trials. This chapter gives an overview of the design and delivery of viral vectors for the transport of a therapeutic gene into a target cell or tissue. The construction and production of retrovirus, lentivirus, and AAV vectors are covered. The focus is on production methods suitable for biopharmaceutical upscaling and for downstream processing. Quality control measures and biological safety considerations for the use of vectors in clinical trials are discussed.
Collapse
|
21
|
Gong J, Zheng H, Wu Z, Chen T, Zhao X. Genome shuffling: Progress and applications for phenotype improvement. Biotechnol Adv 2009; 27:996-1005. [DOI: 10.1016/j.biotechadv.2009.05.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
22
|
Ward P, Walsh CE. Chimeric AAV Cap sequences alter gene transduction. Virology 2009; 386:237-48. [DOI: 10.1016/j.virol.2009.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 12/26/2008] [Accepted: 01/09/2009] [Indexed: 11/25/2022]
|
23
|
Abstract
Viruses can be engineered to efficiently deliver exogenous genes, but their natural gene delivery properties often fail to meet human therapeutic needs. Therefore, engineering viral vectors with new properties, including enhanced targeting abilities and resistance to immune responses, is a growing area of research. This review discusses protein engineering approaches to generate viral vectors with novel gene delivery capabilities. Rational design of viral vectors has yielded successful advances in vitro, and to an extent in vivo. However, there is often insufficient knowledge of viral structure-function relationships to reengineer existing functions or create new capabilities, such as virus-cell interactions, whose molecular basis is distributed throughout the primary sequence of the viral proteins. Therefore, high-throughput library and directed evolution methods offer alternative approaches to engineer viral vectors with desired properties. Parallel and integrated efforts in rational and library-based design promise to aid the translation of engineered viral vectors toward the clinic.
Collapse
Affiliation(s)
- David V Schaffer
- The Department of Chemical Engineering, the Department of Bioengineering, and The Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720-3220, USA.
| | | | | |
Collapse
|
24
|
In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses. J Virol 2008; 82:5887-911. [PMID: 18400866 DOI: 10.1128/jvi.00254-08] [Citation(s) in RCA: 470] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Adeno-associated virus (AAV) serotypes differ broadly in transduction efficacies and tissue tropisms and thus hold enormous potential as vectors for human gene therapy. In reality, however, their use in patients is restricted by prevalent anti-AAV immunity or by their inadequate performance in specific targets, exemplified by the AAV type 2 (AAV-2) prototype in the liver. Here, we attempted to merge desirable qualities of multiple natural AAV isolates by an adapted DNA family shuffling technology to create a complex library of hybrid capsids from eight different wild-type viruses. Selection on primary or transformed human hepatocytes yielded pools of hybrids from five of the starting serotypes: 2, 4, 5, 8, and 9. More stringent selection with pooled human antisera (intravenous immunoglobulin [IVIG]) then led to the selection of a single type 2/type 8/type 9 chimera, AAV-DJ, distinguished from its closest natural relative (AAV-2) by 60 capsid amino acids. Recombinant AAV-DJ vectors outperformed eight standard AAV serotypes in culture and greatly surpassed AAV-2 in livers of naïve and IVIG-immunized mice. A heparin binding domain in AAV-DJ was found to limit biodistribution to the liver (and a few other tissues) and to affect vector dose response and antibody neutralization. Moreover, we report the first successful in vivo biopanning of AAV capsids by using a new AAV-DJ-derived viral peptide display library. Two peptides enriched after serial passaging in mouse lungs mediated the retargeting of AAV-DJ vectors to distinct alveolar cells. Our study validates DNA family shuffling and viral peptide display as two powerful and compatible approaches to the molecular evolution of novel AAV vectors for human gene therapy applications.
Collapse
|
25
|
Vu HN, Ramsey JD, Pack DW. Engineering of a Stable Retroviral Gene Delivery Vector by Directed Evolution. Mol Ther 2008; 16:308-14. [DOI: 10.1038/sj.mt.6300350] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
26
|
Vu HN, Li Y, Casali M, Irimia D, Megeed Z, Yarmush ML. A microfluidic bioreactor for increased active retrovirus output. LAB ON A CHIP 2008; 8:75-80. [PMID: 18094764 DOI: 10.1039/b711577f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Retroviruses are one of the most commonly used vectors in ongoing gene therapy clinical trials. To evaluate and advance virus production on the microscale platform, we have created a novel microfluidic bioreactor for continuous retrovirus production. We investigated the growth kinetics of a retroviral packaging cell line in microfluidic bioreactors for several compartment sizes, and packaging cells perfused in the microdevices showed similar growth kinetics to those cultured in conventional static conditions. To evaluate the efficiency of retrovirus production, virus titers from the microdevices were compared to those obtained from static tissue culture. When retrovirus production and collection were maintained at 37 degrees C, virus production levels were comparable for the microdevices and static tissue culture conditions. However, immediate cold storage downstream of the packaging cells in the microdevices resulted in 1.4- to 3.7-fold greater active virus production levels with the microdevices compared to the conventional static conditions over a 5 day period. Lastly, the use of microfluidics for virus production provides a continuous supply of virus supernatant for immediate infection of target cells or for preservation and storage. Such devices will be valuable for the optimization of production and evaluation of retroviruses and other viral vectors for gene therapy applications.
