Name: production of adeno-associated virus vectors in cell stacks for preclinical studies in large animal models
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Amira D. Rghei, Brenna A. Y. Stevens, Sylvia P. Thomas, and Jacob G. E. Yates were recipients of Ontario Veterinary College Student Stipends as well as Ontario Graduate Scholarships. Amira D. Rghei was the recipient of a Mitacs Accelerate Studentship. This work was funded by the Canadian Institutes for Health Research (CIHR) Project Grant (#66009) and a Collaborative Health Research Projects (NSERC partnered) grant (#433339) to SKW.

1. Double plasmid transfection of HEK293 cells in cell stacks
<ol>
	<li>Thaw a cryo-vial of HEK293 cells in a bead bath set at 37 &#176;C. 
	NOTE: Pre-warm complete DMEM to 37 &#176;C while cells are thawing to ensure the cold temperature does not shock cells when plating. Ensure the cells have a low passage number, ideally less than 20, to ensure optimal growth and transfection efficiency. Ensure that the cells are certified to be mycoplasma-free.</li>
	<li>Transfer the contents of the cryo-vial dropwise into a 1...

<ol>
	<li>Hastie, E., Samulski, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adeno-associated+virus+at+50:+A+golden+anniversary+of+discovery,+research,+and+gene+therapy+success-a+personal+perspective.">Adeno-associated virus at 50: A golden anniversary of discovery, research, and gene therapy success-a personal perspective.</a> Human Gene Therapy. 26 (5), 257-265 (2015).</li><li>Wang, D., Tai, P. W. L., Gao, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adeno-associated+virus+vector+as+a+platform+for+gene+therapy+delivery.">Adeno-associated virus vector as a platform for gene therapy delivery.</a> Nature Reviews Drug Discovery. 18 (5), 358-378 (2019).</li><li>Nathwani, A. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+safety+and+efficacy+of+factor+IX+gene+therapy+in+hemophilia+B.">Long-term safety and efficacy of factor IX gene therapy in hemophilia B.</a> The New England Journal of Medicine. 371 (21), 1994-2004 (2014).</li><li>Kuzmin, D. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+clinical+landscape+for+AAV+gene+therapies.">The clinical landscape for AAV gene therapies.</a> Nature Reviews Drug Discovery. 20 (3), 173-174 (2021).</li><li>Yl&#228;-Herttuala, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endgame:+glybera+finally+recommended+for+approval+as+the+first+gene+therapy+drug+in+the+European+union.">Endgame: glybera finally recommended for approval as the first gene therapy drug in the European union.</a> Molecular Therapy: The Journal of the American Society of Gene Therapy. 20 (10), 1831-1832 (2012).</li><li>FDA approves novel gene therapy to treat patients with a rare form of inherited vision loss. FDA News Release. FDA Available from: <a target="_blank" href="https://www.fda.gov/news-events/press-announcements/fda-approves-novel-gene-therapy-treat-patients-rare-form-inherited-vision-loss">https://www.fda.gov/news-events/press-announcements/fda-approves-novel-gene-therapy-treat-patients-rare-form-inherited-vision-loss</a> (2020)</li><li>FDA approves innovative gene therapy to treat pediatric patients with spinal muscular atrophy, a rare disease and leading genetic cause of infant mortality. FDA News Release. FDA Available from: <a target="_blank" href="https://www.fda.gov/news-events/press-announcements/fda-approves-innovative-gene-therapy-treat-pediatric-patients-spinal-muscular-atrophy-rare-disease">https://www.fda.gov/news-events/press-announcements/fda-approves-innovative-gene-therapy-treat-pediatric-patients-spinal-muscular-atrophy-rare-disease</a> (2020)</li><li>Statement from FDA Commissioner Scott Gottlieb, MD and Peter Marks, MD Ph.D., Director of the Center for Biologics Evaluation and Research on new policies to advance development of safe and effective cell and gene therapies. FDA Available from: <a target="_blank" href="https://www.fda.gov/news-events/press-announcements/statement-fda-commissioner-scott-gottlieb-md-and-peter-marks-md-phd-director-center-biologics">https://www.fda.gov/news-events/press-announcements/statement-fda-commissioner-scott-gottlieb-md-and-peter-marks-md-phd-director-center-biologics</a> (2020)</li><li>Asokan, A., Schaffer, D. V., Samulski, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+AAV+vector+toolkit:+poised+at+the+clinical+crossroads.">The AAV vector toolkit: poised at the clinical crossroads.</a> Molecular Therapy: The Journal of the American Society of Gene Therapy. 20 (4), 699-708 (2012).</li><li>Rose, J. A., Hoggan, M. D., Shatkin, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nucleic+acid+from+an+adeno-associated+virus:+chemical+and+physical+studies.">Nucleic acid from an adeno-associated virus: chemical and physical studies.</a> Proceedings of the National Academy of Sciences of the United States of America. 56 (1), 86-92 (1966).</li><li>Lusby, E., Fife, K. H., Berns, K. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nucleotide+sequence+of+the+inverted+terminal+repetition+in+adeno-associated+virus+DNA.">Nucleotide sequence of the inverted terminal repetition in adeno-associated virus DNA.</a> Journal of Virology. 34 (2), 402-409 (1980).</li><li>Masat, E., Pavani, G., Mingozzi, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Humoral+immunity+to+AAV+vectors+in+gene+therapy:+challenges+and+potential+solutions.">Humoral immunity to AAV vectors in gene therapy: challenges and potential solutions.</a> Discovery Medicine. 15 (85), 379-389 (2013).</li><li>Ling, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhanced+Transgene+Expression+from+Recombinant+Single-Stranded+D-Sequence-Substituted+Adeno-Associated+Virus+Vectors+in+Human+Cell+Lines+In+Vitro+and+in+Murine+Hepatocytes+In+Vivo.">Enhanced Transgene Expression from Recombinant Single-Stranded D-Sequence-Substituted Adeno-Associated Virus Vectors in Human Cell Lines In Vitro and in Murine Hepatocytes In Vivo.</a> Journal of Virology. 89 (2), 952-961 (2014).</li><li>Cathomen, T., Stracker, T. H., Gilbert, L. B., Weitzman, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+genetic+screen+identifies+a+cellular+regulator+of+adeno-associated+virus.">A genetic screen identifies a cellular regulator of adeno-associated virus.