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Oziolor EM, Kumpf SW, Qian J, Gosink M, Sheehan M, Rubitski DM, Newman L, Whiteley LO, Lanz TA. Comparing molecular and computational approaches for detecting viral integration of AAV gene therapy constructs. Mol Ther Methods Clin Dev 2023; 29:395-405. [PMID: 37251978 PMCID: PMC10209688 DOI: 10.1016/j.omtm.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Many current gene therapy targets use recombinant adeno-associated virus (AAV). The majority of delivered AAV therapeutics persist as episomes, separate from host DNA, yet some viral DNA can integrate into host DNA in different proportions and at genomic locations. The potential for viral integration leading to oncogenic transformation has led regulatory agencies to require investigation into AAV integration events following gene therapy in preclinical species. In the present study, tissues were collected from cynomolgus monkeys and mice 6 and 8 weeks, respectively, following administration of an AAV vector delivering transgene cargo. We compared three different next-generation sequencing approaches (shearing extension primer tag selection ligation-mediated PCR, targeted enrichment sequencing [TES], and whole-genome sequencing) to contrast the specificity, scope, and frequency of integration detected by each method. All three methods detected dose-dependent insertions with a limited number of hotspots and expanded clones. While the functional outcome was similar for all three methods, TES was the most cost-effective and comprehensive method of detecting viral integration. Our findings aim to inform the direction of molecular efforts to ensure a thorough hazard assessment of AAV viral integration in our preclinical gene therapy studies.
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Affiliation(s)
- Elias M. Oziolor
- Global Computational Safety Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Steven W. Kumpf
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Jessie Qian
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Mark Gosink
- Global Computational Safety Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Mark Sheehan
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - David M. Rubitski
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Leah Newman
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | | | - Thomas A. Lanz
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
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2
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Tang PZ, Ding B, Reyes C, Papp D, Potter J. Target-seq: single workflow for detection of genome integration site, DNA translocation and off-target events. Biotechniques 2023. [PMID: 37161298 DOI: 10.2144/btn-2023-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Designed donor DNA delivery through viral or nonviral systems to target loci in the host genome is a critical step for gene therapy. Adeno-associated virus and lentivirus are leading vehicles for in vivo and ex vivo delivery of therapeutic genes due to their high delivery and editing efficiency. Nonviral editing tools, such as CRISPR/Cas9, are getting more attention for gene modification. However, there are safety concerns; for example, tumorigenesis due to off-target effects and DNA rearrangement. Analysis tools to detect and characterize on-target and off-target genome modification post editing in the host genome are pivotal for evaluating the success and safety of gene therapy. We developed Target-seq combined with different analysis tools to detect the genome integration site, DNA translocation and off-target events.
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Affiliation(s)
| | - Bo Ding
- Thermo Fisher Scientific, Inc., MA, USA
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3
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Nguyen GN, Everett JK, Kafle S, Roche AM, Raymond HE, Leiby J, Wood C, Assenmacher CA, Merricks EP, Long CT, Kazazian HH, Nichols TC, Bushman FD, Sabatino DE. A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells. Nat Biotechnol 2021; 39:47-55. [PMID: 33199875 PMCID: PMC7855056 DOI: 10.1038/s41587-020-0741-7] [Citation(s) in RCA: 231] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022]
Abstract
Nine dogs with hemophilia A were treated with adeno-associated viral (AAV) gene therapy and followed for up to 10 years. Administration of AAV8 or AAV9 vectors expressing canine factor VIII (AAV-cFVIII) corrected the FVIII deficiency to 1.9-11.3% of normal FVIII levels. In two of nine dogs, levels of FVIII activity increased gradually starting about 4 years after treatment. None of the dogs showed evidence of tumors or altered liver function. Analysis of integration sites in liver samples from six treated dogs identified 1,741 unique AAV integration events in genomic DNA and expanded cell clones in five dogs, with 44% of the integrations near genes involved in cell growth. All recovered integrated vectors were partially deleted and/or rearranged. Our data suggest that the increase in FVIII protein expression in two dogs may have been due to clonal expansion of cells harboring integrated vectors. These results support the clinical development of liver-directed AAV gene therapy for hemophilia A, while emphasizing the importance of long-term monitoring for potential genotoxicity.