Collapse
Affiliation(s)
- Halong N Vu
- Center for Engineering in Medicine and Department of Surgery, BioMEMS Resource Center, Massachusetts General Hospital, Shriners Hospital for Children, and Harvard Medical School, 51 Blossom Street, Rm. 406, Boston, MA 02114, USA
| | | | | | | | | | | |
Collapse
|
27
|
Chaparro-Riggers JF, Loo BL, Polizzi KM, Gibbs PR, Tang XS, Nelson MJ, Bommarius AS. Revealing biases inherent in recombination protocols. BMC Biotechnol 2007; 7:77. [PMID: 18001472 PMCID: PMC2203992 DOI: 10.1186/1472-6750-7-77] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 11/14/2007] [Indexed: 11/23/2022] Open
Abstract
Background The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing. Results We developed different test systems to compare and reveal biases from DNA shuffling and recombination-dependent PCR (RD-PCR), a StEP-like recombination protocol. An assay based on the reactivation of β-lactamase was developed to simulate the recombination of point mutations. Both protocols performed similarly here, with slight advantages for RD-PCR. However, clear differences in the performance of the recombination protocols were observed when applied to homologous genes of varying DNA identities. Most importantly, the recombination-dependent PCR showed a less pronounced bias of the crossovers in regions with high sequence identity. We discovered that template variations, including engineered terminal truncations, have significant influence on the position of the crossovers in the recombination-dependent PCR. In comparison, DNA shuffling can produce higher crossover numbers, while the recombination-dependent PCR frequently results in one crossover. Lastly, DNA shuffling and recombination-dependent PCR both produce counter-productive variants such as parental sequences and have chimeras that are over-represented in a library, respectively. Lastly, only RD-PCR yielded chimeras in the low homology situation of GFP/mRFP (45% DNA identity level). Conclusion By comparing different recombination scenarios, this study expands on existing recombination knowledge and sheds new light on known biases, which should improve library-creation efforts. It could be shown that the recombination-dependent PCR is an easy to perform alternative to DNA shuffling.
Collapse
Affiliation(s)
- Javier F Chaparro-Riggers
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, 315 Ferst Drive, Atlanta, GA 30332-0363, USA.
| | | | | | | | | | | | | |
Collapse
|
28
|
Jang JH, Lim KI, Schaffer DV. Library selection and directed evolution approaches to engineering targeted viral vectors. Biotechnol Bioeng 2007; 98:515-24. [PMID: 17614321 DOI: 10.1002/bit.21541] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gene therapy, to delivery of genetic material to a patient for therapeutic benefit, has significant promise for translating basic knowledge of disease mechanism into biomedical treatments. The clinical development of the field has been slowed, however, by the need for improvements in the properties and capabilities of gene delivery vehicles. Vehicles based on viruses offer the potential for efficient gene delivery, but because viruses did not evolve to serve human therapeutic needs, many of their properties require significant improvement, including their safety, efficiency, and capacity for targeted gene delivery. Since viruses are highly complex biological entities, engineering such properties at the molecular level can be challenging. However, there has been significant progress in developing approaches that mimic the mechanisms by which viruses arose in the first place. In particular, library-based selection, the generation of one diverse genetic library and selection for new properties, and directed evolution, based on the multiple rounds of library generation and selection for iterative improvement of function, have strong potential in engineering novel properties into these complex biomolecular assemblies. This review will discuss progress in the application of peptide display, library selection, and directed evolution technologies toward engineering vectors based on retrovirus, adeno-associated virus, and adenovirus that are capable of targeted delivery to specific cell types. In addition to creating biomedically useful products, these approaches have future potential to yield novel insights into viral structure-function relationships.
Collapse
Affiliation(s)
- Jae-Hyung Jang
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, 201 Gilman Hall, Berkeley, California 94720, USA
| | | | | |
Collapse
|
29
|
Abstract
From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles. They are composed of a small number of different (bio)polymers: proteins and nucleic acids. Many viruses are enveloped in a lipid membrane and all viruses do not have a metabolism of their own, but rather use the metabolic machinery of a living cell for their replication. Their surface carries specific tools designed to cross the barriers of their host cells. The size and shape of viruses, and the number and nature of the functional groups on their surface, is precisely defined. As such, viruses are commonly used in materials science as scaffolds for covalently linked surface modifications. A particular quality of viruses is that they can be tailored by directed evolution by taking advantage of their inbuilt colocalization of geno- and phenotypes. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine.