</a> Proceedings of the National Academy of Sciences of the United States of America. 98 (26), 14991-14996 (2001).</li><li>McCarty, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-complementary+AAV+vectors;+advances+and+applications.">Self-complementary AAV vectors; advances and applications.</a> Molecular Therapy. 16 (10), 1648-1656 (2008).</li><li>Aschauer, D. F., Kreuz, S., Rumpel, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+transduction+efficiency,+tropism+and+axonal+transport+of+aav+serotypes+1,+2,+5,+6,+8+and+9+in+the+mouse+brain.">Analysis of transduction efficiency, tropism and axonal transport of aav serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain.</a> PLOS One. 8 (9), 76310 (2013).</li><li>Zincarelli, C., Soltys, S., Rengo, G., Rabinowitz, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+AAV+serotypes+1-9+mediated+gene+expression+and+tropism+in+mice+after+systemic+injection.">Analysis of AAV serotypes 1-9 mediated gene expression and tropism in mice after systemic injection.</a> Molecular Therapy. 16 (6), 1073-1080 (2008).</li><li>Pillay, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adeno-associated+virus+(AAV)+serotypes+have+distinctive+interactions+with+domains+of+the+cellular+AAV+receptor.">Adeno-associated virus (AAV) serotypes have distinctive interactions with domains of the cellular AAV receptor.</a> Journal of Virology. 91 (18), (2017).</li><li>Merkel, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trafficking+of+adeno-associated+virus+vectors+across+a+model+of+the+blood-brain+barrier;+a+comparative+study+of+transcytosis+and+transduction+using+primary+human+brain+endothelial+cells.">Trafficking of adeno-associated virus vectors across a model of the blood-brain barrier; a comparative study of transcytosis and transduction using primary human brain endothelial cells.</a> Journal of Neurochemistry. 140 (2), 216-230 (2017).</li><li>van Lieshout, L. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+triple-mutant+AAV6+capsid+induces+rapid+and+potent+transgene+expression+in+the+muscle+and+respiratory+tract+of+mice.">A novel triple-mutant AAV6 capsid induces rapid and potent transgene expression in the muscle and respiratory tract of mice.</a> Molecular Therapy. Methods &amp; Clinical Development. 9, 323-329 (2018).</li><li>Wu, Z., Asokan, A., Grieger, J. C., Govindasamy, L., Agbandje-McKenna, M., Samulski, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=single+amino+acid+changes+can+influence+titer,+heparin+binding,+and+tissue+tropism+in+different+adeno-associated+virus+serotypes.">single amino acid changes can influence titer, heparin binding, and tissue tropism in different adeno-associated virus serotypes.</a> Journal of Virology. 80 (22), 11393-11397 (2006).</li><li>Liu, J., Moon, Y. -. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+purification+of+adeno-associated+virus-DJ+for+liver-specific+gene+expression.">Simple purification of adeno-associated virus-DJ for liver-specific gene expression.</a> Yonsei Medical Journal. 57 (3), 790-794 (2016).</li><li>Grimm, D., Kern, A., Rittner, K., Kleinschmidt, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+tools+for+production+and+purification+of+recombinant+adeno-associated+virus+vectors.">Novel tools for production and purification of recombinant adeno-associated virus vectors.</a> Human Gene Therapy. 9 (18), 2745-2760 (1998).</li><li>Kimura, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production+of+adeno-associated+virus+vectors+for+in+vitro+and+in+vivo+applications.">Production of adeno-associated virus vectors for in vitro and in vivo applications.</a> Scientific Reports. 9 (1), 13601 (2019).</li><li>Aurnhammer, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Universal+real-time+PCR+for+the+detection+and+quantification+of+adeno-associated+virus+serotype+2-derived+inverted+terminal+repeat+sequences.">Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences.</a> Human Gene Therapy Methods. 23 (1), 18-28 (2012).</li><li>. Paramyxoviridae: The viruses and their replication. Fields Virology Available from: <a target="_blank" href="https://www.scholars.northwestern.edu/en/publications/paramyxoviridae-the-viruses-and-their-replication">https://www.scholars.northwestern.edu/en/publications/paramyxoviridae-the-viruses-and-their-replication</a> (1996)</li><li>Boussif, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+versatile+vector+for+gene+and+oligonucleotide+transfer+into+cells+in+culture+and+in+vivo:+polyethylenimine.">A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine.</a> Proceedings of the National Academy of Sciences of the United States of America. 92 (16), 7297-7301 (1995).</li><li>Kaludov, N., Brown, K. E., Walters, R. W., Zabner, J., Chiorini, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adeno-associated+virus+serotype+4+(AAV4)+and+AAV5+Both+require+sialic+acid+binding+for+hemagglutination+and+efficient+transduction+but+differ+in+sialic+acid+linkage+specificity.">Adeno-associated virus serotype 4 (AAV4) and AAV5 Both require sialic acid binding for hemagglutination and efficient transduction but differ in sialic acid linkage specificity.</a> Journal of Virology. 75 (15), 6884-6893 (2001).</li><li>Burnham, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+ultracentrifugation+as+an+approach+to+characterize+recombinant+adeno-associated+viral+vectors.">Analytical ultracentrifugation as an approach to characterize recombinant adeno-associated viral vectors.</a> Human Gene Therapy Methods. 26 (6), 228-242 (2015).</li><li>Dobnik, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accurate+quantification+and+characterization+of+adeno-associated+viral+vectors.">Accurate quantification and characterization of adeno-associated viral vectors.</a> Frontiers in Microbiology. 10, 1570 (2019).</li><li>Backovic, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capsid+protein+expression+and+adeno-associated+virus+like+particles+assembly+in+Saccharomyces+cerevisiae.">Capsid protein expression and adeno-associated virus like particles assembly in Saccharomyces cerevisiae.</a> Microbial Cell Factories. 11, 124 (2012).</li></ol>