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Affiliation(s)
- Giang N Nguyen
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John K Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samita Kafle
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aoife M Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hayley E Raymond
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob Leiby
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christian Wood
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Charles-Antoine Assenmacher
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth P Merricks
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Blood Research Center, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - C Tyler Long
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Blood Research Center, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Haig H Kazazian
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Timothy C Nichols
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Blood Research Center, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Denise E Sabatino
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Hematology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Li N, Jin K, Bai Y, Fu H, Liu L, Liu B. Tn5 Transposase Applied in Genomics Research. Int J Mol Sci 2020; 21:ijms21218329. [PMID: 33172005 PMCID: PMC7664229 DOI: 10.3390/ijms21218329] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 11/28/2022] Open
Abstract
The development of high-throughput sequencing (next-generation sequencing technology (NGS)) and the continuous increase in experimental throughput require the upstream sample processing steps of NGS to be as simple as possible to improve the efficiency of the entire NGS process. The transposition system has fast “cut and paste” and “copy and paste” functions, and has been innovatively applied to the NGS field. For example, the Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) uses high-throughput sequencing to detect chromatin regions accessible by Tn5 transposase. Linear Amplification via Transposon Insertion (LIANTI) uses Tn5 transposase for linear amplification, haploid typing, and structural variation detection. Not only is it efficient and simple, it effectively shortens the time for NGS sample library construction, realizes large-scale and rapid sequencing, improves sequencing resolution, and can be flexibly modified for more technological innovation.
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Affiliation(s)
- Niannian Li
- College of Life Sciences, Nankai University, Tianjin 300071, China; (N.L.); (K.J.); (H.F.)
| | - Kairang Jin
- College of Life Sciences, Nankai University, Tianjin 300071, China; (N.L.); (K.J.); (H.F.)
| | - Yanmin Bai
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400700, China;
| | - Haifeng Fu
- College of Life Sciences, Nankai University, Tianjin 300071, China; (N.L.); (K.J.); (H.F.)
| | - Lin Liu
- College of Life Sciences, Nankai University, Tianjin 300071, China; (N.L.); (K.J.); (H.F.)
- Correspondence: (L.L.); (B.L.)
| | - Bin Liu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300071, China
- Correspondence: (L.L.); (B.L.)
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5
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Torres-Torronteras J, Cabrera-Pérez R, Vila-Julià F, Viscomi C, Cámara Y, Hirano M, Zeviani M, Martí R. Long-Term Sustained Effect of Liver-Targeted Adeno-Associated Virus Gene Therapy for Mitochondrial Neurogastrointestinal Encephalomyopathy. Hum Gene Ther 2018; 29:708-718. [PMID: 29284302 DOI: 10.1089/hum.2017.133] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by mutations in TYMP, the gene encoding the enzyme thymidine phosphorylase (TP). TP dysfunction results in systemic accumulation of the noxious TP substrates thymidine and deoxyuridine. Gene therapy using either a lentiviral vector or adeno-associated vector (AAV) has proven to be a feasible strategy, as both vectors restore biochemical homeostasis in a murine model of the disease. This study shows that the effect of an AAV containing the TYMP coding sequence transcriptionally targeted to the liver persists long term in mice. Although the vector copy number was diluted and AAV-mediated liver TP activity eventually reduced or lost after 21 months at the lowest vector doses, the effect was sustained (with a negligible decrease in TP activity) and fully effective on nucleoside homeostasis for at least 21 months at a dose of 2 × 1012 vg/kg. Macroscopic visual inspection of the animals' organs at completion of the study showed no adverse effects associated with the treatment. These results further support the feasibility of gene therapy for MNGIE.
