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Brito-Sierra CA, Lannan MB, Malherbe LP, Siegel RW. The HLA class I immunopeptidomes of AAV capsid proteins. Front Immunol 2023; 14:1212136. [PMID: 37662941 PMCID: PMC10469481 DOI: 10.3389/fimmu.2023.1212136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Cellular immune responses against AAV vector capsid represent an obstacle for successful gene therapy. Previous studies have used overlapping peptides spanning the entire capsid sequence to identify T cell epitopes recognized by AAV-specific CD8+ T cells. However, the repertoire of peptides naturally displayed by HLA class I molecules for CD8 T cell recognition is unknown. Methods Using mRNA transfected monocyte-derived dendritic cells (MDDCs) and MHC-associated peptide proteomics (MAPPs), we identified the HLA class I immunopeptidomes of AAV2, AAV6 and AAV9 capsids. MDDCs were isolated from a panel of healthy donors that have diverse alleles across the US population. mRNA-transfected MDDCs were lysed, the peptide:HLA complexes immunoprecipitated, and peptides eluted and analyzed by mass spectrometry. Results We identified 65 AAV capsid-derived peptides loaded on HLA class I molecules of mRNA transfected monocyte derived dendritic cells. The HLA class I peptides are distributed along the entire capsid and more than 60% are contained within HLA class II clusters. Most of the peptides are organized as single species, however we identified twelve clusters containing at least 2 peptides of different lengths. Only 9% of the identified peptides have been previously identified as T cell epitopes, demonstrating that the immunogenicity potential for the vast majority of the AAV HLA class I immunopeptidome remains uncharacterized. In contrast, 12 immunogenic epitopes identified before were not found to be naturally processed in our study. Remarkably, 11 naturally presented AAV peptides were highly conserved among the three serotypes analyzed suggesting the possibility of cross-reactive AAV-specific CD8 T cells. Discussion This work is the first comprehensive study identifying the naturally displayed HLA class I peptides derived from the capsid of AAVs. The results from this study can be used to generate strategies to assess immunogenicity risk and cross-reactivity among serotypes during gene therapies.
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Affiliation(s)
| | | | - Laurent P. Malherbe
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Robert W. Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
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2
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Piletska E, Veron P, Bertin B, Mingozzi F, Jones D, Norman RL, Earley J, Karim K, Garcia-Cruz A, Piletsky S. Analysis of Adeno-Associated Virus Serotype 8 (AAV8)-antibody complexes using epitope mapping by molecular imprinting leads to the identification of Fab peptides that potentially evade AAV8 neutralisation. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 52:102691. [PMID: 37329939 DOI: 10.1016/j.nano.2023.102691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Gene therapy is a promising approach for treating genetic disorders by delivering therapeutic genes to replace or correct malfunctioning genes. However, the introduced gene therapy vector can trigger an immune response, leading to reduced efficacy and potential harm to the patient. To improve the efficiency and safety of gene therapy, preventing the immune response to the vector is crucial. This can be achieved through the use of immunosuppressive drugs, vector engineering to evade the immune system, or delivery methods that bypass the immune system altogether. By reducing the immune response, gene therapy can deliver therapeutic genes more effectively and potentially cure genetic diseases. In this study, a novel molecular imprinting technique, combined with mass-spectrometry and bioinformatics, was used to identify four antigen-binding fragments (Fab) sequences of Adeno-Associated Virus (AAV) - neutralising antibodies capable of binding to AAV. The identified Fab peptides were shown to prevent AAV8's binding to antibodies, demonstrating their potential to improve gene therapy efficiency by preventing the immune response.
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Affiliation(s)
- Elena Piletska
- School of Chemistry, University of Leicester, LE1 7RH, UK.