The production of recombinant AAV (rAAV) vectors described in this paper uses common materials, reagents, and equipment found in majority of the molecular biology research labs and facilities. This paper allows for high-quality in vitro and in vivo grade rAAV to be produced by the reader. Above all, this protocol for rAAV production, compared to more tedious protocols involving cesium chloride purification, is efficient and avoids the use of ultracentrifugation. Once HEK293 cells have been transfected, ...

Gene therapy utilizing adeno-associated virus (AAV) vectors has made huge strides over the past three decades1,2. Demonstrated improvements in a diverse range of genetic diseases, including congenital blindness, hemophilia, and diseases of the musculoskeletal and central nervous system, have brought AAV gene therapy to the forefront of clinical research3,4. In 2012, the European Medicines Agency (EMA) approved Glybera, an AAV1 vector expressing lipoprotein lipase (LPL) for the treatment of LPL deficiency, making it the first marketing authorization for a gene therapy treatment in either Europe or the United States5. Since then, two additional AAV gene therapies, Luxturna6 and Zolgensma7, have received FDA approval, and the market is expected to expand quickly over the next 5 years with as many as 10-20 gene therapies expected by 20258. Available clinical data indicate that AAV gene therapy is a safe, well-tolerated, and efficacious modality making it one of the most promising viral vectors, with above 244 clinical trials involving AAV registered with ClinicalTrials.gov. The increasing interest in clinical applications involving AAV vectors requires robust and scalable production methods to facilitate the evaluation of AAV therapies in large animal models, as this is a critical step in the translational pipeline9.
For AAV vector production, the two main requirements are the AAV genome and the capsid. The genome of wild-type (wt)-AAV is single-stranded DNA that is approximately 4.7 kb in length10. The wt-AAV genome comprises inverted terminal repeats (ITRs) found at both ends of the genome, which are important for packaging, and the rep and cap genes11. The rep and cap genes, necessary for genome replication, assembly of the viral capsid, and encapsulation of the genome into the viral capsid, are removed from the viral genome and provided in trans for AAV vector production12. The removal of these genes from the viral genome provides room for therapeutic transgenes and all the necessary regulatory elements, including the promoter and polyA signal. The ITRs remain in the vector genome to ensure proper genome replication and viral encapsulation13,14. To improve the kinetics of transgene expression, AAV vector genomes can be engineered to be self-complementary, which mitigates the need for conversion from single-stranded to double-stranded DNA conversion during AAV genome replication, but reduces the coding capacity to ~2.4 kb15.
Beyond AAV genome design, capsid serotype selection determines the tissue and cell tropism of the AAV vector in vivo2. In addition to tissue tropism, different AAV serotypes have been shown to display different gene expression kinetics16. For example, Zincarelli et al.17&#160;classified different AAV serotypes into low expression serotypes (AAV2, 3, 4, 5), moderate expression serotypes (AAV1, 6, 8), and high expression serotypes (AAV7 and 9). They also categorized AAV serotypes into slow-onset expression (AAV2, 3, 4, 5) or rapid-onset expression (AAV1, 6, 7, 8, and 9). These divergent tropisms and gene expression kinetics are due to amino acid variations in the capsid proteins, capsid protein formations, and interactions with host cell receptors/co-receptors18. Some AAV capsids have additional beneficial characteristics such as the ability to cross the blood-brain barrier following intravascular administration (AAV9) or reside in long-living muscle cells for durable transgene expression (AAV6, 6.2FF, 8, and 9)19,20.
This paper aims to detail a cost-effective method for producing high-purity, high-titer, research-grade AAV vectors for use in preclinical large animal models. Production of AAV using this protocol is achieved using dual-plasmid transfection into adherent human embryonic kidney (HEK)293 cells grown in cell stacks. Furthermore, the study describes a protocol for heparin sulfate affinity chromatography purification, which can be used for AAV serotypes that contain heparin-binding domains, including AAV2, 3, 6, 6.2FF, 13, and DJ21,22.
A number of packaging systems are available for the production of AAV vectors. Among these, the use of a two-plasmid co-transfection systems, in which the Rep and Cap genes and Ad helper genes (E1A, E1B55K, E2A, E4orf6, and VA RNA) are contained within one plasmid (pHelper), has some practical advantages over the common three-plasmid (triple) transfection method, including reduced cost for plasmid production23,24. The AAV genome plasmid containing the transgene expression cassette (pTransgene), must be flanked by ITRs, and must not exceed ~4.7 kb in length. Vector titer and purity can be affected by the transgene due to potential cytotoxic effects during transfection. Assessment of vector purity is described herein. Vectors produced using this method, which yield a 1 x 1013 vg/mL for each, were evaluated in mice, hamsters, and ovine animal models.
Table 1: Composition of required solutions. Necessary information, including percentages and volumes, of components needed for various solutions throughout the protocol. <a href="https://www.jove.com/files/ftp_upload/62727/Table 1- 62727_R2.xlsx" target="_blank">Please click here to download this Table.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.22 &#956;m filter</td>
			<td>Millipore Sigma</td>
			<td>S2GPU05RE</td>
			<td></td>
		</tr>
		<tr>
			<td>0.25% Trypsin</td>
			<td>Fisher Scientific</td>
			<td>SM2001C</td>
			<td></td>
		</tr>
		<tr>
			<td>1-Butanol</td>
			<td>Thermo Fisher Scientific</td>
			<td>A399-4</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>10 chamber cellstack</td>
			<td>Corning</td>
			<td>3271</td>
			<td></td>
		</tr>
		<tr>
			<td>1L PETG bottle</td>
			<td>Thermo Fisher Scientific</td>
			<td>2019-1000</td>
			<td></td>
		</tr>
		<tr>
			<td>30% Acrylamide/Bis Solution</td>
			<td>Bio-Rad</td>
			<td>1610158</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well skirted plate</td>
			<td>FroggaBio</td>
			<td>FS-96</td>
			<td></td>
		</tr>
		<tr>
			<td>Adhesive plate seals</td>
			<td>Thermo Fisher Scientific</td>
			<td>08-408-240</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium persulfate (APS)</td>
			<td>Bio-Rad</td>
			<td>161-0700</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>Blood and Tissue Clean up Kit</td>
			<td>Qiagen</td>
			<td>69506</td>
			<td>Use for DNA clean up in section 4.6 of protocol</td>
		</tr>
		<tr>
			<td>Bromophenol blue</td>
			<td>Fisher Scientific</td>
			<td>B392-5</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>Cell Culture Dishes</td>
			<td>Greiner bio-one</td>
			<td>7000232</td>
			<td>15 cm plates</td>
		</tr>
		<tr>
			<td>Culture Conical Tube</td>
			<td>Thermo Fisher Scientific</td>
			<td>339650</td>
			<td>15 mL conical tube</td>
		</tr>
		<tr>
			<td>Culture Conical Tube</td>
			<td>Fisher Scientific</td>
			<td>14955240</td>
			<td>50 mL conical tube</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle Medium (DMEM) with 1000 mg/L D-glucose, L-glutamine</td>
			<td>Cytiva Life Sciences</td>
			<td>SH30022.01</td>
			<td></td>
		</tr>
		<tr>
