paper.bib

@article{ojala_vivo_2018,
	title = {In {Vivo} {Selection} of a {Computationally} {Designed} {SCHEMA} {AAV} {Library} {Yields} a {Novel} {Variant} for {Infection} of {Adult} {Neural} {Stem} {Cells} in the {SVZ}},
	volume = {26},
	issn = {1525-0024},
	doi = {10.1016/j.ymthe.2017.09.006},
	abstract = {Directed evolution continues to expand the capabilities of complex biomolecules for a range of applications, such as adeno-associated virus vectors for gene therapy; however, advances in library design and selection strategies are key to develop variants that overcome barriers to clinical translation. To address this need, we applied structure-guided SCHEMA recombination of the multimeric adeno-associated virus (AAV) capsid to generate a highly diversified chimeric library with minimal structural disruption. A stringent in vivo Cre-dependent selection strategy was implemented to identify variants that transduce adult neural stem cells (NSCs) in the subventricular zone. A novel variant, SCH9, infected 60\% of NSCs and mediated 24-fold higher GFP expression and a 12-fold greater transduction volume than AAV9. SCH9 utilizes both galactose and heparan sulfate as cell surface receptors and exhibits increased resistance to neutralizing antibodies. These results establish the SCHEMA library as a valuable tool for directed evolution and SCH9 as an effective gene delivery vector to investigate subventricular NSCs.},
	language = {eng},
	number = {1},
	journal = {Molecular Therapy: The Journal of the American Society of Gene Therapy},
	author = {Ojala, David S. and Sun, Sabrina and Santiago-Ortiz, Jorge L. and Shapiro, Mikhail G. and Romero, Philip A. and Schaffer, David V.},
	year = {2018},
	pmid = {28988711},
	pmcid = {PMC5762983},
	keywords = {Animals, Dependovirus, Gene Transfer Techniques, Genetic Engineering, Genetic Therapy, Genetic Vectors, Humans, Mice, adeno-associated virus, capsid engineering, Capsid Proteins, CNS, directed evolution, Galactose, Gene Library, gene therapy, Genome, Viral, Heparitin Sulfate, Imaging, Three-Dimensional, Lateral Ventricles, Models, Molecular, Mutation, neural stem cell, Neural Stem Cells, Protein Conformation, subventricular zone, Transduction, Genetic},
	pages = {304--319},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\HDW2REVV\\Ojala et al. - 2018 - In Vivo Selection of a Computationally Designed SC.pdf:application/pdf}
}

@article{hanlon_selection_2019,
	title = {Selection of an {Efficient} {AAV} {Vector} for {Robust} {CNS} {Transgene} {Expression}},
	volume = {15},
	issn = {2329-0501},
	doi = {10.1016/j.omtm.2019.10.007},
	abstract = {Adeno-associated virus (AAV) capsid libraries have generated improved transgene delivery vectors. We designed an AAV library construct, iTransduce, that combines a peptide library on the AAV9 capsid with a Cre cassette to enable sensitive detection of transgene expression. After only two selection rounds of the library delivered intravenously in transgenic mice carrying a Cre-inducible fluorescent protein, we flow sorted fluorescent cells from brain, and DNA sequencing revealed two dominant capsids. One of the capsids, termed AAV-F, mediated transgene expression in the brain cortex more than 65-fold (astrocytes) and 171-fold (neurons) higher than the parental AAV9. High transduction efficiency was sex-independent and sustained in two mouse strains (C57BL/6 and BALB/c), making it a highly useful capsid for CNS transduction of mice. Future work in large animal models will test the translation potential of AAV-F.},
	language = {eng},
	journal = {Molecular Therapy. Methods \& Clinical Development},
	author = {Hanlon, Killian S. and Meltzer, Jonah C. and Buzhdygan, Tetyana and Cheng, Ming J. and Sena-Esteves, Miguel and Bennett, Rachel E. and Sullivan, Timothy P. and Razmpour, Roshanak and Gong, Yi and Ng, Carrie and Nammour, Josette and Maiz, Daniela and Dujardin, Simon and Ramirez, Servio H. and Hudry, Eloise and Maguire, Casey A.},
	month = dec,
	year = {2019},
	pmid = {31788496},
	pmcid = {PMC6881693},
	keywords = {gene therapy, AAV capsid library, AAV vector, adeno-associated virus vector, central nervous system, gene delivery, transduction efficiency},
	pages = {320--332},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\EEH8J9N2\\Hanlon et al. - 2019 - Selection of an Efficient AAV Vector for Robust CN.pdf:application/pdf}
}

