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Stone D, Meumann N, Kuhlmann AS, Peterson CW, Xie H, Roychoudhury P, Loprieno MA, Vu XK, Strongin DE, Kenkel EJ, Haick A, Stensland L, Obenza WM, Parrott J, Nelson V, Murnane RD, Huang ML, Aubert M, Kiem HP, Büning H, Jerome KR. A multiplexed barcode approach to simultaneously evaluate gene delivery by adeno-associated virus capsid variants in nonhuman primates. Hepatol Commun 2023; 7:e0009. [PMID: 37074875 PMCID: PMC10503678 DOI: 10.1097/hc9.0000000000000009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/21/2022] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND AND AIMS Adeno-associated virus (AAV) vectors are widely used to deliver therapeutic transgenes to distinct tissues, including the liver. Vectors based on naturally occurring AAV serotypes as well as vectors using engineered capsids have shown variations in tissue tropism and level of transduction between different mouse models. Moreover, results obtained in rodents frequently lack translatability into large animal studies. In light of the increasing interest in AAV vectors for human gene therapy, an increasing number of studies are being performed in nonhuman primates. To keep animal numbers to a minimum and thus optimize the process of AAV capsid selection, we developed a multiplex barcoding approach to simultaneously evaluate the in vivo vector performance for a set of serotypes and capsid-engineered AAV vectors across multiple organs. APPROACH AND RESULTS Vector biodistribution and transgene expression were assessed by quantitative PCR, quantitative reverse transcription PCR, vector DNA amplicon Illumina sequencing and vRNAseq in male and female rhesus macaques simultaneously dosed with a mixture of barcoded naturally occurring or engineered AAV vectors encoding the same transgene. As expected, our findings show animal-to-animal variation in both the biodistribution and tissue transduction pattern, which was partly influenced by each animal's distinctive serological status. CONCLUSIONS This method offers a robust approach to AAV vector optimization that can be used to identify and validate AAV vectors for gene delivery to potentially any anatomical site or cell type.
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Affiliation(s)
- Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nadja Meumann
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Anne-Sophie Kuhlmann
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Christopher W. Peterson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Michelle A. Loprieno
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Xuan-Khang Vu
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Daniel E. Strongin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Elizabeth J. Kenkel
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Anoria Haick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Laurence Stensland
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Willimark M. Obenza
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob Parrott
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Veronica Nelson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Robert D. Murnane
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, USA
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
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Aubert M, Strongin DE, Roychoudhury P, Loprieno MA, Haick AK, Klouser LM, Stensland L, Huang ML, Makhsous N, Tait A, De Silva Feelixge HS, Galetto R, Duchateau P, Greninger AL, Stone D, Jerome KR. Gene editing and elimination of latent herpes simplex virus in vivo. Nat Commun 2020; 11:4148. [PMID: 32811834 PMCID: PMC7435201 DOI: 10.1038/s41467-020-17936-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/17/2020] [Indexed: 11/08/2022] Open
Abstract
We evaluate gene editing of HSV in a well-established mouse model, using adeno-associated virus (AAV)-delivered meganucleases, as a potentially curative approach to treat latent HSV infection. Here we show that AAV-delivered meganucleases, but not CRISPR/Cas9, mediate highly efficient gene editing of HSV, eliminating over 90% of latent virus from superior cervical ganglia. Single-cell RNA sequencing demonstrates that both HSV and individual AAV serotypes are non-randomly distributed among neuronal subsets in ganglia, implying that improved delivery to all neuronal subsets may lead to even more complete elimination of HSV. As predicted, delivery of meganucleases using a triple AAV serotype combination results in the greatest decrease in ganglionic HSV loads. The levels of HSV elimination observed in these studies, if translated to humans, would likely significantly reduce HSV reactivation, shedding, and lesions. Further optimization of meganuclease delivery and activity is likely possible, and may offer a pathway to a cure for HSV infection.