			<td>ECL Western Blotting Substrate</td>
			<td>Thermo Fisher Scientific</td>
			<td>32209</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Greenfield</td>
			<td>P016EA95</td>
			<td>Dilute ethyl alcohol(95% vol) to 20% for section 3.7.4 and 70% for section 6.1.1.1</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS)</td>
			<td>Thermo Fisher Scientific</td>
			<td>SH30396.03</td>
			<td></td>
		</tr>
		<tr>
			<td>Glacial acetic acid</td>
			<td>Fisher Scientific</td>
			<td>A38-500</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Fisher Scientific</td>
			<td>BP229-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Fisher Scientific</td>
			<td>BP381-500</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS with Mg2+ and Ca2+</td>
			<td>Thermo Fisher Scientific</td>
			<td>SH302268.02</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS without Mg2+ and Ca2+</td>
			<td>Thermo Fisher Scientific</td>
			<td>SH30588.02</td>
			<td></td>
		</tr>
		<tr>
			<td>HEK293 cells</td>
			<td>American Tissue Culture Collection</td>
			<td>CRL-1573</td>
			<td>Upon receipt, thaw the cells and culture as described in manufacturer&#8217;s protocol. Once cells have been minimally passaged and are growing well, freeze a subfraction for future in aliquots and store in liquid nitrogen. Always use cells below passage number 30. Once cultured cells have been passaged more than 30 times, it is recommended to restart a culture from the stored aliquots</td>
		</tr>
		<tr>
			<td>HEK293 host cell protein ELISA kit</td>
			<td>Cygnus Technologies</td>
			<td>F650S</td>
			<td>Follow manufacturer&#8217;s instructions</td>
		</tr>
		<tr>
			<td>Heparin sulfate column</td>
			<td>Cytiva Life Sciences</td>
			<td>17040703</td>
			<td></td>
		</tr>
		<tr>
			<td>Kimwipe</td>
			<td>Thermo Fisher Scientific</td>
			<td>KC34120</td>
			<td></td>
		</tr>
		<tr>
			<td>&#160;L-glutamine (200 mM)</td>
			<td>Thermo Fisher Scientific</td>
			<td>SH30034.02</td>
			<td></td>
		</tr>
		<tr>
			<td>Large Volume Centrifuge Tube Support Cushion</td>
			<td>Corning</td>
			<td>CLS431124</td>
			<td>Support cushion must be used with large volume centrifuge tubes uless the centrifuge rotor has the approriate V-bottom cushions</td>
		</tr>
		<tr>
			<td>Large Volume Centrifuge Tubes</td>
			<td>Corning</td>
			<td>CLS431123-6EA</td>
			<td>500 mL centrifuge tubes</td>
		</tr>
		<tr>
			<td>MgCl2&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>7791-18-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge tube</td>
			<td>Fisher Scientific</td>
			<td>05-408-129</td>
			<td>1.5 mL microcentrifuge tube, sterilize prior to use</td>
		</tr>
		<tr>
			<td>Molecular Grade Water</td>
			<td>Cytiva Life Sciences</td>
			<td>SH30538.03</td>
			<td></td>
		</tr>
		<tr>
			<td>N-Lauroylsarcosine sodium salt</td>
			<td>Sigma Aldrich</td>
			<td>L5125</td>
			<td>CAUTION. Wear gloves</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Thermo Fisher Scientific</td>
			<td>BP35810</td>
			<td></td>
		</tr>
		<tr>
			<td>Optimem, reduced serum medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>31985070</td>
			<td></td>
		</tr>
		<tr>
			<td>Pasteur pipets</td>
			<td>Fisher Scientific</td>
			<td>13-678-20D</td>
			<td>Sterilize prior to use</td>
		</tr>
		<tr>
			<td>PBS (10x)</td>
			<td>Thermo Fisher Scientific</td>
			<td>70011044</td>
			<td>Dilute to 1x for use on cells</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin Solution</td>
			<td>Cytiva Life Sciences</td>
			<td>SV30010</td>
			<td></td>
		</tr>
		<tr>
			<td>pHelper plasmid</td>
			<td>De novo design or obtained from plasmid repository</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipet basin</td>
			<td>Thermo Fisher Scientific</td>
			<td>13-681-502</td>
			<td>Purchase sterile pipet basins</td>
		</tr>
		<tr>
			<td>Polyethylene glycol tert-octylphenyl ether (Triton X-100)</td>
			<td>Thermo Fisher Scientific</td>
			<td>9002-93-1</td>
			<td>CAUTION. Wear gloves</td>
		</tr>
		<tr>
			<td>Polyethylenimine (PEI)</td>
			<td>Polyscience</td>
			<td>24765-1</td>
			<td>Follow manufacturer&#8217;s instructions to produce a 1L solution. 0.22&#956;m filter and store at 4&#176;C</td>
		</tr>
		<tr>
			<td>Polypropylene semi-skirted PCR Plate</td>
			<td>FroggaBio</td>
			<td>WS-96</td>
			<td></td>
		</tr>
		<tr>
			<td>Polysorbate 20 (Tween 20)</td>
			<td>Thermo Fisher Scientific</td>
			<td>BP337-100</td>
			<td>CAUTION. Wear gloves</td>
		</tr>
		<tr>
			<td>polyvinylidene difluoride (PVDF) membrane</td>
			<td>Cytiva Life Sciences</td>
			<td>10600023</td>
			<td>Use forceps to manipulate. Wear gloves.</td>
		</tr>
		<tr>
			<td>Primary antibody</td>
			<td>Progen</td>
			<td>65158</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein Ladder</td>
			<td>FroggaBio</td>
			<td>PM008-0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>Thermo Fisher Scientific</td>
			<td>AM2546</td>
			<td></td>
		</tr>
		<tr>
			<td>pTrangene plasmid</td>
			<td>De novo design or obtained from plasmid repository</td>
			<td>NA</td>
			<td>Must contain SV40 polyA in genome to be compatible with AAV titration in section 5.0</td>
		</tr>
		<tr>
			<td>Pump tubing</td>
			<td>Cole-Parmer</td>
			<td>RK-96440-14</td>
			<td>Optimize length of tubing and containment of virus in fractions E1-E5</td>
		</tr>
		<tr>
			<td>RQ1 Dnase 10 Reaction Buffer</td>
			<td>Promega</td>
			<td>M6101</td>
			<td>Use at 10x concentration in protocol from section 4.0</td>
		</tr>
		<tr>
			<td>RQ1 Rnase-free Dnase</td>
			<td>Promega</td>
			<td>M6101</td>
			<td></td>
		</tr>
		<tr>
			<td>Sample dilutent</td>
			<td>Cygnus Technologies</td>
			<td>I700</td>
			<td>Must be purchased separately for use with HEK293 host cell protein ELISA kit</td>
		</tr>
		<tr>
			<td>Secondary antibody, HRP</td>
			<td>Thermo Fisher Scientific</td>
			<td>G-21040</td>
			<td></td>
		</tr>
		<tr>
			<td>Skim milk powder</td>
			<td>Oxoid</td>
			<td>LP0033B</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate (SDS)</td>
			<td>Thermo Fisher Scientific</td>
			<td>28312</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>Sodium hydroxide (NaOH)</td>
			<td>Thermo Fisher Scientific</td>
			<td>SS266-4</td>
			<td></td>
		</tr>
		<tr>
			<td>SV40 polyA primer probe</td>
			<td>IDT</td>
			<td></td>
			<td>Use sequence in Table X for quote from IDT for synthesis</td>
		</tr>
		<tr>
			<td>Tetramethylethylenediamine (TEMED)</td>
			<td>Thermo Fisher Scientific</td>
			<td>15524010</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>Tris Base</td>
			<td>Fisher Scientific</td>
			<td>BP152-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan blue</td>
			<td>Bio-Rad</td>
			<td>1450021</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra-Filter</td>
			<td>Millipore Sigma</td>
			<td>UFC810024</td>
			<td>Ultra-4 Centrifugal 10K device must be used, as it has a 10000 molecular weight cutoff</td>
		</tr>
		<tr>
			<td>Universal Nuclease for cell lysis</td>
			<td>Thermo Fisher Scientific</td>
			<td>88702</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal qPCR master mix</td>
			<td>NEB</td>
			<td>M3003L</td>
			<td></td>
		</tr>
		<tr>
			<td>Whatman Paper</td>
			<td>Millipore Sigma</td>
			<td>WHA1001325</td>
			<td></td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>Fisher Scientific</td>
			<td>21985023</td>
			<td>CAUTION. Use under a laminar flow hood. Wear gloves</td>
		</tr>
		<tr>
			<td>CAUTION:&#160;Refer to the Materials Table for guidelines on the use of dangerous chemicals.</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