@article{deverman_cre-dependent_2016,
	title = {Cre-dependent selection yields {AAV} variants for widespread gene transfer to the adult brain},
	volume = {34},
	issn = {1546-1696},
	doi = {10.1038/nbt.3440},
	abstract = {Recombinant adeno-associated viruses (rAAVs) are commonly used vehicles for in vivo gene transfer. However, the tropism repertoire of naturally occurring AAVs is limited, prompting a search for novel AAV capsids with desired characteristics. Here we describe a capsid selection method, called Cre recombination-based AAV targeted evolution (CREATE), that enables the development of AAV capsids that more efficiently transduce defined Cre-expressing cell populations in vivo. We use CREATE to generate AAV variants that efficiently and widely transduce the adult mouse central nervous system (CNS) after intravenous injection. One variant, AAV-PHP.B, transfers genes throughout the CNS with an efficiency that is at least 40-fold greater than that of the current standard, AAV9 (refs. 14,15,16,17), and transduces the majority of astrocytes and neurons across multiple CNS regions. In vitro, it transduces human neurons and astrocytes more efficiently than does AAV9, demonstrating the potential of CREATE to produce customized AAV vectors for biomedical applications.},
	language = {eng},
	number = {2},
	journal = {Nature Biotechnology},
	author = {Deverman, Benjamin E. and Pravdo, Piers L. and Simpson, Bryan P. and Kumar, Sripriya Ravindra and Chan, Ken Y. and Banerjee, Abhik and Wu, Wei-Li and Yang, Bin and Huber, Nina and Pasca, Sergiu P. and Gradinaru, Viviana},
	month = feb,
	year = {2016},
	pmid = {26829320},
	pmcid = {PMC5088052},
	keywords = {Animals, Dependovirus, Female, Genetic Engineering, Genetic Vectors, Humans, Mice, HEK293 Cells, Integrases, Transfection},
	pages = {204--209},
	file = {Accepted Version:C\:\\Users\\damien.marsic\\Zotero\\storage\\9GPM4DE7\\Deverman et al. - 2016 - Cre-dependent selection yields AAV variants for wi.pdf:application/pdf}
}

@article{excoffon_directed_2009,
	title = {Directed evolution of adeno-associated virus to an infectious respiratory virus},
	volume = {106},
	issn = {1091-6490},
	doi = {10.1073/pnas.0813365106},
	abstract = {Respiratory viruses evolve to maintain infectivity levels that permit spread yet prevent host and virus extinction, resulting in surprisingly low infection rates. Respiratory viruses harnessed as gene therapy vectors have illustrated this limitation. We used directed evolution in an organotypic human airway model to generate a highly infectious adeno-associated virus. This virus mediated gene transfer more than 100-fold better than parental strains and corrected the cystic fibrosis epithelial Cl(-) transport defect. Thus, under appropriate selective pressures, viruses can evolve to be more infectious than observed in nature, a finding that holds significant implications for designing vectors for gene therapy and for understanding emerging pathogens.},
	language = {eng},
	number = {10},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Excoffon, Katherine J. D. A. and Koerber, James T. and Dickey, David D. and Murtha, Matthew and Keshavjee, Shaf and Kaspar, Brian K. and Zabner, Joseph and Schaffer, David V.},
	month = mar,
	year = {2009},
	pmid = {19237554},
	pmcid = {PMC2646629},
	keywords = {Animals, Dependovirus, Genetic Vectors, Humans, Gene Library, Models, Molecular, Mutation, Transduction, Genetic, Capsid, Cell Line, Cell Polarity, Cystic Fibrosis, Cystic Fibrosis Transmembrane Conductance Regulator, Directed Molecular Evolution, Epithelial Cells, N-Acetylneuraminic Acid, Parvoviridae Infections, Phenotype, Selection, Genetic, Virus Attachment},
	pages = {3865--3870},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\TPQY2K9I\\Excoffon et al. - 2009 - Directed evolution of adeno-associated virus to an.pdf:application/pdf}
}