| | - Philippe Veron
- Laboratory of Immunology, Genethon, 91002 Evry Cedex, France
| | | | | | - Donald Jones
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, UK; Department of Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Rachel L Norman
- Cancer Research Centre, RKCSB, University of Leicester, Leicester LE1 7RH, UK; Van Geest MS Omics Facility, University of Leicester, Leicester LE1 9HN, UK
| | - Joseph Earley
- School of Chemistry, University of Leicester, LE1 7RH, UK
| | - Kal Karim
- School of Chemistry, University of Leicester, LE1 7RH, UK
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3
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Brito-Sierra CA, Lannan MB, Siegel RW, Malherbe LP. The HLA class-II immunopeptidomes of AAV capsids proteins. Front Immunol 2022; 13:1067399. [PMID: 36605211 PMCID: PMC9807805 DOI: 10.3389/fimmu.2022.1067399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Gene therapies are using Adeno-associated viruses (AAVs) as vectors, but immune responses against the capsids pose challenges to their efficiency and safety. Helper T cell recognition of capsid-derived peptides bound to human leukocyte antigen (HLA) class II molecules is an essential step in the AAV-specific adaptive immunity. Methods Using MHC-associated peptide proteomics, we identified the HLA-DR and HLA-DQ immunopeptidomes of the capsid proteins of three different AAV serotypes (AAV2, AAV6, and AAV9) from a panel of healthy donors selected to represent a majority of allele usage. Results The identified sequences span the capsids of all serotypes, with AAV2 having the highest peptide count. For all the serotypes, multiple promiscuous peptides were identified and displayed by both HLA-DR and -DQ. However, despite high sequence homology, there were few identical peptides among AAV2, AAV6, and AAV9 immunopeptidomes, and none were promiscuous. Discussion Results from this work represent a comprehensive immunopeptidomics research of potential CD4+ T cell epitopes and provide the basis for immunosurveillance efforts for safer and more efficient AAV-based gene therapies.
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Affiliation(s)
| | | | - Robert W. Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Laurent P. Malherbe
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
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4
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Differential T cell immune responses to deamidated adeno-associated virus vector. Mol Ther Methods Clin Dev 2022; 24:255-267. [PMID: 35211638 PMCID: PMC8829777 DOI: 10.1016/j.omtm.2022.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/16/2022] [Indexed: 01/09/2023]
Abstract
Despite the high safety profile demonstrated in clinical trials, the immunogenicity of adeno-associated virus (AAV)-mediated gene therapy remains a major hurdle. Specifically, T-cell-mediated immune responses to AAV vectors are related to loss of efficacy and potential liver toxicities. As post-translational modifications in T cell epitopes have the potential to affect immune reactions, the cellular immune responses to peptides derived from spontaneously deamidated AAV were investigated. Here, we report that highly deamidated sites in AAV9 contain CD4 T cell epitopes with a Th1 cytokine pattern in multiple human donors with diverse human leukocyte antigen (HLA) backgrounds. Furthermore, some peripheral blood mononuclear cell (PBMC) samples demonstrated differential T cell activation to deamidated or non-deamidated epitopes. Also, in vitro and in silico HLA binding assays showed differential binding to the deamidated or non-deamidated peptides in some HLA alleles. This study provides critical attributes to vector-immune-mediated responses, as AAV deamidation can impact the immunogenicity, safety, and efficacy of AAV-mediated gene therapy in some patients.
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Singh N, Bhatnagar S. Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host-pathogen Interaction Network Parameters. Mol Inform 2021; 41:e2100115. [PMID: 34676983 DOI: 10.1002/minf.202100115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Host-pathogen interactions play a crucial role in invasion, infection, and induction of immune response in humans. In this work, four machine learning algorithms, namely Logistic regression, K-nearest neighbor, Support Vector Machine, and Random Forest were implemented for the classification of drug targets. The algorithms were trained using 3400 hosts and 3800 pathogen drug and non-drug target proteins as learning instances. For each protein, 68 pathogen and 73 host features were computed that included sequence, structure, biological and host-pathogen network centrality characteristics. The Random Forest classifier model achieved the best accuracy after 10-fold cross-validation. 99 % accuracy was achieved with a ROC-AUC score of 0.99±0.01 for both pathogen and host training sets. The Eigenvector Centrality of host-pathogen interactions and host-host interactions was the top feature in performing classification of pathogen and host targets respectively. Other features important for classification were the presence of catalytic and binding sites, low instability/aliphatic index, and cellular location. The Random Forest classifier was then used for prediction of drug targets involved in Microbe Associated Cardiovascular Diseases. 331 host and 743 pathogen proteins were predicted as drug targets by the random forest model and can be validated experimentally for therapeutic intervention in Microbe Associated Cardiovascular Diseases.