production of adeno-associated virus vectors in cell stacks for preclinical studies in large animal models

Adeno-associated virus (AAV) vectors are among the most clinically advanced gene therapy vectors, with three AAV gene therapies approved for humans. Clinical advancement of novel applications for AAV involves transitioning from small animal models, such as mice, to larger animal models, including dogs, sheep, and nonhuman primates. One of the limitations of administering AAV to larger animals is the requirement for large quantities of high-titer virus. While suspension cell culture is a scalable method for AAV vector production, few research labs have the equipment (e.g., bioreactors) or know how to produce AAV in this manner. Moreover, AAV titers are often significantly lower when produced in suspension HEK 293 cells as compared to adherent HEK293 cells. Described here is a method for producing large quantities of high-titer AAV using cell stacks. A detailed protocol for titering AAV as well as methods for validating vector purity are also described. Finally, representative results of AAV-mediated transgene expression in a sheep model are presented. This optimized protocol for large-scale production of AAV vectors in adherent cells will enable molecular biology laboratories to advance the testing of their novel AAV therapies in larger animal models.

Translation from small rodent models to larger animal models and eventual clinical application presents a significant challenge due to the large amount of AAV required to transduce larger animals and achieve therapeutic effects. To compare transduction efficiency of the rationally designed AAV6.2FF capsid, previously demonstrated a 101-fold increase in transduction efficiency in murine muscle cells compared to AAV63, mice, hamsters, and lambs were all administered AAV6.2FF expressing a human monoc...

Watch this Scientific Journal Video about Production of Adeno-Associated Virus Vectors in Cell Stacks for Preclinical Studies in Large Animal Models at JoVE.com

Production of Adeno-Associated Virus Vectors in Cell Stacks for Preclinical Studies in Large Animal Models

Here we provide a detailed procedure for large-scale production of research-grade AAV vectors using adherent HEK 293 cells grown in cell stacks and affinity chromatography purification. This protocol consistently yields &#62;1 x 1013 vector genomes/mL, providing vector quantities appropriate for large animal studies.

Adeno-associated virus (AAV) vectors are among the most clinically advanced gene therapy vectors, with three AAV gene therapies approved for humans. ...

This protocol for production of AAV viral vectors is cost-effective and yields high purity, high titer, research-grade AAV for use in preclinical, large animal models. This technique uses adherent HEK293 cells in cell culture chambers, which is time efficient and less hands-on, allowing for fewer disruptions to the cells. This protocol can greatly aid in viral vector production for the field of gene therapy, and can also be used for the production of other AAV serotypes that also bind heparan sulfate.To begin, collect HEK293 cells from the culture when it reaches 80%confluency. Aspirate the media before gently washing the cell culture plate with three milliliters of PBS. Then aspirate PBS and add three milliliters of trypsin.Incubate the plates for two minutes at 37 degrees Celsius. After incubation, neutralize trypsin, by adding seven milliliters of complete DMEM to the plate, and collect the supernatant in 50 milliliter conical tubes. Gently invert the tubes to ensure the cells are homogenous.To determine the cell density, mix 10 microliters of the cell samples with 10 microliters of trypan blue. And add the mixture to a cell counting slide to analyze in the cell counter. Mix the cell suspension with one liter of pre warmed complete DMEM to see the culture chamber.Gently rotate the chamber to distribute the cells evenly. Incubate the chamber at 37 degrees Celsius with 5%carbon dioxide. In addition to the cell culture chamber, culture cells at 10 to the fourth cells per centimeter squared in a 15 centimeter plate as a reference for confluency.After 65 hours of incubation, when the cells are 80 to 90%confluent, slowly add the polyethyleneimine-DNA and DMEM mixture into the cell culture chamber port. Distribute the liquid evenly to all the rows before incubating at 37 degrees Celsius, and 5%carbon dioxide for 72 hours. After incubation, shake the cell culture chamber vigorously to dislodge the cells until the media appears cloudy, and pour it into four or 500 milliliter centrifuge tubes.Pellet the cells by centrifugation at 18, 000 times G for 30 minutes at four degrees Celsius. Pour the clarified supernatant into a one-liter PETG bottle, and resuspend the cell pellets in 50 milliliters of licensed buffer in 500 milliliter centrifuge tubes. Incubate the tubes for 60 minutes at 37 degrees Celsius.After incubation, centrifuge the tubes at 18, 000 times G for 30 minutes, and transfer the supernatant into the same one-liter PETG bottle. Store at minus 80 degrees Celsius. Thaw the crude lysate at four degrees Celsius overnight.Once thawed, filter it using a 0.22 micron filter. Immediately before the purification steps, passivate the centrifugal concentrator by adding four milliliters of filter pretreatment buffer for each heparin-Sepharose column being used. Place the tubing in a peristaltic pump.Sequentially run the solutions and media. Prepare for chromatography by attaching a five milliliter heparin-Sepharose column to the tubing, and running 25 milliliters of Bazell DMEM through the column. Then load 0.2 micromolar of the filtered crude lysate onto the column at a flow rate of one to two drops per second.Wash the column sequentially to elute five milliliters five times with 300 millimolar of sodium chloride HBSS, with magnesium and calcium, and label the five elutions as E1 to E5.When ready, spin the centrifugal concentrator containing the pretreatment buffer at 900 times G for two minutes. Discard the flow-through. Wash the centrifugal concentrator filter with four milliliters of HBSS with magnesium and calcium by spinning at 1000 times G for two minutes.Then add the elution E2 to the centrifugal concentrator, and spin at 1000 times G for five minutes. Discard the flow-through. Similarly spin the elution E3 into the centrifugal concentrator until the concentrated virus is approximately one milliliter.Remove the concentrated virus from the centrifugal concentrator using a P200 filtered tip, and collect it into a sterile 1.5 milliliter centrifuge tube. After collection of the virus, rinse the centrifugal concentrator with 200 microliters of HBSS with magnesium and calcium. Pipette up and down vigorously for 30 seconds to dislodge any virus adhered to the membrane, and collect the concentrated virus in the same 1.5 milliliter centrifuge tube.Mix the tube well. Wash the column and saturate with 20%ethanol before storing at four degrees Celsius. Store the pump tubing in one molar sodium hydroxide.The transduction efficiency of the AAV6.2FF capsid was compared in mice, hamsters, and lambs for 28 days upon intramuscular administration. Mice administered five times 10 to the 12th vector genomes per kilogram of AAV6.2FF human IgG, expressed between 171 to 237 micrograms per milliliter of human IgG in the serum. Hamster is administered at two times 10 to the 13th vector genomes per kilogram of AAV6.2FF human IgG, expressed much higher levels of human IgG than the mice.While the large animal model was able to express an average 35 micrograms per milliliter of human IgG levels in the plasma. Large animal models can determine the expression of the AAV transgene in vivo, and determine if the transgenes have therapeutic effect against the disorder or disease of interest. The study has showcased the great transduction ability of AAV6.2FF, a novel AAV 6 serotype vector in the skeletal muscle, as well as the low immunogenicity of AAV viral vectors in vivo.