@article{marsic_vector_2014,
	title = {Vector design {Tour} de {Force}: integrating combinatorial and rational approaches to derive novel adeno-associated virus variants},
	volume = {22},
	copyright = {All rights reserved},
	issn = {1525-0024},
	shorttitle = {Vector design {Tour} de {Force}},
	doi = {10.1038/mt.2014.139},
	abstract = {Methodologies to improve existing adeno-associated virus (AAV) vectors for gene therapy include either rational approaches or directed evolution to derive capsid variants characterized by superior transduction efficiencies in targeted tissues. Here, we integrated both approaches in one unified design strategy of "virtual family shuffling" to derive a combinatorial capsid library whereby only variable regions on the surface of the capsid are modified. Individual sublibraries were first assembled in order to preselect compatible amino acid residues within restricted surface-exposed regions to minimize the generation of dead-end variants. Subsequently, the successful families were interbred to derive a combined library of {\textasciitilde}8 × 10(5) complexity. Next-generation sequencing of the packaged viral DNA revealed capsid surface areas susceptible to directed evolution, thus providing guidance for future designs. We demonstrated the utility of the library by deriving an AAV2-based vector characterized by a 20-fold higher transduction efficiency in murine liver, now equivalent to that of AAV8.},
	language = {eng},
	number = {11},
	journal = {Molecular Therapy: The Journal of the American Society of Gene Therapy},
	author = {Marsic, Damien and Govindasamy, Lakshmanan and Currlin, Seth and Markusic, David M. and Tseng, Yu-Shan and Herzog, Roland W. and Agbandje-McKenna, Mavis and Zolotukhin, Sergei},
	month = nov,
	year = {2014},
	pmid = {25048217},
	pmcid = {PMC4429732},
	keywords = {Animals, Dependovirus, Genetic Therapy, Genetic Vectors, Humans, Mice, Mice, Inbred C57BL, Capsid Proteins, Gene Library, Transduction, Genetic, HEK293 Cells, Amino Acid Sequence, Amino Acids, DNA, Viral, High-Throughput Nucleotide Sequencing, Liver, Male, Organ Specificity, Sequence Analysis, DNA},
	pages = {1900--1909},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\E2RDKZMG\\Marsic et al. - 2014 - Vector design Tour de Force integrating combinato.pdf:application/pdf}
}

@article{paulk_bioengineered_2018,
	title = {Bioengineered {AAV} {Capsids} with {Combined} {High} {Human} {Liver} {Transduction} {In} {Vivo} and {Unique} {Humoral} {Seroreactivity}},
	volume = {26},
	issn = {1525-0024},
	doi = {10.1016/j.ymthe.2017.09.021},
	abstract = {Existing recombinant adeno-associated virus (rAAV) serotypes for delivering in vivo gene therapy treatments for human liver diseases have not yielded combined high-level human hepatocyte transduction and favorable humoral neutralization properties in diverse patient groups. Yet, these combined properties are important for therapeutic efficacy. To bioengineer capsids that exhibit both unique seroreactivity profiles and functionally transduce human hepatocytes at therapeutically relevant levels, we performed multiplexed sequential directed evolution screens using diverse capsid libraries in both primary human hepatocytes in vivo and with pooled human sera from thousands of patients. AAV libraries were subjected to five rounds of in vivo selection in xenografted mice with human livers to isolate an enriched human-hepatotropic library that was then used as input for a sequential on-bead screen against pooled human immunoglobulins. Evolved variants were vectorized and validated against existing hepatotropic serotypes. Two of the evolved AAV serotypes, NP40 and NP59, exhibited dramatically improved functional human hepatocyte transduction in vivo in xenografted mice with human livers, along with favorable human seroreactivity profiles, compared with existing serotypes. These novel capsids represent enhanced vector delivery systems for future human liver gene therapy applications.},
	language = {eng},
	number = {1},
	journal = {Molecular Therapy: The Journal of the American Society of Gene Therapy},
	author = {Paulk, Nicole K. and Pekrun, Katja and Zhu, Erhua and Nygaard, Sean and Li, Bin and Xu, Jianpeng and Chu, Kirk and Leborgne, Christian and Dane, Allison P. and Haft, Annelise and Zhang, Yue and Zhang, Feijie and Morton, Chris and Valentine, Marcus B. and Davidoff, Andrew M. and Nathwani, Amit C. and Mingozzi, Federico and Grompe, Markus and Alexander, Ian E. and Lisowski, Leszek and Kay, Mark A.},
	year = {2018},
	pmid = {29055620},
	pmcid = {PMC5763027},
	keywords = {Animals, Dependovirus, Female, Gene Transfer Techniques, Genetic Engineering, Genetic Vectors, Humans, Mice, Capsid Proteins, Models, Molecular, Protein Conformation, Transduction, Genetic, Liver, Male, AAV, Hepatocytes, evolution, hepatocyte, Heterografts, human, library, liver, neutralization, screen, transduction},
	pages = {289--303},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\FY2WGKBZ\\Paulk et al. - 2018 - Bioengineered AAV Capsids with Combined High Human.pdf:application/pdf}
}