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Affiliation(s)
- Javier Torres-Torronteras
- 1 Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona , Barcelona, Spain .,2 Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III , Madrid, Spain
| | - Raquel Cabrera-Pérez
- 1 Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona , Barcelona, Spain .,2 Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III , Madrid, Spain
| | - Ferran Vila-Julià
- 1 Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona , Barcelona, Spain .,2 Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III , Madrid, Spain
| | - Carlo Viscomi
- 3 MRC-Mitochondrial Biology Unit, MRC MBU, Wellcome Trust/MRC Building, Hills Road, Cambridge, United Kingdom
| | - Yolanda Cámara
- 1 Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona , Barcelona, Spain .,2 Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III , Madrid, Spain
| | - Michio Hirano
- 4 H. Houston Merritt Center, Department of Neurology, Columbia University Medical Center , New York, New York
| | - Massimo Zeviani
- 3 MRC-Mitochondrial Biology Unit, MRC MBU, Wellcome Trust/MRC Building, Hills Road, Cambridge, United Kingdom
| | - Ramon Martí
- 1 Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona , Barcelona, Spain .,2 Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III , Madrid, Spain
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Kondratov O, Marsic D, Crosson SM, Mendez-Gomez HR, Moskalenko O, Mietzsch M, Heilbronn R, Allison JR, Green KB, Agbandje-McKenna M, Zolotukhin S. Direct Head-to-Head Evaluation of Recombinant Adeno-associated Viral Vectors Manufactured in Human versus Insect Cells. Mol Ther 2017; 25:2661-2675. [PMID: 28890324 DOI: 10.1016/j.ymthe.2017.08.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022] Open
Abstract
The major drawback of the Baculovirus/Sf9 system for recombinant adeno-associated viral (rAAV) manufacturing is that most of the Bac-derived rAAV vector serotypes, with few exceptions, demonstrate altered capsid compositions and lower biological potencies. Here, we describe a new insect cell-based production platform utilizing attenuated Kozak sequence and a leaky ribosome scanning to achieve a serotype-specific modulation of AAV capsid proteins stoichiometry. By way of example, rAAV5 and rAAV9 were produced and comprehensively characterized side by side with HEK293-derived vectors. A mass spectrometry analysis documented a 3-fold increase in both viral protein (VP)1 and VP2 capsid protein content compared with human cell-derived vectors. Furthermore, we conducted an extensive analysis of encapsidated single-stranded viral DNA using next-generation sequencing and show a 6-fold reduction in collaterally packaged contaminating DNA for rAAV5 produced in insect cells. Consequently, the re-designed rAAVs demonstrated significantly higher biological potencies, even in a comparison with HEK293-manufactured rAAVs mediating, in the case of rAAV5, 4-fold higher transduction of brain tissues in mice. Thus, the described system yields rAAV vectors of superior infectivity and higher genetic identity providing a scalable platform for good manufacturing practice (GMP)-grade vector production.
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Affiliation(s)
- Oleksandr Kondratov
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Damien Marsic
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Sean M Crosson
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Hector R Mendez-Gomez
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Oleksandr Moskalenko
- UFIT Research Computing, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA; Institute of Virology, Campus Benjamin Franklin, Charité Medical School, Berlin, Germany
| | - Regine Heilbronn
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, Berlin, Germany
| | | | - Kari B Green
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Sergei Zolotukhin
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA.
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7
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Tedesco FS. Human artificial chromosomes for Duchenne muscular dystrophy and beyond: challenges and hopes. Chromosome Res 2015; 23:135-41. [PMID: 25596829 DOI: 10.1007/s10577-014-9460-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Safe and efficacious vectors able to carry large or several transgenes are of key importance for gene therapy. Human artificial chromosomes can fulfil this essential requirement; moreover, they do not integrate into the host genome. However, drawbacks such as the low efficiency of chromosome transfer and their relatively complex engineering still limit their widespread use. In this article, I summarise the key steps that brought human artificial chromosomes into preclinical research for Duchenne muscular dystrophy, an X-linked, monogenic disorder. I will also review possible future pre-clinical and clinical perspectives for this technology.
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Affiliation(s)
- Francesco Saverio Tedesco
- Department of Cell and Developmental Biology, University College London, 21 University Street, London, WC1E 6DE, UK,
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8
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Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e260. [PMID: 26506038 PMCID: PMC4881760 DOI: 10.1038/mtna.2015.32] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022]
Abstract
Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.