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Research

JoVE Journal

Immunology and Infection

Estimating Virus Production Rates in Aquatic Systems

Viruses are pervasive components of marine and freshwater systems, and are known to be significant agents of microbial mortality. Developing quantitative estimates of this process is critical as we can then develop better models of microbial community structure and function as well as advance our understanding of how viruses work to alter aquatic biogeochemical cycles. The virus reduction technique allows researchers to estimate the rate at which virus particles are released from the endemic microbial community. In brief, the abundance of free (extracellular) viruses is reduced in a sample while the microbial community is maintained at near ambient concentration. The microbial community is then incubated in the absence of free viruses and the rate at which viruses reoccur in the sample (through the lysis of already infected members of the community) can be quantified by epifluorescence microscopy or, in the case of specific viruses, quantitative PCR. These rates can then be used to estimate the rate of microbial mortality due to virus-mediated cell lysis.

The turnover rate of viruses in marine and freshwater systems can be estimated by a reduction and reoccurrence technique. The data allow researchers to infer rates of virus-mediated microbial mortality in aquatic systems.

Viruses are pervasive components of marine and freshwater systems, and are known to be significant agents of microbial mortality. Developing quantitative ...

Visualizing Dengue Virus through Alexa Fluor Labeling

The early events in the interaction between virus and cell can have profound influence on the outcome of infection. Determining the factors 
that influence this interaction could lead to improved understanding of disease pathogenesis and thus influence vaccine or therapeutic design. Hence, the development 
of methods to probe this interaction would be useful. Recent advancements in fluorophores development1-3 and imaging technology4 can be exploited to 
improve our current knowledge on dengue pathogenesis and thus pave the way to reduce the millions of dengue infections occurring annually.

The enveloped dengue virus has an external scaffold consisting of 90 envelope glycoprotein (E) dimers protecting the nucleocapsid shell, 
which contains a single positive strand RNA genome5. The identical protein subunits on the virus surface can thus be labeled with an amine reactive dye and visualized 
through immunofluorescent microscopy. Here, we present a simple method of labeling of dengue virus with Alexa Fluor succinimidyl ester dye dissolved directly in a sodium 
bicarbonate buffer that yielded highly viable virus after labeling. There is no standardized procedure for the labeling of live virus and existing manufacturer&#x2019;s protocol 
for protein labeling usually requires the reconstitution of dye in dimethyl sulfoxide. The presence of dimethyl sulfoxide, even in minute quantities, can block 
productive infection of virus and also induce cell cytotoxicity6. The exclusion of the use of dimethyl sulfoxide in this protocol thus reduced this possibility. 
Alexa Fluor dyes have superior photostability and are less pH-sensitive than the common dyes, such as fluorescein and rhodamine2, making them ideal for 
studies on cellular uptake and endosomal transport of the virus. The conjugation of Alexa Fluor dye did not affect the recognition of labeled dengue 
virus by virus-specific antibody and its putative receptors in host cells7. This method could have useful applications in virological studies.

Taking advantage of the advancements in fluorophore development and imaging technology, a simple method of Alexa Fluor labeling of dengue virus was devised to visualize the early interactions between virus and cell.

The early events in the interaction between virus and cell can have profound influence on the outcome of infection. Determining the factors 
that ...

Production and Titering of Recombinant Adeno-associated Viral Vectors

In recent years recombinant adeno-associated viral vectors (AAV) have become increasingly valuable for in vivo studies in animals, and are also currently being tested in human clinical trials. Wild-type AAV is a non-pathogenic member of the parvoviridae family and inherently replication-deficient. The broad transduction profile, low immune response as well as the strong and persistent transgene expression achieved with these vectors has made them a popular and versatile tool for in vitro and in vivo gene delivery. rAAVs can be easily and cheaply produced in the laboratory and, based on their favourable safety profile, are generally given a low safety classification. Here, we describe a method for the production and titering of chimeric rAAVs containing the capsid proteins of both AAV1 and AAV2. The use of these so-called chimeric vectors combines the benefits of both parental serotypes such as high titres stocks (AAV1) and purification by affinity chromatography (AAV2). These AAV serotypes are the best studied of all AAV serotypes, and individually have a broad infectivity pattern. The chimeric vectors described here should have the infectious properties of AAV1 and AAV2 and can thus be expected to infect a large range of tissues, including neurons, skeletal muscle, pancreas, kidney among others. The method described here uses heparin column purification, a method believed to give a higher viral titer and cleaner viral preparation than other purification methods, such as centrifugation through a caesium chloride gradient. Additionally, we describe how these vectors can be quickly and easily titered to give accurate reading of the number of infectious particles produced.

Recombinant adeno-associated virus (rAAVs) vectors are becoming increasingly valuable for in vivo studies in animals. We describe how rAAVs can be produced in the laboratory and how these vectors can be titered to give an accurate reading of the number of infectious particles produced.

In recent years recombinant adeno-associated viral vectors (AAV) have become increasingly valuable for in vivo studies in animals, and are also currently ...

Engineering and Evolution of Synthetic Adeno-Associated Virus (AAV) Gene Therapy Vectors via DNA Family Shuffling

Adeno-associated viral (AAV) vectors represent some of the most potent and promising vehicles for therapeutic human gene transfer due to a unique combination of beneficial properties1. These include the apathogenicity of the underlying wildtype viruses and the highly advanced methodologies for production of high-titer, high-purity and clinical-grade recombinant vectors2. A further particular advantage of the AAV system over other viruses is the availability of a wealth of naturally occurring serotypes which differ in essential properties yet can all be easily engineered as vectors using a common protocol1,2. Moreover, a number of groups including our own have recently devised strategies to use these natural viruses as templates for the creation of synthetic vectors which either combine the assets of multiple input serotypes, or which enhance the properties of a single isolate. The respective technologies to achieve these goals are either DNA family shuffling3, i.e. fragmentation of various AAV capsid genes followed by their re-assembly based on partial homologies (typically &gt;80% for most AAV serotypes), or peptide display4,5, i.e. insertion of usually seven amino acids into an exposed loop of the viral capsid where the peptide ideally mediates re-targeting to a desired cell type. For maximum success, both methods are applied in a high-throughput fashion whereby the protocols are up-scaled to yield libraries of around one million distinct capsid variants. Each clone is then comprised of a unique combination of numerous parental viruses (DNA shuffling approach) or contains a distinctive peptide within the same viral backbone (peptide display approach). The subsequent final step is iterative selection of such a library on target cells in order to enrich for individual capsids fulfilling most or ideally all requirements of the selection process. The latter preferably combines positive pressure, such as growth on a certain cell type of interest, with negative selection, for instance elimination of all capsids reacting with anti-AAV antibodies. This combination increases chances that synthetic capsids surviving the selection match the needs of the given application in a manner that would probably not have been found in any naturally occurring AAV isolate. Here, we focus on the DNA family shuffling method as the theoretically and experimentally more challenging of the two technologies. We describe and demonstrate all essential steps for the generation and selection of shuffled AAV libraries (Fig. 1), and then discuss the pitfalls and critical aspects of the protocols that one needs to be aware of in order to succeed with molecular AAV evolution.