@article{powell_characterization_2016,
	title = {Characterization of a novel adeno-associated viral vector with preferential oligodendrocyte tropism},
	volume = {23},
	issn = {1476-5462},
	doi = {10.1038/gt.2016.62},
	abstract = {No adeno-associated virus (AAV) capsid has been described in the literature to exhibit a primary oligodendrocyte tropism when a constitutive promoter drives gene expression, which is a significant barrier for efficient in vivo oligodendrocyte gene transfer. The vast majority of AAV vectors, such as AAV1, 2, 5, 6, 8 or 9, exhibit a dominant neuronal tropism in the central nervous system. However, a novel AAV capsid (Olig001) generated using capsid shuffling and directed evolution was recovered after rat intravenous delivery and subsequent capsid clone rescue, which exhibited a {\textgreater}95\% tropism for striatal oligodendrocytes after rat intracranial infusion where a constitutive promoter drove gene expression. Olig001 contains a chimeric mixture of AAV1, 2, 6, 8 and 9, but unlike these parental serotypes after intravenous administration Olig001 has very low affinity for peripheral organs, especially the liver. Furthermore, in mixed glial cell cultures, Olig001 exhibits a 9-fold greater binding when compared with AAV8. This novel oligodendrocyte-preferring AAV vector exhibits characteristics that are a marked departure from previously described AAV serotypes.},
	language = {eng},
	number = {11},
	journal = {Gene Therapy},
	author = {Powell, S. K. and Khan, N. and Parker, C. L. and Samulski, R. J. and Matsushima, G. and Gray, S. J. and McCown, T. J.},
	year = {2016},
	pmid = {27628693},
	pmcid = {PMC5541369},
	keywords = {Animals, Dependovirus, Female, Gene Transfer Techniques, Genetic Therapy, Genetic Vectors, Humans, Mice, Mice, Inbred C57BL, Capsid Proteins, HEK293 Cells, Male, Infusions, Intraventricular, Injections, Intravenous, Oligodendroglia, Promoter Regions, Genetic, Rats, Rats, Sprague-Dawley},
	pages = {807--814},
	file = {Accepted Version:C\:\\Users\\damien.marsic\\Zotero\\storage\\LYKJAKHN\\Powell et al. - 2016 - Characterization of a novel adeno-associated viral.pdf:application/pdf}
}