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Affiliation(s)
- Nirupma Singh
- Department of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Sonika Bhatnagar
- Department of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India.,Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology Dwarka, New Delhi, 110078, India
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Mary B, Maurya S, Kumar M, Bammidi S, Kumar V, Jayandharan GR. Molecular Engineering of Adeno-Associated Virus Capsid Improves Its Therapeutic Gene Transfer in Murine Models of Hemophilia and Retinal Degeneration. Mol Pharm 2019; 16:4738-4750. [PMID: 31596095 PMCID: PMC7035104 DOI: 10.1021/acs.molpharmaceut.9b00959] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recombinant adeno-associated virus (AAV)-based gene therapy has been promising, but several host-related transduction or immune challenges remain. For this mode of therapy to be widely applicable, it is crucial to develop high transduction and permeating vectors that infect the target at significantly low doses. Because glycosylation of capsid proteins is known to be rate limiting in the life cycle of many viruses, we reasoned that perturbation of glycosylation sites in AAV2 capsid will enhance gene delivery. In our first set experiments, pharmacological modulation of the glycosylation status in host cells, modestly decreased (1-fold) AAV2 packaging efficacy while it improved their gene expression (∼74%) in vitro. We then generated 24 mutant AAV2 vectors modified to potentially create or disrupt a glycosylation site in its capsid. Three of them demonstrated a 1.3-2.5-fold increase in transgene expression in multiple cell lines (HeLa, Huh7, and ARPE-19). Hepatic gene transfer of these vectors in hemophilia B mice, resulted in a 2-fold increase in human coagulation factor (F)IX levels, while its T/B-cell immunogenic response was unaltered. Subsequently, intravitreal gene transfer of glycosylation site-modified vectors in C57BL6/J mice demonstrated an increase in green fluorescence protein expression (∼2- to 4-fold) and enhanced permeation across retina. Subretinal administration of these modified vectors containing RPE65 gene further rescued the photoreceptor response in a murine model of Leber congenital amarousis. Our studies highlight the translational potential of glycosylation site-modified AAV2 vectors for hepatic and ocular gene therapy applications.
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Affiliation(s)
- Bertin Mary
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Shubham Maurya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Mohit Kumar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Sridhar Bammidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Vikas Kumar
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha 68198, Nebraska, United States
| | - Giridhara R. Jayandharan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
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Dhanda SK, Karosiene E, Edwards L, Grifoni A, Paul S, Andreatta M, Weiskopf D, Sidney J, Nielsen M, Peters B, Sette A. Predicting HLA CD4 Immunogenicity in Human Populations. Front Immunol 2018; 9:1369. [PMID: 29963059 PMCID: PMC6010533 DOI: 10.3389/fimmu.2018.01369] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022] Open
Abstract
Background Prediction of T cell immunogenicity is a topic of considerable interest, both in terms of basic understanding of the mechanisms of T cells responses and in terms of practical applications. HLA binding affinity is often used to predict T cell epitopes, since HLA binding affinity is a key requisite for human T cell immunogenicity. However, immunogenicity at the population it is complicated by the high level of variability of HLA molecules, potential other factors beyond HLA as well as the frequent lack of HLA typing data. To overcome those issues, we explored an alternative approach to identify the common characteristics able to distinguish immunogenic peptides from non-recognized peptides. Methods Sets of dominant epitopes derived from peer-reviewed published papers were used in conjunction with negative peptides from the same experiments/donors to train neural networks and generate an “immunogenicity score.” We also compared the performance of the immunogenicity score with previously described method for immunogenicity prediction based on HLA class II binding at the population level. Results The immunogenicity score was validated on a series of independent datasets derived from the published literature, representing 57 independent studies where immunogenicity in human populations was assessed by testing overlapping peptides spanning different antigens. Overall, these testing datasets corresponded to over 2,000 peptides and tested in over 1,600 different human donors. The 7-allele method prediction and the immunogenicity score were associated with similar performance [average area under the ROC curve (AUC) values of 0.703 and 0.702, respectively] while the combined methods reached an average AUC of 0.725. This increase in average AUC value is significant compared with the immunogenicity score (p = 0.0135) and a strong trend toward significance is observed when compared to the 7-allele method (p = 0.0938). The new immunogenicity score method is now freely available using CD4 T cell immunogenicity prediction tool on the Immune Epitope Database website (http://tools.iedb.org/CD4episcore). Conclusion The new immunogenicity score predicts CD4 T cell immunogenicity at the population level starting from protein sequences and with no need for HLA typing. Its efficacy has been validated in the context of different antigen sources, ethnicities, and disparate techniques for epitope identification.