Collapse
Affiliation(s)
- Martin Fischlechner
- Institute of Medical Physics and Biophysics, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | | |
Collapse
|
30
|
Fischlechner M, Donath E. Viren als Bauelemente für Materialien und Strukturen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603445] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
31
|
Schaffer DV, Maheshri N. Directed evolution of AAV mutants for enhanced gene delivery. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007; 2004:3520-3. [PMID: 17271049 DOI: 10.1109/iembs.2004.1403990] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Gene therapy vehicles must be engineered to overcome numerous barriers that limit delivery efficiency. These barriers arise at every step of the delivery process, including the transit of the vector from injection to a cell surface, receptor binding and uptake, intracellular trafficking, and nuclear entry. The gene transfer properties of the highly promising adeno-associated viral (AAV) vector at each step are determined by its capsid structure. Previous capsid modifications that alter AAV tropism, as well as the existence of multiple AAV serotypes, suggest that the AAV capsid is reasonably plastic. We have taken advantage of this remarkable capsid plasticity to generate a large mutant AAV library (1e6) and select for mutant AAV virons that can overcome several barriers to infection. Specifically, we have selected AAV2 library for infectious particles with altered heparan sulfate (HS) affinity and for the ability to evade an AAV2 immune response. We have generated mutants with lower and higher affinity to heparin, which could prove valuable in controlling the therapeutic zone of an AAV vector in tissues where ECM HS hinders AAV2 diffusion. Furthermore, we have generated vector variants that have resistance to human serum that neutralizes wild type AAV2, yet retain AAV2 gene delivery efficiency. These vectors may enable high gene delivery efficiency even in patients with preexisting immunity, and the locations of point mutations on the capsid surface suggest new regions of functional importance to the virus. These AAV libraries therefore both provide useful variants for gene therapy application and offer a means to dissect AAV biology.
Collapse
Affiliation(s)
- D V Schaffer
- Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California at Berkeley, Berkeley, CA, USA
| | | |
Collapse
|
32
|
Abstract
A possible origin of novel coding sequences is the removal of stop codons, leading to the inclusion of 3' untranslated regions (3' UTRs) within genes. We classified changes in the position of stop codons in closely related Saccharomyces species and in a mouse/rat comparison as either additions to or subtractions from coding regions. In both cases, the position of stop codons is highly labile, with more subtractions than additions found. The subtraction bias may be balanced by the input of new coding regions through gene duplication. Saccharomyces shows less stop codon lability than rodents, probably due to greater selective constraint. A higher proportion of 3' UTR incorporation events preserve frame in Saccharomyces. This higher proportion is consistent with the action of the [PSI(+)] prion as an evolutionary capacitor to facilitate 3' UTR incorporation in yeast.
Collapse
Affiliation(s)
| | | | - Joanna Masel
- Dpt. Ecology & Evolutionary Biology, University of
Arizona
| |
Collapse
|
33
|
Rodrigues T, Carvalho A, Carmo M, Carrondo MJT, Alves PM, Cruz PE. Scaleable purification process for gene therapy retroviral vectors. J Gene Med 2007; 9:233-43. [PMID: 17428003 DOI: 10.1002/jgm.1021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Retroviral vectors (RVs) constitute one of the preferred gene therapy tools against inherited and acquired diseases. Development of scaleable downstream processes allowing purification under mild conditions and yielding viral preparations with high titer, potency and purity is critical for the success of clinical trials and subsequent clinical use of this technology. METHODS A purification process for murine leukaemia virus (MLV)-derived vector supernatants was developed based on membrane separation and anion-exchange chromatography (AEXc). Initial clarification of the vector stocks was performed using 0.45 microm membranes followed by concentration with 500 kDa molecular weight cut-off (MWCO) membranes; further purification was performed by AEXc using a tentacle matrix bearing DEAE functional ligands. Finally, concentration/diafiltration was performed by 500 kDa MWCO membranes. To validate final product quality the process was scaled up 16-fold. RESULTS Optimization of microfiltration membrane pore size and ultrafiltration transmembrane pressure allowed the recovery of nearly 100% infectious particles. Further purification of the RVs by AEXc resulted in high removal of protein contaminants while maintaining high recoveries of infectious vectors (77+/-11%). Up-scaling of the process resulted in high titer vector preparations, 3.2x10(8) infectious particles (IP)/ml (85-fold concentration), with an overall recovery reaching 26%. The process yielded vectors with transduction efficiencies higher than the starting material and more than 99% pure, relative to protein contamination. CONCLUSIONS The combination of membrane separation and AEXc processes results in a feasible and scaleable purification strategy for MLV-derived vectors, allowing the removal of inhibitory contaminants thus yielding pure vectors with increased transduction efficiencies.