Engineering and Evolution of Synthetic Adeno-Associated Virus AAV Gene Therapy Vectors via DNA Family Shuffling

We demonstrate the basic technique to molecularly engineer and evolve synthetic Adeno-associated viral (AAV) gene therapy vectors via DNA family shuffling. Moreover, we provide general guidelines and representative examples for selection and analysis of individual chimeric capsids with enhanced properties on target cells in culture or in mice.

Adeno-associated viral (AAV) vectors represent some of the most potent and promising vehicles for therapeutic human gene transfer due to a unique ...

Bioluminescence Imaging of NADPH Oxidase Activity in Different Animal Models

NADPH oxidase is a critical enzyme that mediates antibacterial and antifungal host defense. In addition to its role in antimicrobial host defense, NADPH oxidase has critical signaling functions that modulate the inflammatory response 1. Thus, the development of a method to measure in "real-time" the kinetics of NADPH oxidase-derived ROS generation is expected to be a valuable research tool to understand mechanisms relevant to host defense, inflammation, and injury.
Chronic granulomatous disease (CGD) is an inherited disorder of the NADPH oxidase characterized by severe infections and excessive inflammation. Activation of the phagocyte NADPH oxidase requires translocation of its cytosolic subunits (p47phox, p67phox, and p40phox) and Rac to a membrane-bound flavocytochrome (composed of a gp91phox and p22phox heterodimer). Loss of function mutations in any of these NADPH oxidase components result in CGD. Similar to patients with CGD, gp91phox -deficient mice and p47phox-deficient mice have defective phagocyte NADPH oxidase activity and impaired host defense 2, 13. In addition to phagocytes, which contain the NADPH oxidase components described above, a variety of other cell types express different isoforms of NADPH oxidase.
Here, we describe a method to quantify ROS production in living mice and to delineate the contribution of NADPH oxidase to ROS generation in models of inflammation and injury. This method is based on ROS reacting with L-012 (an analogue of luminol) to emit luminescence that is recorded by a charge-coupled device (CCD). In the original description of the L-012 probe, L-012-dependent chemiluminescence was completely abolished by superoxide dismutase, indicating that the main ROS detected in this reaction was superoxide anion 14. Subsequent studies have shown that L-012 can detect other free radicals, including reactive nitrogen species 15, 16. Kielland et al. 16 showed that topical application of phorbol myristate acetate, a potent activator of NADPH oxidase, led to NADPH oxidase-dependent ROS generation that could be detected in mice using the luminescent probe L-012. In this model, they showed that L-012-dependent luminescence was abolished in p47phox-deficient mice.
We compared ROS generation in wildtype mice and NADPH oxidase-deficient p47phox-/- mice 2 in the following three models: 1) intratracheal administration of zymosan, a pro-inflammatory fungal cell wall-derived product that can activate NADPH oxidase; 2) cecal ligation and puncture (CLP), a model of intra-abdominal sepsis with secondary acute lung inflammation and injury; and 3) oral carbon tetrachloride (CCl4), a model of ROS-dependent hepatic injury. These models were specifically selected to evaluate NADPH oxidase-dependent ROS generation in the context of non-infectious inflammation, polymicrobial sepsis, and toxin-induced organ injury, respectively. Comparing bioluminescence in wildtype mice to p47phox-/- mice enables us to delineate the specific contribution of ROS generated by p47phox-containing NADPH oxidase to the bioluminescent signal in these models.
Bioluminescence imaging results that demonstrated increased ROS levels in wildtype mice compared to p47phox-/- mice indicated that NADPH oxidase is the major source of ROS generation in response to inflammatory stimuli. This method provides a minimally invasive approach for "real-time" monitoring of ROS generation during inflammation in vivo.

NADPH oxidase is the major source of reactive oxygen species (ROS) in phagocytes. Because of the ephemeral nature of ROS, it is difficult to measure and monitor ROS levels in living animals. A minimally invasive method for serial quantification of ROS in living mice is described.

NADPH oxidase is a critical enzyme that mediates antibacterial and antifungal host defense. In addition to its role in antimicrobial host defense, NADPH ...

Neutrophil Isolation and Analysis to Determine their Role in Lymphoma Cell Sensitivity to Therapeutic Agents

Neutrophils are the most abundant (40% to 75%) type of white blood cells and among the first inflammatory cells to migrate towards the site of inflammation. They are key players in the innate immune system and play major roles in cancer biology. Neutrophils have been proposed as key mediators of malignant transformation, tumor progression, angiogenesis and in the modulation of the antitumor immunity; through their release of soluble factors or their interaction with tumor cells. To characterize the specific functions of neutrophils, a fast and reliable method is coveted for in vitro isolation of neutrophils from human blood. Here, a density gradient separation method is demonstrated to isolate neutrophils as well as mononuclear cells from the blood. The procedure consists of layering the density gradient solution such as Ficoll carefully above the diluted blood obtained from patients diagnosed with chronic lymphocytic leukemia (CLL), followed by centrifugation, isolation of mononuclear layer, separation of neutrophils from RBCsby dextran then lysis of residual erythrocytes. This method has been shown to isolate neutrophils &#8805; 90 % pure. To mimic the tumor microenvironment, 3-dimensional (3D) experiments were performed using basement membrane matrix such as Matrigel. Given the short half-life of neutrophils in vitro, 3D experiments with fresh human neutrophils cannot be performed. For this reason promyelocytic HL60 cells are differentiated along the granulocytic pathway using the differentiation inducers dimethyl sulfoxide (DMSO) and retinoic acid (RA). The aim of our experiments is to study the role of neutrophils on the sensitivity of lymphoma cells to anti-lymphoma agents. However these methods can be generalized to study the interactions of neutrophils or neutrophil-like cells with a large range of cell types in different situations.

Neutrophils are the most abundant type of white blood cells. The isolation of neutrophils from human blood by density gradient separation method and the differentiation of human promyelocytic (HL60) cells along the granulocytic pathway are described here; to test their role on sensitivity of lymphoma cells to anti-lymphoma agents.