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Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Edita Karosiene
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Lindy Edwards
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
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8
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Adeno-Associated Virus Gene Therapy: Translational Progress and Future Prospects in the Treatment of Heart Failure. Heart Lung Circ 2018; 27:1285-1300. [PMID: 29703647 DOI: 10.1016/j.hlc.2018.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/03/2018] [Indexed: 02/06/2023]
Abstract
Despite advances in treatment over the past decade, heart failure remains a significant public health burden and a leading cause of death in the developed world. Gene therapy provides a promising approach for preventing and reversing cardiac abnormalities, however, clinical application has shown limited success to date. A substantial effort is being invested into the development of recombinant adeno-associated viruses (AAVs) for cardiac gene therapy as AAV gene therapy offers a high safety profile and provides sustained and efficient transgene expression following a once-off administration. Due to the physiological, anatomical and genetic similarities between large animals and humans, preclinical studies using large animal models for AAV gene therapy are crucial stepping stones between the laboratory and the clinic. Many molecular targets selected to treat heart failure using AAV gene therapy have been chosen because of their potential to regulate and restore cardiac contractility. Other genes targeted with AAV are involved with regulating angiogenesis, beta-adrenergic sensitivity, inflammation, physiological signalling and metabolism. While significant progress continues to be made in the field of AAV cardiac gene therapy, challenges remain in overcoming host neutralising antibodies, improving AAV vector cardiac-transduction efficiency and selectivity, and optimising the dose, route and method of delivery.
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9
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Nelson CE, Robinson-Hamm JN, Gersbach CA. Genome engineering: a new approach to gene therapy for neuromuscular disorders. Nat Rev Neurol 2017; 13:647-661. [DOI: 10.1038/nrneurol.2017.126] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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10
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Bera A, Sen D. Promise of adeno-associated virus as a gene therapy vector for cardiovascular diseases. Heart Fail Rev 2017; 22:795-823. [DOI: 10.1007/s10741-017-9622-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Bello A, Chand A, Aviles J, Soule G, Auricchio A, Kobinger GP. Novel adeno-associated viruses derived from pig tissues transduce most major organs in mice. Sci Rep 2014; 4:6644. [PMID: 25335510 PMCID: PMC4205840 DOI: 10.1038/srep06644] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/30/2014] [Indexed: 01/12/2023] Open
Abstract
Recently, development of Adeno-associated virus (AAV) vectors has been focusing on expanding the genetic diversity of vectors from existing sequences via directed evolution or epitope remapping. Apart from intelligent design, AAV isolation from natural sources remains an important source of new AAVs with unique biological features. In this study, several new AAV sequences were isolated from porcine tissues (AAVpo2.1, -po4, -po5, and -po6), which aligned in divergent new clades. Viral particles generated from these sequences displayed tissue tropism and transduction efficiency profile specific to each porcine-derived AAV. When delivered systemically, AAVpo2.1 targeted the heart, kidney, and muscle, AAVpo5 performed poorly but was able to transduce muscle fibers when injected intramuscularly, whereas AAVpo4 and -po6 efficiently transduced all the major organs sampled, contending with ‘gold-standard’ AAVs. When delivered systemically, AAVpo4 and -po6 were detected by polymerase chain reaction (PCR) and histochemical staining of the transgene product in adult mouse brain, suggesting that these vectors can pass through the blood-brain barrier with efficiencies that may be useful for the development of therapeutic approaches. Porcine tissues are antigenically similar to human tissues and by inference, porcine AAVs may provide fresh tools to contribute to the development of gene therapy-based solutions to human diseases.