Collapse
|
34
|
Rodrigues T, Carrondo MJT, Alves PM, Cruz PE. Purification of retroviral vectors for clinical application: Biological implications and technological challenges. J Biotechnol 2007; 127:520-41. [PMID: 16950534 DOI: 10.1016/j.jbiotec.2006.07.028] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 07/12/2006] [Accepted: 07/25/2006] [Indexed: 11/16/2022]
Abstract
For centuries mankind led a difficult battle against viruses, the smallest infectious agents at the surface of the earth. Nowadays it is possible to use viruses for our benefit, both at a prophylactic level in the production of vaccines and at a therapeutic level in the promising field of gene therapy. Retroviruses were discovered at the end of the 19th century and constitute one of the most effective entities for gene transfer and insertion into the genome of mammalian cells. This attractive feature has intensified research in retroviral vectors development and production over the past years, mainly due to the expectations raised by the concept of gene therapy. The demand for high quality retroviral vectors that meet standard requisites from the regulatory agencies (FDA and EMEA) is therefore increasing, as the technology has moved into clinical trials. The development of safer producer cell lines that can be used in large-scale production will result in the production of large quantities of retroviral stocks. Cost-efficient and scalable purification processes are essential for production of injectable-grade preparations to achieve final implementation of these vectors as therapeutics. Several preparative purification steps already established for proteins can certainly be applied to retroviral vectors, in particular membrane filtration and chromatographic methods. Nevertheless, the special properties of these complex products require technological improvement of the existing purification steps and/or development of particular purification steps to increase productivity and throughput, while maintaining biological activity of the final product. This review focuses on downstream process development in relation to the retroviral vectors characteristics and quality assessment of retroviral stocks for intended use in gene therapy.
Collapse
Affiliation(s)
- Teresa Rodrigues
- IBET/ITQB, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | | | | | | |
Collapse
|
35
|
Wu Z, Asokan A, Samulski RJ. Adeno-associated virus serotypes: vector toolkit for human gene therapy. Mol Ther 2006; 14:316-27. [PMID: 16824801 DOI: 10.1016/j.ymthe.2006.05.009] [Citation(s) in RCA: 590] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 05/17/2006] [Accepted: 05/17/2006] [Indexed: 01/11/2023] Open
Abstract
Recombinant adeno-associated viral (AAV) vectors have rapidly advanced to the forefront of gene therapy in the past decade. The exponential progress of AAV-based vectors has been made possible by the isolation of several naturally occurring AAV serotypes and over 100 AAV variants from different animal species. These isolates are ideally suited to development into human gene therapy vectors due to their diverse tissue tropisms and potential to evade preexisting neutralizing antibodies against the common human AAV serotype 2. Despite their prolific application in several animal models of disease, the mechanisms underlying selective tropisms of AAV serotypes remain largely unknown. Efforts to understand cell surface receptor usage and intracellular trafficking pathways exploited by AAV continue to provide significant insight into the biology of AAV vectors. Such unique traits are thought to arise from differences in surface topology of the capsids of AAV serotypes and variants. In addition to the aforementioned naturally evolved AAV isolates, several strategies to engineer hybrid AAV serotype vectors have been formulated in recent years. The generation of mosaic or chimeric vectors through the transcapsidation or marker-rescue/domain-swapping approach, respectively, is notable in this regard. More recently, combinatorial strategies for engineering AAV vectors using error-prone PCR, DNA shuffling, and other molecular cloning techniques have been established. The latter library-based approaches can serve as powerful tools in the generation of low-immunogenic and cell/tissue type-specific AAV vectors for gene delivery. This review is focused on recent developments in the isolation of novel AAV serotypes and isolates, their production and purification, diverse tissue tropisms, mechanisms of cellular entry/trafficking, and capsid structure. Strategies for engineering hybrid AAV vectors derived from AAV serotypes and potential implications of the rapidly expanding AAV vector toolkit are discussed.
Collapse
Affiliation(s)
- Zhijian Wu
- Gene Therapy Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | |
Collapse
|
36
|
Rodrigues T, Carvalho A, Roldão A, Carrondo MJT, Alves PM, Cruz PE. Screening anion-exchange chromatographic matrices for isolation of onco-retroviral vectors. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 837:59-68. [PMID: 16697280 DOI: 10.1016/j.jchromb.2006.03.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 03/01/2006] [Accepted: 03/30/2006] [Indexed: 11/25/2022]
Abstract
The adsorption kinetics of retroviral vectors to several chromatographic media, DEAE FF, Streamlinetrade mark Q XL and CHTtrade mark Ceramic Hydroxyapatite, in batch mode was investigated. The effects of buffer type, pH and operational temperature were studied. A mathematical model describing viral adsorption kinetics that considers viral degradation in solution was developed. The best results, either in terms of speed and extent of adsorbed infectious particles, were obtained with DEAE FF and Streamlinetrade mark Q XL. Fixed-bed chromatography was further investigated using DEAE FF, Q XL and Q FF, for validation of the batch adsorption process. Fixed-bed DEAE FF and Q XL proved to be good candidates for purification of MoMLV derived vectors due to resulting high yields, 53+/-13% and 51+/-7%, respectively, while removing more than 99% of protein and 90% of the DNA contaminants.
