Name: combined genetic and chemical capsid modifications of adenovirus-based gene transfer vectors for shielding and targeting
Uploaded: 2018-10-26T14:30:00
Description: Watch this Scientific Journal Video about Combined Genetic and Chemical Capsid Modifications of Adenovirus-Based Gene Transfer Vectors for Shielding and Targeting at JoVE.com

NOTE: In the following, a protocol for geneti-chemical PEGylation of an Ad vector is described to detail. To enable specific coupling of the PEG moiety, an Ad5 vector was beforehand genetically modified by introducing a cysteine residue into the hexon protein at the hypervariable loop 5 as described in a previous publication36, and a maleimide-activated PEG compound is used as coupling compound.
1. Preparation of Buffers for Vector Purification by CsCL Step Gradients
...

<ol>
	<li>Benko, M., Harrach, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+evolution+of+adenoviruses.">Molecular evolution of adenoviruses.</a> Current Topics in Microbiology and Immunology. , 3-35 (2003).</li><li>Davison, A. J., Benko, M., Harrach, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+content+and+evolution+of+adenoviruses.">Genetic content and evolution of adenoviruses.</a> Journal of Genetic Virology. 84, 2895-2908 (2003).</li><li>Rowe, W. P., Huebner, R. J., Gilmore, L. K., Parrott, R. H., Ward, T. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+a+cytopathogenic+agent+from+human+adenoids+undergoing+spontaneous+degeneration+in+tissue+culture.">Isolation of a cytopathogenic agent from human adenoids undergoing spontaneous degeneration in tissue culture.</a> Proceedings of the Society for Experimental Biology and Medicine. 84, 570-573 (1953).</li><li>van Oostrum, J., Burnett, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+composition+of+the+adenovirus+type+2+virion.">Molecular composition of the adenovirus type 2 virion.</a> Journal of Virology. 56, 439-448 (1985).</li><li>Stewart, P. L., Fuller, S. D., Burnett, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Difference+imaging+of+adenovirus:+bridging+the+resolution+gap+between+X-ray+crystallography+and+electron+microscopy.">Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy.</a> TheEMBO Journal. 12, 2589-2599 (1993).</li><li>Stewart, P. L., Burnett, R. M., Cyrklaff, M., Fuller, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Image+reconstruction+reveals+the+complex+molecular+organization+of+adenovirus.">Image reconstruction reveals the complex molecular organization of adenovirus.</a> Cell. 67, 145-154 (1991).</li><li>Meier, 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=Adenovirus+triggers+macropinocytosis+and+endosomal+leakage+together+with+its+clathrin-mediated+uptake.">Adenovirus triggers macropinocytosis and endosomal leakage together with its clathrin-mediated uptake.</a> Journal of Cellular Biology. 158, 1119-1131 (2002).</li><li>Xu, Z., 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=Coagulation+factor+X+shields+adenovirus+type+5+from+attack+by+natural+antibodies+and+complement.">Coagulation factor X shields adenovirus type 5 from attack by natural antibodies and complement.</a> Nature Medicine. 19, 452-457 (2013).</li><li>Qiu, Q., 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=Impact+of+natural+IgM+concentration+on+gene+therapy+with+adenovirus+type+5+vectors.">Impact of natural IgM concentration on gene therapy with adenovirus type 5 vectors.</a> Journal of Virology. 89, 3412-3416 (2015).</li><li>Alemany, R., Suzuki, K., Curiel, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blood+clearance+rates+of+adenovirus+type+5+in+mice.">Blood clearance rates of adenovirus type 5 in mice.</a> Journal of Genetic Virology. 81, 2605-2609 (2000).</li><li>Smith, J. S., Xu, Z., Tian, J., Stevenson, S. C., Byrnes, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interaction+of+systemically+delivered+adenovirus+vectors+with+Kupffer+cells+in+mouse+liver.">Interaction of systemically delivered adenovirus vectors with Kupffer cells in mouse liver.</a> Human Gene Therapy. 19, 547-554 (2008).</li><li>Schiedner, G., 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+hemodynamic+response+to+intravenous+adenovirus+vector+particles+is+caused+by+systemic+Kupffer+cell-mediated+activation+of+endothelial+cells.">A hemodynamic response to intravenous adenovirus vector particles is caused by systemic Kupffer cell-mediated activation of endothelial cells.</a> Human Gene Therapy. 14, 1631-1641 (2003).