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Affiliation(s)
- Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel E Strongin
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Michelle A Loprieno
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anoria K Haick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lindsay M Klouser
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurence Stensland
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Alexander Tait
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
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3
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Abstract
Gene loci on different chromosomes can preferentially colocalize in the cell nucleus. However, many of the mechanisms mediating this spatial proximity remain to be elucidated. The IgH locus on Chromosome 12 and the Myc locus on Chromosome 15 are a well-studied model for gene colocalization in murine B cells, where the two loci are positioned in close proximity at a higher than expected frequency. These gene loci are also partners in the chromosomal translocation that causes murine plasmacytoma and Burkitt’s lymphoma. Because both Chromosome 12 and Chromosome 15 carry nucleolar organizer regions (NORs) in the most commonly studied mouse strains, we hypothesized that NOR-mediated tethering of the IgH and Myc loci to shared nucleoli could serve as a mechanism to drive IgH:Myc colocalization. Using mouse strains that naturally carry nucleolar organizer regions (NORs) on different sets of chromosomes, we establish that IgH and Myc are positioned proximal to nucleoli in a NOR dependent manner and show that their joint association with nucleoli significantly increases the frequency of IgH and Myc pairing. Thus we demonstrate that simple nucleolar tethering can increase the colocalization frequency of genes on NOR-bearing chromosomes.
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Affiliation(s)
- Daniel E Strongin
- a Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA
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Ali M, Daze KD, Strongin DE, Rothbart SB, Rincon-Arano H, Allen HF, Li J, Strahl BD, Hof F, Kutateladze TG. Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes. J Biol Chem 2015; 290:22919-30. [PMID: 26229108 DOI: 10.1074/jbc.m115.669333] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Indexed: 11/06/2022] Open
Abstract
Plant homeodomain (PHD) finger-containing proteins are implicated in fundamental biological processes, including transcriptional activation and repression, DNA damage repair, cell differentiation, and survival. The PHD finger functions as an epigenetic reader that binds to posttranslationally modified or unmodified histone H3 tails, recruiting catalytic writers and erasers and other components of the epigenetic machinery to chromatin. Despite the critical role of the histone-PHD interaction in normal and pathological processes, selective inhibitors of this association have not been well developed. Here we demonstrate that macrocyclic calixarenes can disrupt binding of PHD fingers to methylated lysine 4 of histone H3 in vitro and in vivo. The inhibitory activity relies on differences in binding affinities of the PHD fingers for H3K4me and the methylation state of the histone ligand, whereas the composition of the aromatic H3K4me-binding site of the PHD fingers appears to have no effect. Our approach provides a novel tool for studying the biological roles of methyllysine readers in epigenetic signaling.
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Affiliation(s)
- Muzaffar Ali
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Kevin D Daze
- the Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Daniel E Strongin
- the Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Scott B Rothbart
- the Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Hector Rincon-Arano
- the Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Hillary F Allen
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Janessa Li
- the Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Brian D Strahl
- the Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Fraser Hof
- the Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada,
| | - Tatiana G Kutateladze
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045,
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5
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Abstract
Like GFP, the fluorescent protein DsRed has a chromophore that forms autocatalytically within the folded protein, but the mechanism of DsRed chromophore formation has been unclear. It was proposed that an initial oxidation generates a green chromophore, and that a final oxidation yields the red chromophore. However, this model does not adequately explain why a mature DsRed sample contains a mixture of green and red chromophores. We present evidence that the maturation pathway for DsRed branches upstream of chromophore formation. After an initial oxidation step, a final oxidation to form the acylimine of the red chromophore is in kinetic competition with a dehydration to form the green chromophore. This scheme explains why green and red chromophores are alternative end points of the maturation pathway.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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Strack RL, Strongin DE, Bhattacharyya D, Tao W, Berman A, Broxmeyer HE, Keenan RJ, Glick BS. A noncytotoxic DsRed variant for whole-cell labeling. Nat Methods 2008; 5:955-7. [PMID: 18953349 DOI: 10.1038/nmeth.1264] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/23/2008] [Indexed: 11/09/2022]
Abstract
A common application of fluorescent proteins is to label whole cells, but many RFPs are cytotoxic when used with standard high-level expression systems. We engineered a rapidly maturing tetrameric fluorescent protein called DsRed-Express2 that has minimal cytotoxicity. DsRed-Express2 exhibits strong and stable expression in bacterial and mammalian cells, and it outperforms other available RFPs with regard to photostability and phototoxicity.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center W238, Chicago, Illinois 60637, USA
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Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ. Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants. Protein Eng Des Sel 2007; 20:525-34. [PMID: 17962222 DOI: 10.1093/protein/gzm046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The red fluorescent protein DsRed has been extensively engineered for use as an in vivo research tool. In fast maturing DsRed variants, the chromophore maturation half-time is approximately 40 min, compared to approximately 12 h for wild-type DsRed. Further, DsRed has been converted from a tetramer into a monomer, a task that entailed mutating approximately 20% of the amino acids. These engineered variants of DsRed have proven extremely valuable for biomedical research, but the structural basis for the improved characteristics has not been thoroughly investigated. Here we present a 1.7 A crystal structure of the fast maturing tetrameric variant DsRed.T4. We also present a biochemical characterization and 1.6 A crystal structure of the monomeric variant DsRed.M1, also known as DsRed-Monomer. Analysis of the crystal structures suggests that rearrangements of Ser69 and Glu215 contribute to fast maturation, and that positioning of the Lys70 side chain modulates fluorescence quantum yield. Despite the 45 mutations in DsRed.M1 relative to wild-type DsRed, there is a root-mean-square deviation of only 0.3 A between the two structures. We propose that novel intramolecular interactions in DsRed.M1 partially compensate for the loss of intermolecular interactions found in the tetramer.