@article{asokan_reengineering_2010,
	title = {Reengineering a receptor footprint of adeno-associated virus enables selective and systemic gene transfer to muscle},
	volume = {28},
	issn = {1546-1696},
	doi = {10.1038/nbt.1599},
	abstract = {Reengineering the receptor footprints of adeno-associated virus (AAV) isolates may yield variants with improved properties for clinical applications. We generated a panel of synthetic AAV2 vectors by replacing a hexapeptide sequence in a previously identified heparan sulfate receptor footprint with corresponding residues from other AAV strains. This approach yielded several chimeric capsids displaying systemic tropism after intravenous administration in mice. Of particular interest, an AAV2/AAV8 chimera designated AAV2i8 displayed an altered antigenic profile, readily traversed the blood vasculature, and selectively transduced cardiac and whole-body skeletal muscle tissues with high efficiency. Unlike other AAV serotypes, which are preferentially sequestered in the liver, AAV2i8 showed markedly reduced hepatic tropism. These features of AAV2i8 suggest that it is well suited to translational studies in gene therapy of musculoskeletal disorders.},
	language = {eng},
	number = {1},
	journal = {Nature Biotechnology},
	author = {Asokan, Aravind and Conway, Julia C. and Phillips, Jana L. and Li, Chengwen and Hegge, Julia and Sinnott, Rebecca and Yadav, Swati and DiPrimio, Nina and Nam, Hyun-Joo and Agbandje-McKenna, Mavis and McPhee, Scott and Wolff, Jon and Samulski, R. Jude},
	month = jan,
	year = {2010},
	pmid = {20037580},
	pmcid = {PMC2912150},
	keywords = {Animals, Dependovirus, Gene Transfer Techniques, Genetic Engineering, Genetic Vectors, Mice, Models, Molecular, Organ Specificity, Viral Tropism, Muscles, Receptors, Virus, Structure-Activity Relationship},
	pages = {79--82},
	file = {Accepted Version:C\:\\Users\\damien.marsic\\Zotero\\storage\\HYT2HS3Z\\Asokan et al. - 2010 - Reengineering a receptor footprint of adeno-associ.pdf:application/pdf}
}

@article{petrs-silva_novel_2011,
	title = {Novel properties of tyrosine-mutant {AAV2} vectors in the mouse retina},
	volume = {19},
	issn = {1525-0024},
	doi = {10.1038/mt.2010.234},
	abstract = {Vectors based on adeno-associated virus serotype 2 (AAV2) have been used extensively in many gene-delivery applications, including several successful clinical trials for one type of Leber congenital amaurosis in the retina. Many studies have focused on improving AAV2 transduction efficiency and cellular specificity by genetically engineering its capsid. We have previously shown that vectors-containing single-point mutations of capsid surface tyrosines in serotypes AAV2, AAV8, and AAV9 displayed significantly increased transduction efficiency in the retina compared with their wild-type counterparts. In the present study, we evaluated the transduction characteristics of AAV2 vectors containing combinations of multiple tyrosine to phenylalanine mutations in seven highly conserved surface-exposed capsid tyrosine residues following subretinal or intravitreal delivery in adult mice. The multiply mutated vectors exhibited different in vivo transduction properties, with some having a unique ability of transgene expression in all retinal layers. Such novel vectors may be useful in developing valuable new therapeutic strategies for the treatment of many genetic diseases.},
	language = {eng},
	number = {2},
	journal = {Molecular Therapy: The Journal of the American Society of Gene Therapy},
	author = {Petrs-Silva, Hilda and Dinculescu, Astra and Li, Qiuhong and Deng, Wen-Tao and Pang, Ji-Jing and Min, Seok-Hong and Chiodo, Vince and Neeley, Andy W. and Govindasamy, Lakshmanan and Bennett, Antonette and Agbandje-McKenna, Mavis and Zhong, Li and Li, Baozheng and Jayandharan, Giridhara R. and Srivastava, Arun and Lewin, Alfred S. and Hauswirth, William W.},
	month = feb,
	year = {2011},
	pmid = {21045809},
	pmcid = {PMC3034844},
	keywords = {Animals, Dependovirus, Genetic Vectors, Mice, Mice, Inbred C57BL, Mutation, Retina, Tyrosine, Mutagenesis, Site-Directed, Point Mutation},
	pages = {293--301},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\6BCX86CT\\Petrs-Silva et al. - 2011 - Novel properties of tyrosine-mutant AAV2 vectors i.pdf:application/pdf}
}