Neutrophils are the most abundant (40% to 75%) type of white blood cells and among the first inflammatory cells to migrate towards the site of ...

A Simple and Efficient Approach to Construct Mutant Vaccinia Virus Vectors

The CRISPR-associated endonuclease Cas9 can edit particular genomic loci directed by a single guide RNA (gRNA). The CRISPR/Cas9 system has been successfully employed for editing genomes of various organisms. Here we describe a protocol for editing the vaccinia virus (VV) genome in the cytoplasm of VV-infected CV-1 cells using the RNA-guided Cas9. RNA-guided Cas9 induces double-stranded DNA breaks facilitating homologous recombination efficiently and specifically in the targeted site of VV and a transgene can be incorporated into these sites by homologous recombination. By using a site-specific homologous vector with transgene(s), a N1L gene-deleted VV with the red fluorescence protein (RFP) gene incorporated in this region was generated with a successful recombination efficiency 10 times greater than that obtained from the conventional homologous recombination method. This protocol demonstrates successful use of RNA-guided Cas9 system to generate mutant VVs with enhanced efficiency.

Vaccinia virus (VV) has been widely used in biomedical research and the improvement of human health. This article describes a simple, highly efficient method to edit the VV genome using a CRISPR-Cas9 system.

The CRISPR-associated endonuclease Cas9 can edit particular genomic loci directed by a single guide RNA (gRNA). The CRISPR/Cas9 system has been ...

Evaluation of the Efficacy And Toxicity of RNAs Targeting HIV-1 Production for Use in Gene or Drug Therapy

Small RNA therapies targeting post-integration steps in the HIV-1 replication cycle are among the top candidates for gene therapy and have the potential to be used as drug therapies for HIV-1 infection. Post-integration inhibitors include ribozymes, short hairpin (sh) RNAs, small interfering (si) RNAs, U1 interference (U1i) RNAs and RNA aptamers. Many of these have been identified using transient co-transfection assays with an HIV-1 expression plasmid and some have advanced to clinical trials. In addition to measures of efficacy, small RNAs have been evaluated for their potential to affect the expression of human RNAs, alter cell growth and/or differentiation, and elicit innate immune responses. In the protocols described here, a set of transient transfection assays designed to evaluate the efficacy and toxicity of RNA molecules targeting post-integration steps in the HIV-1 replication cycle are described. We have used these assays to identify new ribozymes and optimize the format of shRNAs and siRNAs targeting HIV-1 RNA. The methods provide a quick set of assays that are useful for screening new anti-HIV-1 RNAs and could be adapted to screen other post-integration inhibitors of HIV-1 replication.

Methods to evaluate the efficacy and toxicity of RNA molecules targeting post-integration steps of the HIV-1 replication cycle are described. These methods are useful for screening new molecules and optimizing the format of existing ones.

Small RNA therapies targeting post-integration steps in the HIV-1 replication cycle are among the top candidates for gene therapy and have the potential ...

Collection and Processing of Lymph Nodes from Large Animals for RNA Analysis: Preparing for Lymph Node Transcriptomic Studies of Large Animal Species

Large animals (both livestock and wildlife) serve as important reservoirs of zoonotic pathogens, including Brucella, Mycobacterium bovis, Salmonella, and E. coli, and are useful for the study of pathogenesis and/or spread of the bacteria in natural hosts. With the key function of lymph nodes in the host immune response, lymph node tissues serve as a potential source of RNA for downstream transcriptomic analyses, in order to assess the temporal changes in gene expression in cells over the course of an infection. This article presents an overview of the process of lymph node collection, tissue sampling, and downstream RNA processing in livestock, using cattle (Bos taurus) as a model, with additional examples provided from the American bison (Bison bison). The protocol includes information about the location, identification, and removal of lymph nodes from multiple key sites in the body. Additionally, a biopsy sampling methodology is presented that allows for a consistency of sampling across multiple animals. Several considerations for sample preservation are discussed, including the generation of RNA suitable for downstream methodologies like RNA-sequencing and RT-PCR. Due to the long delays inherent in large animal vs. mouse time course studies, representative results from bison and bovine lymph node tissues are presented to describe the time course of the degradation in this tissue type, in the context of a review of previous methodological work on RNA degradation in other tissues. Overall, this protocol will be useful to both veterinary researchers beginning transcriptome projects on large animal samples and to molecular biologists interested in learning techniques for in vivo tissue sampling and in vitro processing.

This protocol provides an overview of procedures for the isolation of RNA for the transcriptomic profiling of lymph node tissues from large animals, including steps in the identification and excision of lymph nodes from livestock and wildlife, sampling approaches to provide consistency across multiple animals, and considerations plus representative results for the post-collection preservation and processing for RNA analysis.

Large animals (both livestock and wildlife) serve as important reservoirs of zoonotic pathogens, including Brucella, Mycobacterium bovis, Salmonella, and ...

Evaluation of Zika Virus-specific T-cell Responses in Immunoprivileged Organs of Infected Ifnar1-/- Mice

The Zika virus (ZIKV) can induce inflammation in immunoprivileged organs (e.g., the brain and testis), leading to the Guillain-Barr&#233; syndrome and damaging the testes. During an infection with the ZIKV, immune cells have been shown to infiltrate into the tissues. However, the cellular mechanisms that define the protection and/or immunopathogenesis of these immune cells during a ZIKV infection are still largely unknown. Herein, we describe methods to evaluate the virus-specific T-cell functionality in these immunoprivileged organs of ZIKV-infected mice. These methods include a) a ZIKV infection and vaccine inoculation in Ifnar1-/- mice; b) histopathology, immunofluorescence, and immunohistochemistry assays to detect the virus infection and inflammation in the brain, testes, and spleen; c) the preparation of a tetramer of ZIKV-derived T-cell epitopes; d) the detection of ZIKV-specific T cells in the monocytes isolated from the brain, testes, and spleen. Using these approaches, it is possible to detect the antigen-specific T cells that have infiltrated into the immunoprivileged organs and to evaluate the functions of these T cells during the infection: potential immune protection via virus clearance and/or immunopathogenesis to exacerbate the inflammation. These findings may also help to clarify the contribution of T cells induced by the immunization against ZIKV.

Evaluation of Zika Virus-specific T-cell Responses in Immunoprivileged Organs of Infected Ifnar1-/- Mice

A protocol to evaluate antigen-specific T-cell responses in the immunoprivileged organs of the Ifnar1-/- murine model for the Zika virus (ZIKV) infection is described. This method is pivotal for investigating the cellular mechanisms of the protection and immunopathogenesis of ZIKV vaccines and is also valuable for their efficacy evaluation.

The Zika virus (ZIKV) can induce inflammation in immunoprivileged organs (e.g., the brain and testis), leading to the Guillain-Barr&#233; syndrome and ...