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Affiliation(s)
- Daniel E Strongin
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA
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8
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Losev E, Reinke CA, Jellen J, Strongin DE, Bevis BJ, Glick BS. Golgi maturation visualized in living yeast. Nature 2006; 441:1002-6. [PMID: 16699524 DOI: 10.1038/nature04717] [Citation(s) in RCA: 282] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 03/07/2006] [Indexed: 11/08/2022]
Abstract
The Golgi apparatus is composed of biochemically distinct early (cis, medial) and late (trans, TGN) cisternae. There is debate about the nature of these cisternae. The stable compartments model predicts that each cisterna is a long-lived structure that retains a characteristic set of Golgi-resident proteins. In this view, secretory cargo proteins are transported by vesicles from one cisterna to the next. The cisternal maturation model predicts that each cisterna is a transient structure that matures from early to late by acquiring and then losing specific Golgi-resident proteins. In this view, secretory cargo proteins traverse the Golgi by remaining within the maturing cisternae. Various observations have been interpreted as supporting one or the other mechanism. Here we provide a direct test of the two models using three-dimensional time-lapse fluorescence microscopy of the yeast Saccharomyces cerevisiae. This approach reveals that individual cisternae mature, and do so at a consistent rate. In parallel, we used pulse-chase analysis to measure the transport of two secretory cargo proteins. The rate of cisternal maturation matches the rate of protein transport through the secretory pathway, suggesting that cisternal maturation can account for the kinetics of secretory traffic.
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Affiliation(s)
- Eugene Losev
- Department of Molecular Genetics and Cell Biology, and Institute for Biophysical Dynamics, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
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9
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Connerly PL, Esaki M, Montegna EA, Strongin DE, Levi S, Soderholm J, Glick BS. Sec16 is a determinant of transitional ER organization. Curr Biol 2006; 15:1439-47. [PMID: 16111939 DOI: 10.1016/j.cub.2005.06.065] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2005] [Revised: 06/29/2005] [Accepted: 06/30/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Proteins are exported from the ER at transitional ER (tER) sites, which produce COPII vesicles. However, little is known about how COPII components are concentrated at tER sites. The budding yeast Pichia pastoris contains discrete tER sites and is, therefore, an ideal system for studying tER organization. RESULTS We show that the integrity of tER sites in P. pastoris requires the peripheral membrane protein Sec16. P. pastoris Sec16 is an order of magnitude less abundant than a COPII-coat protein at tER sites and seems to show a saturable association with these sites. A temperature-sensitive mutation in Sec16 causes tER fragmentation at elevated temperature. This effect is specific because when COPII assembly is inhibited with a dominant-negative form of the Sar1 GTPase, tER sites remain intact. The tER fragmentation in the sec16 mutant is accompanied by disruption of Golgi stacks. CONCLUSIONS Our data suggest that Sec16 helps to organize patches of COPII-coat proteins into clusters that represent tER sites. The Golgi disruption that occurs in the sec16 mutant provides evidence that Golgi structure in budding yeasts depends on tER organization.
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Affiliation(s)
- Pamela L Connerly
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60615, USA
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Silver RB, Strongin DE, Hurwitz LR, Reeves AP. Identification of Phospholipase A 2 and Phospholipase C Activities in Calcium Regulatory Endomembranes of Sand Dollar Cells. Biol Bull 1997; 193:236-237. [PMID: 28575619 DOI: 10.1086/bblv193n2p236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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