</li><li>Xu, Z., Tian, J., Smith, J. S., Byrnes, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clearance+of+adenovirus+by+Kupffer+cells+is+mediated+by+scavenger+receptors,+natural+antibodies,+and+complement.">Clearance of adenovirus by Kupffer cells is mediated by scavenger receptors, natural antibodies, and complement.</a> Journal of Virology. 82, 11705-11713 (2008).</li><li>Khare, R., Reddy, V. S., Nemerow, G. R., Barry, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+adenovirus+serotype+5+hexon+regions+that+interact+with+scavenger+receptors.">Identification of adenovirus serotype 5 hexon regions that interact with scavenger receptors.</a> Journal of Virology. 86, 2293-2301 (2012).</li><li>Piccolo, P., Annunziata, P., Mithbaokar, P., Brunetti-Pierri, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SR-A+and+SREC-I+binding+peptides+increase+HDAd-mediated+liver+transduction.">SR-A and SREC-I binding peptides increase HDAd-mediated liver transduction.</a> Gene Therapy. 21, 950-957 (2014).</li><li>Pl&#252;ddemann, A., Neyen, C., Gordon, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Macrophage+scavenger+receptors+and+host-derived+ligands.">Macrophage scavenger receptors and host-derived ligands.</a> Methods (San Diego, Calif). 43, 207-217 (2007).</li><li>Ganesan, 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=Rapid+and+efficient+clearance+of+blood-borne+virus+by+liver+sinusoidal+endothelium.">Rapid and efficient clearance of blood-borne virus by liver sinusoidal endothelium.</a> PLoS Pathogen. 7, e1002281 (2011).</li><li>Cichon, G., 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=Titer+determination+of+Ad5+in+blood:+a+cautionary+note.">Titer determination of Ad5 in blood: a cautionary note.</a> Gene Therapy. 10, 1012-1017 (2003).</li><li>Carlisle, R. 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=Human+erythrocytes+bind+and+inactivate+type+5+adenovirus+by+presenting+Coxsackie+virus-adenovirus+receptor+and+complement+receptor+1.">Human erythrocytes bind and inactivate type 5 adenovirus by presenting Coxsackie virus-adenovirus receptor and complement receptor 1.</a> Blood. 113, 1909-1918 (2009).</li><li>Waddington, S. N., 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=Adenovirus+serotype+5+hexon+mediates+liver+gene+transfer.">Adenovirus serotype 5 hexon mediates liver gene transfer.</a> Cell. 132, 397-409 (2008).</li><li>Kalyuzhniy, 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=Adenovirus+serotype+5+hexon+is+critical+for+virus+infection+of+hepatocytes+in+vivo.">Adenovirus serotype 5 hexon is critical for virus infection of hepatocytes in vivo.</a> Proceedings of the National Academy of Sciences USA. 105, 5483-5488 (2008).</li><li>Vigant, F., 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=Substitution+of+hexon+hypervariable+region+5+of+adenovirus+serotype+5+abrogates+blood+factor+binding+and+limits+gene+transfer+to+liver.+Molecular+Therapy.">Substitution of hexon hypervariable region 5 of adenovirus serotype 5 abrogates blood factor binding and limits gene transfer to liver. Molecular Therapy.</a> The Journal of the American Society of Gene Therapy. 16, 1474-1480 (2008).</li><li>Jonsson, M. I., 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=Coagulation+factors+IX+and+X+enhance+binding+and+infection+of+adenovirus+types+5+and+31+in+human+epithelial+cells.">Coagulation factors IX and X enhance binding and infection of adenovirus types 5 and 31 in human epithelial cells.</a> Journal of Virology. 83, 3816-3825 (2009).</li><li>Bradshaw, 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=Requirements+for+receptor+engagement+during+infection+by+adenovirus+complexed+with+blood+coagulation+factor+X.">Requirements for receptor engagement during infection by adenovirus complexed with blood coagulation factor X.</a> PLoS Pathogen. 6, e1001142 (2010).</li><li>Duffy, M. R., Bradshaw, A. C., Parker, A. L., McVey, J. H., Baker, A. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+cluster+of+basic+amino+acids+in+the+factor+X+serine+protease+mediates+surface+attachment+of+adenovirus/FX+complexes.">A cluster of basic amino acids in the factor X serine protease mediates surface attachment of adenovirus/FX complexes.</a> Journal of Virology. 85, 10914-10919 (2011).</li><li>Xu, Z., 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=Coagulation+factor+X+shields+adenovirus+type+5+from+attack+by+natural+antibodies+and+complement.">Coagulation factor X shields adenovirus type 5 from attack by natural antibodies and complement.</a> Nature Medicine. 19, 452-457 (2013).