Collapse
|
37
|
Perabo L, Endell J, King S, Lux K, Goldnau D, Hallek M, Büning H. Combinatorial engineering of a gene therapy vector: directed evolution of adeno-associated virus. J Gene Med 2006; 8:155-62. [PMID: 16285001 DOI: 10.1002/jgm.849] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Viruses are being exploited as vectors to deliver therapeutic genetic information into target cells. The success of this approach will depend on the ability to overcome current limitations, especially in terms of safety and efficiency, through molecular engineering of the viral particles. METHODS Here we show that in vitro directed evolution can be successfully performed to randomize the viral capsid by error prone PCR and to obtain mutants with improved phenotype. RESULTS To demonstrate the potential of this technology we selected several adeno-associated virus (AAV) capsid variants that are less efficiently neutralized by human antibodies. These mutations can be used to generate novel vectors for the treatment of patients with pre-existing immunity to AAV. CONCLUSIONS Our results demonstrate that combinatorial engineering overcomes the limitations of rational design approaches posed by incomplete understanding of the infectious process and at the same time offers a powerful tool to dissect basic viral biology by reverse genetics.
Collapse
Affiliation(s)
- Luca Perabo
- Gene Center, Ludwig-Maximilians-University of Munich, Germany.
| | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
The biological weapons are different from conventional weapons, because living germs hold an extraordinary and predictable potential for multiplication, propagation and genetic variation during their dissemination in a susceptible population. Only natural pathogens (1rst generation weapons) have been used in the past (smallpox virus, plague, anthrax, toxins...). However, new threats are emerging, due to the rapid progress of scientific knowledge and its exponential worldwide diffusion. It is possible to synthesize microorganisms from in silico sequences widely diffused on Internet (poliovirus, influenza...), thus resulting in the accessibility of very dangerous virus confined today in high-security laboratories (virus Ebola...). It is possible also to "improve" pathogens by genetic manipulations, becoming more resistant or virulent (2nd generation weapons). Finally, one can now create de novo new pathogens by molecular breeding (DNA shuffling), potentially highly dangerous for naive populations (3rd generation weapons). Making biological weapons does not require too much technological resources and appears accessible to terrorists, due to low cost and easy use. Although the destructive consequences are difficult to predict, the psychological and social damages should be considerable, because of the highly emotional burden in the population associated to the transgression by man of a taboo of life.
Collapse
Affiliation(s)
- Patrick Berche
- Service de microbiologie, Hôpital Necker- Enfants-malades, 149, rue de Sèvres, 75015 Paris, France.
| |
Collapse
|
39
|
Abstract
Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.
Collapse
Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | | | | | | |
Collapse
|
40
|
Conant GC, Wagner A. The rarity of gene shuffling in conserved genes. Genome Biol 2005; 6:R50. [PMID: 15960802 PMCID: PMC1175970 DOI: 10.1186/gb-2005-6-6-r50] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 03/23/2005] [Accepted: 04/13/2005] [Indexed: 12/02/2022] Open
Abstract
The incidence of gene shuffling is estimated in conserved genes in 10 organisms from the three domains of life. Successful gene shuffling is found to be very rare among such conserved genes. This suggests that gene shuffling may not be a major force in reshaping the core genomes of eukaryotes. Background Among three sources of evolutionary innovation in gene function - point mutations, gene duplications, and gene shuffling (recombination between dissimilar genes) - gene shuffling is the most potent one. However, surprisingly little is known about its incidence on a genome-wide scale. Results We have studied shuffling in genes that are conserved between distantly related species. Specifically, we estimated the incidence of gene shuffling in ten organisms from the three domains of life: eukaryotes, eubacteria, and archaea, considering only genes showing significant sequence similarity in pairwise genome comparisons. We found that successful gene shuffling is very rare among such conserved genes. For example, we could detect only 48 successful gene-shuffling events in the genome of the fruit fly Drosophila melanogaster which have occurred since its common ancestor with the worm Caenorhabditis elegans more than half a billion years ago. Conclusion The incidence of gene shuffling is roughly an order of magnitude smaller than the incidence of single-gene duplication in eukaryotes, but it can approach or even exceed the gene-duplication rate in prokaryotes. If true in general, this pattern suggests that gene shuffling may not be a major force in reshaping the core genomes of eukaryotes. Our results also cast doubt on the notion that introns facilitate gene shuffling, both because prokaryotes show an appreciable incidence of gene shuffling despite their lack of introns and because we find no statistical association between exon-intron boundaries and recombined domains in the two multicellular genomes we studied.