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9
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Consequences of zygote injection and germline transfer of mutant human mitochondrial DNA in mice. Proc Natl Acad Sci U S A 2015; 112:E5689-98. [PMID: 26438859 DOI: 10.1073/pnas.1506129112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Considerable evidence supports mutations in mitochondrial genes as the cause of maternally inherited diseases affecting tissues that rely primarily on oxidative energy metabolism, usually the nervous system, the heart, and skeletal muscles. Mitochondrial diseases are diverse, and animal models currently are limited. Here we introduced a mutant human mitochondrial gene responsible for Leber hereditary optic neuropathy (LHON) into the mouse germ line using fluorescence imaging for tissue-specific enrichment in the target retinal ganglion cells. A mitochondria-targeted adeno-associated virus (MTS-AAV) containing the mutant human NADH ubiquinone oxidoreductase subunit 4 (ND4) gene followed by mitochondrial-encoded mCherry was microinjected into zygotes. Female founders with mCherry fluorescence on ophthalmoscopy were backcrossed with normal males for eight generations. Mutant human ND4 DNA was 20% of mouse ND4 and did not integrate into the host genome. Translated human ND4 protein assembled into host respiratory complexes, decreasing respiratory chain function and increasing oxidative stress. Swelling of the optic nerve head was followed by progressive demise of ganglion cells and their axons, the hallmarks of human LHON. Early visual loss that began at 3 mo and progressed to blindness 8 mo after birth was reversed by intraocular injection of MTS-AAV expressing wild-type human ND4. The technology of introducing human mitochondrial genes into the mouse germ line has never been described, to our knowledge, and has implications not only for creating animal models recapitulating the counterpart human disorder but more importantly for reversing the adverse effects of the mutant gene using gene therapy to deliver the wild-type allele.
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10
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Sherrill-Mix S, Ocwieja KE, Bushman FD. Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. Retrovirology 2015; 12:79. [PMID: 26377088 PMCID: PMC4574318 DOI: 10.1186/s12977-015-0205-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/28/2015] [Indexed: 02/07/2023] Open
Abstract
Background HIV infection has been reported to alter cellular gene activity, but published studies have commonly assayed transformed cell lines and lab-adapted HIV strains, yielding inconsistent results. Here we carried out a deep RNA-Seq analysis of primary human T cells infected with the low passage HIV isolate HIV89.6. Results Seventeen percent of cellular genes showed altered activity 48 h after infection. In a meta-analysis including four other studies, our data differed from studies of HIV infection in cell lines but showed more parallels with infections of primary cells. We found a global trend toward retention of introns after infection, suggestive of a novel cellular response to infection. HIV89.6 infection was also associated with activation of several human endogenous retroviruses (HERVs) and retrotransposons, of interest as possible novel antigens that could serve as vaccine targets. The most highly activated group of HERVs was a subset of the ERV-9. Analysis showed that activation was associated with a particular variant of ERV-9 long terminal repeats that contains an indel near the U3-R border. These data also allowed quantification of >70 splice forms of the HIV89.6 RNA and specified the main types of chimeric HIV89.6-host RNAs. Comparison to over 100,000 integration site sequences from the same infected cell populations allowed quantification of authentic versus artifactual chimeric reads, showing that 5′ read-in, splicing out of HIV89.6 from the D4 donor and 3′ read-through were the most common HIV89.6-host cell chimeric RNA forms. Conclusions Analysis of RNA abundance after infection of primary T cells with the low passage HIV89.6 isolate disclosed multiple novel features of HIV-host interactions, notably intron retention and induction of transcription of retrotransposons and endogenous retroviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Karen E Ocwieja
- Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA, 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
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11
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Kaeppel C, Beattie SG, Fronza R, van Logtenstein R, Salmon F, Schmidt S, Wolf S, Nowrouzi A, Glimm H, von Kalle C, Petry H, Gaudet D, Schmidt M. Reply to: NGS library preparation may generate artifactual integration sites of AAV vectors. Nat Med 2014; 20:578-9. [PMID: 24901561 DOI: 10.1038/nm.3584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christine Kaeppel
- 1] National Center for Tumor Diseases, Heidelberg, Germany. [2] German Cancer Research Center, Heidelberg, Germany
| | | | - Raffaele Fronza
- 1] National Center for Tumor Diseases, Heidelberg, Germany. [2] German Cancer Research Center, Heidelberg, Germany
| | | | | | - Sabine Schmidt
- Genomics and Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Ali Nowrouzi
- 1] National Center for Tumor Diseases, Heidelberg, Germany. [2] German Cancer Research Center, Heidelberg, Germany
| | - Hanno Glimm
- 1] National Center for Tumor Diseases, Heidelberg, Germany. [2] German Cancer Research Center, Heidelberg, Germany
| | - Christof von Kalle
- 1] National Center for Tumor Diseases, Heidelberg, Germany. [2] German Cancer Research Center, Heidelberg, Germany
| | | | - Daniel Gaudet
- ECOGENE-21 Clinical Research Center, Department of Medicine, Université de Montréal, Chicoutimi, Canada
| | - Manfred Schmidt
- 1] National Center for Tumor Diseases, Heidelberg, Germany. [2] German Cancer Research Center, Heidelberg, Germany
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