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Affiliation(s)
- Alexander Bello
- 1] Public Health Agency of Canada, National Microbiology Laboratory, Special Pathogens Program, Winnipeg, Canada [2] University of Manitoba, Department of Medical Microbiology
| | - Allan Chand
- 1] Public Health Agency of Canada, National Microbiology Laboratory, Special Pathogens Program, Winnipeg, Canada [2] University of Manitoba, Department of Medical Microbiology
| | - Jenna Aviles
- 1] Public Health Agency of Canada, National Microbiology Laboratory, Special Pathogens Program, Winnipeg, Canada [2] Department of Immunology, Winnipeg, Canada
| | - Geoff Soule
- Public Health Agency of Canada, National Microbiology Laboratory, Special Pathogens Program, Winnipeg, Canada
| | - Alberto Auricchio
- 1] Telethon Institute of Genetics and Medicine, Naples, Italy [2] Medical Genetics, Translational Medicine, "Federico II" University, Naples, Italy
| | - Gary P Kobinger
- 1] Public Health Agency of Canada, National Microbiology Laboratory, Special Pathogens Program, Winnipeg, Canada [2] University of Manitoba, Department of Medical Microbiology [3] Department of Immunology, Winnipeg, Canada
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12
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Manzano-Szalai K, Thell K, Willensdorfer A, Weghofer M, Pfanzagl B, Singer J, Ritter M, Stremnitzer C, Flaschberger I, Michaelis U, Jensen-Jarolim E. Adeno-associated virus-like particles as new carriers for B-cell vaccines: testing immunogenicity and safety in BALB/c mice. Viral Immunol 2014; 27:438-48. [PMID: 25247267 DOI: 10.1089/vim.2014.0059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Adeno-associated viruses (AAVs) are established vectors for gene therapy of different human diseases. AAVs are assembled of 60 capsomers, which can be genetically modified, allowing high-density display of short peptide sequences at their surface. The aim of our study was to evaluate the immunogenicity and safety of an adeno-associated virus-like particle (AAVLP)-displayed B-cell peptide epitope taking ovalbumin (OVA) as a model antigen or allergen from egg, respectively. An OVA-derived B-cell epitope was expressed as fusion protein with the AAV-2 capsid protein of VP3 (AAVLP-OVA) and for control, with the nonrelated peptide TP18 (AAVLP-TP18). Cellular internalization studies revealed an impaired uptake of AAVLP-OVA by mouse BMDC, macrophages, and human HeLa cells. Nevertheless, BALB/c mice immunized subcutaneously with AAVLP-OVA formed similarly high titers of OVA-specific IgG1 compared to mice immunized with the native OVA. The extent of the immune response was independent whether aluminum hydroxide or water in oil emulsion was used as adjuvant. Furthermore, in mice immunized with native OVA, high OVA-specific IgE levels were observed, which permitted OVA-specific mast-cell degranulation in a β-hexosaminidase release assay, whereas immunizations with AAVLP-OVA rendered background IgE levels only. Accordingly, OVA-immunized mice, but not AAVLP-OVA immunized mice, displayed an anaphylactic reaction with a significant drop of body temperature upon intravenous OVA challenge. From this mouse model, we conclude that AAVLPs that display B-cell epitope peptides on their surface are suitable vaccine candidates, especially in the field of allergy.
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Affiliation(s)
- Krisztina Manzano-Szalai
- 1 Comparative Medicine, Messerli Research Institute, University of Veterinary Medicine Vienna , Medical University of Vienna and University of Vienna, Vienna, Austria
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Abstract
Clinical gene therapy has been increasingly successful owing both to an enhanced molecular understanding of human disease and to progressively improving gene delivery technologies. Among these technologies, delivery vectors based on adeno-associated viruses (AAVs) have emerged as safe and effective and, in one recent case, have led to regulatory approval. Although shortcomings in viral vector properties will render extension of such successes to many other human diseases challenging, new approaches to engineer and improve AAV vectors and their genetic cargo are increasingly helping to overcome these barriers.
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Affiliation(s)
- Melissa A. Kotterman
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - David V. Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Sen D, Balakrishnan B, Gabriel N, Agrawal P, Roshini V, Samuel R, Srivastava A, Jayandharan GR. Improved adeno-associated virus (AAV) serotype 1 and 5 vectors for gene therapy. Sci Rep 2013; 3:1832. [PMID: 23665951 PMCID: PMC3652085 DOI: 10.1038/srep01832] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/22/2013] [Indexed: 12/19/2022] Open
Abstract
Despite significant advancements with recombinant AAV2 or AAV8 vectors for liver directed gene therapy in humans, it is well-recognized that host and vector-related immune challenges need to be overcome for long-term gene transfer. To overcome these limitations, alternate AAV serotypes (1–10) are being rigorously evaluated. AAV5 is the most divergent (55% similarity vs. other serotypes) and like AAV1 vector is known to transduce liver efficiently. AAV1 and AAV5 vectors are also immunologically distinct by virtue of their low seroprevalence and minimal cross reactivity against pre-existing AAV2 neutralizing antibodies. Here, we demonstrate that targeted bio-engineering of these vectors, augment their gene expression in murine hepatocytes in vivo (up to 16-fold). These studies demonstrate the feasibility of the use of these novel AAV1 and AAV5 vectors for potential gene therapy of diseases like hemophilia.