@article{tervo_designer_2016,
	title = {A {Designer} {AAV} {Variant} {Permits} {Efficient} {Retrograde} {Access} to {Projection} {Neurons}},
	volume = {92},
	issn = {1097-4199},
	doi = {10.1016/j.neuron.2016.09.021},
	abstract = {Efficient retrograde access to projection neurons for the delivery of sensors and effectors constitutes an important and enabling capability for neural circuit dissection. Such an approach would also be useful for gene therapy, including the treatment of neurodegenerative disorders characterized by pathological spread through functionally connected and highly distributed networks. Viral vectors, in particular, are powerful gene delivery vehicles for the nervous system, but all available tools suffer from inefficient retrograde transport or limited clinical potential. To address this need, we applied in vivo directed evolution to engineer potent retrograde functionality into the capsid of adeno-associated virus (AAV), a vector that has shown promise in neuroscience research and the clinic. A newly evolved variant, rAAV2-retro, permits robust retrograde access to projection neurons with efficiency comparable to classical synthetic retrograde tracers and enables sufficient sensor/effector expression for functional circuit interrogation and in vivo genome editing in targeted neuronal populations. VIDEO ABSTRACT.},
	language = {eng},
	number = {2},
	journal = {Neuron},
	author = {Tervo, D. Gowanlock R. and Hwang, Bum-Yeol and Viswanathan, Sarada and Gaj, Thomas and Lavzin, Maria and Ritola, Kimberly D. and Lindo, Sarah and Michael, Susan and Kuleshova, Elena and Ojala, David and Huang, Cheng-Chiu and Gerfen, Charles R. and Schiller, Jackie and Dudman, Joshua T. and Hantman, Adam W. and Looger, Loren L. and Schaffer, David V. and Karpova, Alla Y.},
	month = oct,
	year = {2016},
	pmid = {27720486},
	pmcid = {PMC5872824},
	keywords = {Animals, Dependovirus, Female, Gene Transfer Techniques, Genetic Vectors, Mice, Capsid, Male, Rats, Cerebellum, Gene Editing, Neurons},
	pages = {372--382},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\E838AHNC\\Tervo et al. - 2016 - A Designer AAV Variant Permits Efficient Retrograd.pdf:application/pdf}
}

@article{gruning_bioconda_2018,
	title = {Bioconda: sustainable and comprehensive software distribution for the life sciences},
	volume = {15},
	issn = {1548-7105},
	shorttitle = {Bioconda},
	doi = {10.1038/s41592-018-0046-7},
	language = {eng},
	number = {7},
	journal = {Nature Methods},
	author = {Grüning, Björn and Dale, Ryan and Sjödin, Andreas and Chapman, Brad A. and Rowe, Jillian and Tomkins-Tinch, Christopher H. and Valieris, Renan and Köster, Johannes and {Bioconda Team}},
	year = {2018},
	pmid = {29967506},
	keywords = {Computational Biology, Software, User-Computer Interface},
	pages = {475--476},
	file = {Submitted Version:C\:\\Users\\damien.marsic\\Zotero\\storage\\L54584PW\\Grüning et al. - 2018 - Bioconda sustainable and comprehensive software d.pdf:application/pdf}
}

@article{herrmann_robust_2019,
	title = {A {Robust} and {All}-{Inclusive} {Pipeline} for {Shuffling} of {Adeno}-{Associated} {Viruses}},
	volume = {8},
	issn = {2161-5063},
	doi = {10.1021/acssynbio.8b00373},
	abstract = {Adeno-associated viruses (AAV) are attractive templates for engineering of synthetic gene delivery vectors. A particularly powerful technology for breeding of novel vectors with improved properties is DNA family shuffling, i.e., generation of chimeric capsids by homology-driven DNA recombination. Here, to make AAV DNA shuffling available to a wider community, we present a robust experimental and bioinformatical pipeline comprising: (i) standardized and partially codon-optimized plasmids carrying 12 different AAV capsid genes; (ii) a scalable protocol including troubleshooting guide for viral library production; and (iii) the freely available software SALANTO for comprehensive analysis of chimeric AAV DNA and protein sequences. Moreover, we describe a set of 12 premade and ready-to-use AAV libraries. Finally, we demonstrate the usefulness of DNA barcoding technology to trace AAV capsid libraries within a complex mixture. Our protocols and resources facilitate the implementation and tailoring of AAV evolution technology in any laboratory interested in customized viral gene transfer.},
	language = {eng},
	number = {1},
	journal = {ACS synthetic biology},
	author = {Herrmann, Anne-Kathrin and Bender, Christian and Kienle, Eike and Grosse, Stefanie and El Andari, Jihad and Botta, Julia and Schürmann, Nina and Wiedtke, Ellen and Niopek, Dominik and Grimm, Dirk},
	year = {2019},
	pmid = {30513195},
	keywords = {Dependovirus, Evolution, Molecular, Gene Transfer Techniques, Genetic Vectors, AAV, Adeno-associated virus, DNA family shuffling, DNA recombination, molecular evolution, virus engineering},
	pages = {194--206}
}