Collapse
Affiliation(s)
- Gavin C Conant
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Andreas Wagner
- Department of Biology, The University of New Mexico, Albuquerque, NM 87131-0001, USA
| |
Collapse
|
41
|
Ho YC, Chen HC, Wang KC, Hu YC. Highly efficient baculovirus-mediated gene transfer into rat chondrocytes. Biotechnol Bioeng 2005; 88:643-51. [PMID: 15472927 DOI: 10.1002/bit.20239] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To explore the potential of baculovirus serving as a gene delivery vector in tissue engineering of articular cartilage, the efficiencies of baculovirus-mediated gene delivery into primary rat chondrocytes were evaluated and the transduction protocol commonly employed by others (using concentrated virus at multiplicity of infection [MOI] 200 for 1 h) was found to be ineffective (<1%). Therefore, a modified protocol was adopted, which markedly enhanced the efficiency (68%). Optimization of the transduction parameters, such as incubation time (8 h), temperature (25 degrees C), and surrounding solutions (PBS), further increased the efficiency to 88% and prolonged the duration of expression to 21 days, suggesting that the cells previously considered nonpermissive to baculovirus transduction may be reexamined for their permissiveness using alternative transduction protocols. The elevated efficiency correlated well with increased virus uptake upon extended incubation time, as demonstrated by quantitative real-time polymerase chain reaction (Q-PCR). The Q-PCR also revealed the degradation of viral DNA over culture time. Although the virus transduction somewhat hindered the cell proliferation, growth rate could be restored in the long-term culture. More importantly, transduced cells could secrete articular cartilage-specific type II collagen and glycosaminoglycan as well as mock-transduced cells, confirming that normal differentiation state of rat chondrocytes is retained upon baculovirus transduction. Taken together, these data indicate that baculovirus is a safe and highly efficient gene delivery vehicle into rat chondrocytes.
Collapse
Affiliation(s)
- Yi-Chen Ho
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | | | | | | |
Collapse
|
42
|
Locher CP, Heinrichs V, Apt D, Whalen RG. Overcoming antigenic diversity and improving vaccines using DNA shuffling and screening technologies. Expert Opin Biol Ther 2005; 4:589-97. [PMID: 15102607 DOI: 10.1517/14712598.4.4.589] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viral, bacterial and parasitic pathogens have evolved multiple strategies to evade the immune response, facilitate transmission and establish chronic infections. One of the underlying strategies that pathogens have evolved is antigenic variation of immune response targets that reduce the affinity of antigen binding to antibodies and major histocompatability complex class I and II receptors. Vaccine candidates generally target a limited number of these antigen variants or combine antigens from several variants to include in multivalent vaccine formulations. DNA shuffling and screening technologies, also known as MolecularBreeding (Maxygen, Inc.) directed molecular evolution, have been successfully used to identify and develop novel and chimaeric vaccine candidates capable of inducing immune responses that recognise and control multiple antigenic variants. DNA shuffling and screening strategies also select vaccine candidates with improved immunogenicity, increased expression as recombinant polypeptides and improved growth of whole viruses in cell culture. As DNA shuffling and screening strategies can be applied to many pathogens, there remain numerous applications of DNA shuffling to solve challenging problems in vaccine process development and manufacture.
Collapse
|
43
|
Hsu CS, Ho YC, Wang KC, Hu YC. Investigation of optimal transduction conditions for baculovirus-mediated gene delivery into mammalian cells. Biotechnol Bioeng 2005; 88:42-51. [PMID: 15384054 DOI: 10.1002/bit.20213] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Although baculovirus-mediated gene delivery into mammalian cells has been documented in a wealth of the literature, systematic investigation of the optimal transduction conditions remains unavailable. In this work, a transduction protocol using unconcentrated baculovirus is proposed for simple and efficient gene delivery into HeLa cells. We found that approximately 75-85% of the cells could be readily transduced and express the reporter protein when virus transduction occurred for 4 h at 25 degrees C using Dulbecco's phosphate-buffered saline (D-PBS) as the surrounding solution. This method contrasts with previous protocols in which transduction occurs for 1 h at 37 degrees C using growth medium (e.g., DMEM) as the surrounding solution. Investigation of the physical parameters led to the findings that: 1) baculovirus uptake by HeLa cells continued for at least 4 h in the event of high virus dosage, which led to higher gene expression; 2) the half-life of baculovirus dramatically decreased at 37 degrees C; 3) EGTA pretreatment did not apparently facilitate the gene delivery when the cells grew to multilayers; and 4) lower transduction efficiency and gene expression were obtained when DMEM was used (in comparison with D-PBS and TNM-FH), suggesting that DMEM contains certain inhibitory factors for baculovirus transduction. Our data uncovered several aspects that were not investigated before and the optimized transduction conditions allowed for gene delivery as efficient as that by the protocols commonly employed by others, but eliminated the need for virus ultracentrifugation. The protocol not only represented a simpler approach, but also considerably reduced possible virus inactivation during ultracentrifugation, thus making it easier to convert the baculovirus/mammalian cell system to a tool for eukaryotic protein production on a larger scale.