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Affiliation(s)
- Dwaipayan Sen
- Department of Hematology, Christian Medical College, Vellore, Tamil Nadu, India
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15
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CD8+ T cell recognition of epitopes within the capsid of adeno-associated virus 8-based gene transfer vectors depends on vectors' genome. Mol Ther 2013; 22:42-51. [PMID: 24077034 DOI: 10.1038/mt.2013.218] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 08/28/2013] [Indexed: 02/06/2023] Open
Abstract
Self-complementary adeno-associated viral (AAV) vectors expressing human factor IX (hF.IX) have achieved transient or sustained correction of hemophilia B in human volunteers. High doses of AAV2 or AAV8 vectors delivered to the liver caused in several patients an increase in transaminases accompanied by a rise in AAV capsid-specific T cells and a decrease in circulating hF.IX levels suggesting immune-mediated destruction of vector-transduced cells. Kinetics of these adverse events differed in patients receiving AAV2 or AAV8 vectors causing rise in transaminases at 3 versus 8 weeks after vector injection, respectively. To test if CD8+ T cells to AAV8 vectors, which are similar to AAV2 vectors are fully-gutted vectors and thereby fail to encode structural viral proteins, could cause damage at this late time point, we tested in a series of mouse studies how long major histocompatibility (MHC) class I epitopes within AAV8 capsid can be presented to CD8+ T cells. Our results clearly show that depending on the vectors' genome, CD8+ T cells can detect such epitopes on AAV8's capsid for up to 6 months indicating that the capsid of AAV8 degrades slowly in mice.
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16
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San Sebastian W, Samaranch L, Kells AP, Forsayeth J, Bankiewicz KS. Gene therapy for misfolding protein diseases of the central nervous system. Neurotherapeutics 2013; 10:498-510. [PMID: 23700209 PMCID: PMC3701766 DOI: 10.1007/s13311-013-0191-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein aggregation as a result of misfolding is a common theme underlying neurodegenerative diseases. Accordingly, most recent studies aim to prevent protein misfolding and/or aggregation as a strategy to treat these pathologies. For instance, state-of-the-art approaches, such as silencing protein overexpression by means of RNA interference, are being tested with positive outcomes in preclinical models of animals overexpressing the corresponding protein. Therapies designed to treat central nervous system diseases should provide accurate delivery of the therapeutic agent and long-term or chronic expression by means of a nontoxic delivery vehicle. After several years of technical advances and optimization, gene therapy emerges as a promising approach able to fulfill those requirements. In this review we will summarize the latest improvements achieved in gene therapy for central nervous system diseases associated with protein misfolding (e.g., amyotrophic lateral sclerosis, Alzheimer's, Parkinson's, Huntington's, and prion diseases), as well as the most recent approaches in this field to treat these pathologies.
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Affiliation(s)
- Waldy San Sebastian
- Department of Neurological Surgery, University of California San Francisco, 1855 Folsom Street, San Francisco, CA USA
| | - Lluis Samaranch
- Department of Neurological Surgery, University of California San Francisco, 1855 Folsom Street, San Francisco, CA USA
| | - Adrian P. Kells
- Department of Neurological Surgery, University of California San Francisco, 1855 Folsom Street, San Francisco, CA USA
| | - John Forsayeth
- Department of Neurological Surgery, University of California San Francisco, 1855 Folsom Street, San Francisco, CA USA
| | - Krystof S. Bankiewicz
- Department of Neurological Surgery, University of California San Francisco, 1855 Folsom Street, San Francisco, CA USA
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Deshmukh TM, Shah RR, Gurav YK, Arankalle VA. Serum immunoglobulin G subclass responses in different phases of hepatitis E virus infection. J Med Virol 2013; 85:828-32. [DOI: 10.1002/jmv.23537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2013] [Indexed: 12/17/2022]
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18
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In vivo reduction or blockade of interleukin-1β in primary osteoarthritis influences expression of mediators implicated in pathogenesis. Osteoarthritis Cartilage 2012; 20:1610-8. [PMID: 22935786 PMCID: PMC3478416 DOI: 10.1016/j.joca.2012.08.011] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 08/10/2012] [Accepted: 08/18/2012] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Diminish interleukin-1β (IL-1β) signaling in a model of primary osteoarthritis by RNA interference-based transcript reduction or receptor blockade, and quantify changes incurred on transcript expression of additional mediators. METHODS Knees of Hartley guinea pigs were collected at 120 and 180 days of age following injection with viral vectors (N = 4/treatment group/date) at 60 days. Two groups received either adeno-associated viral serotype 5 vector containing a knockdown sequence (TV), or adenoviral vector encoding for IL-1 receptor antagonist protein (Ad-IRAP); treatments were contrasted with opposite knees administered corresponding vector controls. A third group evaluated TV relative to saline-only injected knees. Chondropathy and immunohistochemistry findings were compared to untreated guinea pigs. Transcript expression levels in cartilage were calculated using the comparative CT (2(-ΔΔCT)) method and analyzed by one-way analysis of variance (ANOVA) with pairwise comparisons using Tukey 95% confidence intervals. RESULTS Vector transduction was confirmed at both harvest dates. TV and Ad-IRAP, relative to vector controls, significantly decreased IL-1β. Inflammatory mediators [tumor necrosis factor-α (TNF-α), IL-8, interferon-γ (IFN-γ)], and catabolic matrix metalloproteinase 13 (MMP13) were also decreased, while anabolic transforming growth factor-β1 (TGF-β1) was increased. IL-1β was also decreased by TV vs saline, with a decrease in MMP13 and increase TGF-β1; TNF-α, IL-8, and IFN-γ were transiently increased. CONCLUSIONS This work confirmed that a reduction in IL-1β signaling was accomplished by either method, resulting in decreased expression of three inflammatory mediators and one catabolic agent, and increased expression of an anabolic molecule. Thus, evidence is provided that IL-1β serves a role in vivo in spontaneous osteoarthritis and that these translational tools may provide beneficial disease modification.