@article{grimm_vitro_2008,
	title = {In {Vitro} and {In} {Vivo} {Gene} {Therapy} {Vector} {Evolution} via {Multispecies} {Interbreeding} and {Retargeting} of {Adeno}-{Associated} {Viruses}},
	volume = {82},
	issn = {0022-538X, 1098-5514},
	url = {https://JVI.asm.org/content/82/12/5887},
	doi = {10.1128/JVI.00254-08},
	abstract = {ABSTRACT
            Adeno-associated virus (AAV) serotypes differ broadly in transduction efficacies and tissue tropisms and thus hold enormous potential as vectors for human gene therapy. In reality, however, their use in patients is restricted by prevalent anti-AAV immunity or by their inadequate performance in specific targets, exemplified by the AAV type 2 (AAV-2) prototype in the liver. Here, we attempted to merge desirable qualities of multiple natural AAV isolates by an adapted DNA family shuffling technology to create a complex library of hybrid capsids from eight different wild-type viruses. Selection on primary or transformed human hepatocytes yielded pools of hybrids from five of the starting serotypes: 2, 4, 5, 8, and 9. More stringent selection with pooled human antisera (intravenous immunoglobulin [IVIG]) then led to the selection of a single type 2/type 8/type 9 chimera, AAV-DJ, distinguished from its closest natural relative (AAV-2) by 60 capsid amino acids. Recombinant AAV-DJ vectors outperformed eight standard AAV serotypes in culture and greatly surpassed AAV-2 in livers of naïve and IVIG-immunized mice. A heparin binding domain in AAV-DJ was found to limit biodistribution to the liver (and a few other tissues) and to affect vector dose response and antibody neutralization. Moreover, we report the first successful in vivo biopanning of AAV capsids by using a new AAV-DJ-derived viral peptide display library. Two peptides enriched after serial passaging in mouse lungs mediated the retargeting of AAV-DJ vectors to distinct alveolar cells. Our study validates DNA family shuffling and viral peptide display as two powerful and compatible approaches to the molecular evolution of novel AAV vectors for human gene therapy applications.},
	language = {en},
	number = {12},
	urldate = {2020-11-18},
	journal = {Journal of Virology},
	author = {Grimm, Dirk and Lee, Joyce S. and Wang, Lora and Desai, Tushar and Akache, Bassel and Storm, Theresa A. and Kay, Mark A.},
	month = jun,
	year = {2008},
	pages = {5887--5911},
	file = {Full Text:C\:\\Users\\damien.marsic\\Zotero\\storage\\2R3ZJ47H\\Grimm et al. - 2008 - In Vitro and In Vivo Gene Therapy Vector Evolution.pdf:application/pdf}
}

@article{dalkara_vivo-directed_2013,
	title = {In {Vivo}-{Directed} {Evolution} of a {New} {Adeno}-{Associated} {Virus} for {Therapeutic} {Outer} {Retinal} {Gene} {Delivery} from the {Vitreous}},
	volume = {5},
	issn = {1946-6234, 1946-6242},
	url = {https://stm.sciencemag.org/lookup/doi/10.1126/scitranslmed.3005708},
	doi = {10.1126/scitranslmed.3005708},
	language = {en},
	number = {189},
	urldate = {2020-11-18},
	journal = {Science Translational Medicine},
	author = {Dalkara, D. and Byrne, L. C. and Klimczak, R. R. and Visel, M. and Yin, L. and Merigan, W. H. and Flannery, J. G. and Schaffer, D. V.},
	month = jun,
	year = {2013},
	pages = {189ra76--189ra76}
}