Collapse
Affiliation(s)
- Ching-Suei Hsu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan 300
| | | | | | | |
Collapse
|
44
|
Chan AWS. Transgenic nonhuman primates for neurodegenerative diseases. Reprod Biol Endocrinol 2004; 2:39. [PMID: 15200672 PMCID: PMC441412 DOI: 10.1186/1477-7827-2-39] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Accepted: 06/16/2004] [Indexed: 01/08/2023] Open
Abstract
Animal models that represent human diseases constitute an important tool in understanding the pathogenesis of the diseases, and in developing effective therapies. Neurodegenerative diseases are complex disorders involving neuropathologic and psychiatric alterations. Although transgenic and knock-in mouse models of Alzheimer's disease, (AD), Parkinson's disease (PD) and Huntington's disease (HD) have been created, limited representation in clinical aspects has been recognized and the rodent models lack true neurodegeneration. Chemical induction of HD and PD in nonhuman primates (NHP) has been reported, however, the role of intrinsic genetic factors in the development of the diseases is indeterminable. Nonhuman primates closely parallel humans with regard to genetic, neuroanatomic, and cognitive/behavioral characteristics. Accordingly, the development of NHP models for neurodegenerative diseases holds greater promise for success in the discovery of diagnoses, treatments, and cures than approaches using other animal species. Therefore, a transgenic NHP carrying a mutant gene similar to that of patients will help to clarify our understanding of disease onset and progression. Additionally, monitoring disease onset and development in the transgenic NHP by high resolution brain imaging technology such as MRI, and behavioral and cognitive testing can all be carried out simultaneously in the NHP but not in other animal models. Moreover, because of the similarity in motor repertoire between NHPs and humans, it will also be possible to compare the neurologic syndrome observed in the NHP model to that in patients. Understanding the correlation between genetic defects and physiologic changes (e.g. oxidative damage) will lead to a better understanding of disease progression and the development of patient treatments, medications and preventive approaches for high risk individuals. The impact of the transgenic NHP model in understanding the role which genetic disorders play in the development of efficacious interventions and medications is foreseeable.
Collapse
Affiliation(s)
- Anthony W S Chan
- Yerkes National Primate Research Center and Department of Human Genetics, Emory University, Atlanta, Georgia, USA.
| |
Collapse
|
45
|
Das AT, Zhou X, Vink M, Klaver B, Verhoef K, Marzio G, Berkhout B. Viral evolution as a tool to improve the tetracycline-regulated gene expression system. J Biol Chem 2004; 279:18776-82. [PMID: 14761948 DOI: 10.1074/jbc.m313895200] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present viral evolution as a novel and powerful method to optimize non-viral proteins. We used this approach to optimize the tetracycline (Tc)-regulated gene expression system (Tet system) for its function in mammalian cells. The components of the Tet system were incorporated in the human immunodeficiency virus (HIV)-1 virus such that viral replication is controlled by this regulatory system. Upon long term replication of this HIV-rtTA virus in human T cells, we obtained a virus variant with an enhanced replication potential resulting from an improved rtTA component of the introduced Tet system. We identified a single amino acid exchange, F86Y, which enhances the transcriptional activity and doxycycline (dox) sensitivity of rtTA. We generated a new rtTA variant that is 5-fold more active at high dox levels than the initial rtTA, and 25-fold more sensitive to dox, whereas the background activity in the absence of dox is not increased. This new rtTA variant will be very useful in biological applications that require a more sensitive or active Tet system. Our results demonstrate that the viral evolution strategy can be used to improve the activity of genes by making them an integral and essential part of the virus.