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Rapti K, Chaanine AH, Hajjar RJ. Targeted gene therapy for the treatment of heart failure. Can J Cardiol 2011; 27:265-83. [PMID: 21601767 PMCID: PMC5902317 DOI: 10.1016/j.cjca.2011.02.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 02/10/2011] [Accepted: 02/11/2011] [Indexed: 12/18/2022] Open
Abstract
Chronic heart failure is one of the leading causes of morbidity and mortality in Western countries and is a major financial burden to the health care system. Pharmacologic treatment and implanting devices are the predominant therapeutic approaches. They improve survival and have offered significant improvement in patient quality of life, but they fall short of producing an authentic remedy. Cardiac gene therapy, the introduction of genetic material to the heart, offers great promise in filling this void. In-depth knowledge of the underlying mechanisms of heart failure is, obviously, a prerequisite to achieve this aim. Extensive research in the past decades, supported by numerous methodological breakthroughs, such as transgenic animal model development, has led to a better understanding of the cardiovascular diseases and, inadvertently, to the identification of several candidate genes. Of the genes that can be targeted for gene transfer, calcium cycling proteins are prominent, as abnormalities in calcium handling are key determinants of heart failure. A major impediment, however, has been the development of a safe, yet efficient, delivery system. Nonviral vectors have been used extensively in clinical trials, but they fail to produce significant gene expression. Viral vectors, especially adenoviral, on the other hand, can produce high levels of expression, at the expense of safety. Adeno-associated viral vectors have emerged in recent years as promising myocardial gene delivery vehicles. They can sustain gene expression at a therapeutic level and maintain it over extended periods of time, even for years, and, most important, without a safety risk.
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Affiliation(s)
- Kleopatra Rapti
- Cardiovascular Research Center, Mount Sinai School of Medicine, New York, New York, USA
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Li H, Tuyishime S, Wu TL, Giles-Davis W, Zhou D, Xiao W, High KA, Ertl HCJ. Adeno-associated virus vectors serotype 2 induce prolonged proliferation of capsid-specific CD8+ T cells in mice. Mol Ther 2011; 19:536-46. [PMID: 21157435 PMCID: PMC3048183 DOI: 10.1038/mt.2010.267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 11/02/2010] [Indexed: 12/18/2022] Open
Abstract
Using adoptive transfer models we determined that an adeno-associated viral vector of serotype 2 (AAV2) induces in mice proliferation of CD8(+) T cells that recognize an epitope within the viral capsid. Proliferation to an endogenous epitope within viral protein (VP)3 could be observed for at least 3 weeks while a foreign epitope placed at multiple copies within VP2 elicited CD8(+) T cell expansion for at least 10 weeks. These data show that capsid antigens of AAV2 degrade slowly over a period of weeks and during this period provide targets to CD8(+) T cells.