Collapse
Affiliation(s)
- Atze T Das
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
46
|
Hu YC, Tsai CT, Chung YC, Lu JT, Hsu JTA. Generation of chimeric baculovirus with histidine-tags displayed on the envelope and its purification using immobilized metal affinity chromatography. Enzyme Microb Technol 2003. [DOI: 10.1016/s0141-0229(03)00143-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
47
|
Maheshri N, Schaffer DV. Computational and experimental analysis of DNA shuffling. Proc Natl Acad Sci U S A 2003; 100:3071-6. [PMID: 12626764 PMCID: PMC152248 DOI: 10.1073/pnas.0537968100] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2002] [Accepted: 12/30/2002] [Indexed: 12/25/2022] Open
Abstract
We describe a computational model of DNA shuffling based on the thermodynamics and kinetics of this process. The model independently tracks a representative ensemble of DNA molecules and records their states at every stage of a shuffling reaction. These data can subsequently be analyzed to yield information on any relevant metric, including reassembly efficiency, crossover number, type and distribution, and DNA sequence length distributions. The predictive ability of the model was validated by comparison to three independent sets of experimental data, and analysis of the simulation results led to several unique insights into the DNA shuffling process. We examine a tradeoff between crossover frequency and reassembly efficiency and illustrate the effects of experimental parameters on this relationship. Furthermore, we discuss conditions that promote the formation of useless "junk" DNA sequences or multimeric sequences containing multiple copies of the reassembled product. This model will therefore aid in the design of optimal shuffling reaction conditions.
Collapse
Affiliation(s)
- Narendra Maheshri
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720-1462, USA
| | | |
Collapse
|
48
|
Lassner MW, McElroy D. Directed molecular evolution: bridging the gap between genomics leads and commercial products. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2003; 6:153-62. [PMID: 12143961 DOI: 10.1089/153623102760092751] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Agricultural crops, engineered to express transgenic traits, have been rapidly adopted by farmers since the initial commercialization of this technology in 1996. However, despite nearly 20 years of research in agricultural biotechnology, only two product categories have achieved commercial success: plants containing transgenes conferring tolerance to herbicides and plants containing insecticidal protein genes derived from Bacillus thuringensis. A number of transgenic concepts, while exhibiting promising phenotypes in laboratory experiments, have failed to generate commercially viable crops. Many of the leads produced by modern integrative approaches to understanding plant biology will need further optimization to deliver economically viable crops. Directed molecular evolution represents a powerful technology to optimize newly discovered leads towards product objectives. In this review, we show by example how directed molecular evolution can be used to develop enabling technologies for plant biologists; how genes can be optimized to generate improved input traits such as those conferring insect tolerance, disease control and herbicide tolerance; and how plant quality can be altered to improve yield, produce novel industrial feedstocks and improve nutritional qualities.
Collapse
|
49
|
Leong SR, Chang JCC, Ong R, Dawes G, Stemmer WPC, Punnonen J. Optimized expression and specific activity of IL-12 by directed molecular evolution. Proc Natl Acad Sci U S A 2003; 100:1163-8. [PMID: 12529500 PMCID: PMC298744 DOI: 10.1073/pnas.0237327100] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2002] [Accepted: 12/03/2002] [Indexed: 01/01/2023] Open
Abstract
DNA delivery of IL-12 has shown promise in reducing the toxic side effects associated with administration of recombinant human (h)IL-12 protein while maintaining the ability to inhibit tumor growth and abolish tumor metastases in animal models. We have developed a more potent version of IL-12 by using DNA shuffling and screening to improve its expression in human cells and specific activity on human T cells. The most improved evolved IL-12 (EvIL-12) derived from seven mammalian genes encoding both the p35 and p40 subunits of IL-12 showed a 128-fold improvement in human T cell proliferation compared with native hIL-12 during the initial screening of supernatants from transected cells. When purified hIL-12 and EvIL-12 proteins were compared in vitro in human T cell proliferation and Th1 differentiation assays, it was demonstrated that EvIL-12 exhibited a concomitant 10-fold increase in the specific activity of the protein compared with hIL-12. Furthermore, DNA shuffling improved the level of expression and homogeneity of the heterodimer synthesized by 293 human embryonic kidney cells transfected with EvIL-12 by at least 10-fold. Molecular analysis of the variant revealed strategic placement of amino acid substitutions that potentially may facilitate heterodimer formation and product expression. The enhanced expression and biological activity of EvIL-12 may improve the effectiveness of IL-12 gene-based vaccines and therapeutics without the toxic side effects sometimes associated with hIL-12 protein administration.
Collapse
Affiliation(s)
- Steven R Leong
- Department of Vaccines, Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063, USA
| | | | | | | | | | | |
Collapse
|
50
|
Abstract
Thanks to biotechnology, proteins are becoming increasingly important tools to fight disease, both as therapeutics in their own right and as catalysts for the synthesis of small molecule drugs. However, the properties of these proteins are not necessarily optimal for their intended tasks. In vitro evolution is a set of technologies useful to address their shortcomings. Moreover, in vitro evolution can help illuminate natural evolutionary pathways, thus potentially enabling prediction of drug resistance evolution. We consider here recent developments in the area of in vitro evolution, as well as its application to proteins of interest to medical science.
Collapse
Affiliation(s)
- Simon Delagrave
- Center for Molecular Biotechnology, Fraunhofer USA, 9 Innovation Way, Suite 200, Newark, DE 19711, USA.
| | | |
Collapse
|