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Affiliation(s)
- Hua Li
- Immunology Program, Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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21
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Mitchell AM, Nicolson SC, Warischalk JK, Samulski RJ. AAV's anatomy: roadmap for optimizing vectors for translational success. Curr Gene Ther 2010; 10:319-340. [PMID: 20712583 PMCID: PMC3920455 DOI: 10.2174/156652310793180706] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 07/20/2010] [Indexed: 12/14/2022]
Abstract
Adeno-Associated Virus based vectors (rAAV) are advantageous for human gene therapy due to low inflammatory responses, lack of toxicity, natural persistence, and ability to transencapsidate the genome allowing large variations in vector biology and tropism. Over sixty clinical trials have been conducted using rAAV serotype 2 for gene delivery with a number demonstrating success in immunoprivileged sites, including the retina and the CNS. Furthermore, an increasing number of trials have been initiated utilizing other serotypes of AAV to exploit vector tropism, trafficking, and expression efficiency. While these trials have demonstrated success in safety with emerging success in clinical outcomes, one benefit has been identification of issues associated with vector administration in humans (e.g. the role of pre-existing antibody responses, loss of transgene expression in non-immunoprivileged sites, and low transgene expression levels). For these reasons, several strategies are being used to optimize rAAV vectors, ranging from addition of exogenous agents for immune evasion to optimization of the transgene cassette for enhanced therapeutic output. By far, the vast majority of approaches have focused on genetic manipulation of the viral capsid. These methods include rational mutagenesis, engineering of targeting peptides, generation of chimeric particles, library and directed evolution approaches, as well as immune evasion modifications. Overall, these modifications have created a new repertoire of AAV vectors with improved targeting, transgene expression, and immune evasion. Continued work in these areas should synergize strategies to improve capsids and transgene cassettes that will eventually lead to optimized vectors ideally suited for translational success.
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Affiliation(s)
- Angela M. Mitchell
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah C. Nicolson
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jayme K. Warischalk
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - R. Jude Samulski
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Boutin S, Monteilhet V, Veron P, Leborgne C, Benveniste O, Montus MF, Masurier C. Prevalence of serum IgG and neutralizing factors against adeno-associated virus (AAV) types 1, 2, 5, 6, 8, and 9 in the healthy population: implications for gene therapy using AAV vectors. Hum Gene Ther 2010; 21:704-12. [PMID: 20095819 DOI: 10.1089/hum.2009.182] [Citation(s) in RCA: 700] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Adeno-associated viruses (AAVs) are small, nonenveloped single-stranded DNA viruses that require helper viruses to facilitate efficient replication. Despite the presence of humoral responses to the wild-type AAV in humans, AAV remains one of the most promising candidates for therapeutic gene transfer to treat many genetic and acquired diseases. Characterization of the IgG subclass responses to AAV and study of the prevalence of both IgG and neutralizing factors to AAV types 1, 2, 5, 6, 8, and 9 in the human population are of importance for the development of new strategies to overcome these immune responses. Natural exposure to AAV types 1, 2, 5, 6, 8, and 9 can result in the production of antibodies from all four IgG subclasses, with a predominant IgG1 response and low IgG2, IgG3, and IgG4 responses. Prevalences of anti-AAV1 and -AAV2 total IgG determined by enzyme-linked immunosorbent assay were higher (67 and 72%) than those of anti-AAV5 (40%), anti-AAV6 (46%), anti-AAV8 (38%), and anti-AAV9 (47%). Furthermore, data showed that cross-reactions are important. The two highest neutralizing factor seroprevalences were observed for AAV2 (59%) and AAV1 (50.5%) and the lowest were observed for AAV8 (19%) and AAV5 (3.2%). Vectors based on AAV5, AAV8, and AAV9 may have an advantage for gene therapy in humans. Furthermore, among individuals seropositive for AAV5, AAV8, and AAV9, about 70-100% present low titers. Better characterization of the preexisting humoral responses to the AAV capsid and cross-reactivity will allow development of new strategies to circumvent AAV acquired immune responses.
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Affiliation(s)
- Sylvie Boutin
- Laboratoire d'Immunologie, Genethon R&D, Evry Cedex, France
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Progress and prospects: Immunobiology of gene therapy for neurodegenerative disease: prospects and risks. Gene Ther 2010; 17:448-58. [PMID: 20147982 DOI: 10.1038/gt.2010.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gene therapy for neurological, and in particular neurodegenerative, disease is now a reality. A number of early phase clinical trials have been completed and several are currently in progress. In view of this, it is critically important to evaluate the immunological risk associated with neurological gene therapy, which has clear implications for trial safety and efficacy. Moreover, it is imperative in particular to identify factors indicating potential high risk. In the light of recent advances in understanding immune regulation in the central nervous system (CNS) and with the continued development of new gene delivery vectors, this review critically assesses the current knowledge of immunobiology within the CNS in terms of likely immunological risk pertaining to viral vectors and gene therapy applications for neurodegenerative disease.
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