</li><li>Prill, J. -. M., 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=Modifications+of+adenovirus+hexon+allow+for+either+hepatocyte+detargeting+or+targeting+with+potential+evasion+from+Kupffer+cells.+Molecular+Therapy.">Modifications of adenovirus hexon allow for either hepatocyte detargeting or targeting with potential evasion from Kupffer cells. Molecular Therapy.</a> The Journal of the American Society of Gene Therapy. 19, 83-92 (2011).</li><li>Zaiss, A. K., 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=Hepatocyte+Heparan+Sulfate+Is+Required+for+Adeno-Associated+Virus+2+but+Dispensable+for+Adenovirus+5+Liver+Transduction+In+Vivo.">Hepatocyte Heparan Sulfate Is Required for Adeno-Associated Virus 2 but Dispensable for Adenovirus 5 Liver Transduction In Vivo.</a> Journal of Virology. 90, 412-420 (2015).</li><li>Delgado, C., Francis, G. E., Fisher, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+uses+and+properties+of+PEG-linked+proteins.">The uses and properties of PEG-linked proteins.</a> Critical Reviews in Therapeutic Drug Carrier Systems. 9, 249-304 (1992).</li><li>Parveen, S., Sahoo, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanomedicine:+clinical+applications+of+polyethylene+glycol+conjugated+proteins+and+drugs.">Nanomedicine: clinical applications of polyethylene glycol conjugated proteins and drugs.</a> Clin. Pharmacokinet. 45, 965-988 (2006).</li><li>O'Riordan, C. R., 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=PEGylation+of+adenovirus+with+retention+of+infectivity+and+protection+from+neutralizing+antibody+in+vitro+and+in+vivo.">PEGylation of adenovirus with retention of infectivity and protection from neutralizing antibody in vitro and in vivo.</a> Human Gene Therapy. 10, 1349-1358 (1999).</li><li>Subr, V., 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=Coating+of+adenovirus+type+5+with+polymers+containing+quaternary+amines+prevents+binding+to+blood+components.">Coating of adenovirus type 5 with polymers containing quaternary amines prevents binding to blood components.</a> Journal of Controlled Release. 135, 152-158 (2009).</li><li>Kreppel, F., Gackowski, J., Schmidt, E., Kochanek, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combined+genetic+and+chemical+capsid+modifications+enable+flexible+and+efficient+de-+and+retargeting+of+adenovirus+vectors.+Molecular+Therapy.">Combined genetic and chemical capsid modifications enable flexible and efficient de- and retargeting of adenovirus vectors. Molecular Therapy.</a> The Journal of the American Society of Gene Therapy. 12, 107-117 (2005).</li><li>Corjon, 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=Targeting+of+adenovirus+vectors+to+the+LRP+receptor+family+with+the+high-affinity+ligand+RAP+via+combined+genetic+and+chemical+modification+of+the+pIX+capsomere.">Targeting of adenovirus vectors to the LRP receptor family with the high-affinity ligand RAP via combined genetic and chemical modification of the pIX capsomere.</a> Molecular Therapy: The Journal of the American Society of Gene Therapy. 16 (11), 1813-1824 (2008).</li><li>Prill, J. -. M., 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=Modifications+of+adenovirus+hexon+allow+for+either+hepatocyte+detargeting+or+targeting+with+potential+evasion+from+Kupffer+cells.+Molecular+Therapy.">Modifications of adenovirus hexon allow for either hepatocyte detargeting or targeting with potential evasion from Kupffer cells. Molecular Therapy.</a> The Journal of the American Society of Gene Therapy. 19, 83-92 (2011).</li><li>Krutzke, L., 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=Substitution+of+blood+coagulation+factor+X-binding+to+Ad5+by+position-specific+PEGylation:+Preventing+vector+clearance+and+preserving+infectivity.">Substitution of blood coagulation factor X-binding to Ad5 by position-specific PEGylation: Preventing vector clearance and preserving infectivity.</a> Journal of Controlled Release. 235, 379-392 (2016).</li><li>Prill, J. -. M., 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=Traceless+bioresponsive+shielding+of+adenovirus+hexon+with+HPMA+copolymers+maintains+transduction+capacity+in+vitro+and+in+vivo.">Traceless bioresponsive shielding of adenovirus hexon with HPMA copolymers maintains transduction capacity in vitro and in vivo.</a> PloS One. 9, e82716 (2014).</li><li>Kratzer, R. F., Kreppel, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production,+Purification,+and+Titration+of+First-Generation+Adenovirus+Vectors.">Production, Purification, and Titration of First-Generation Adenovirus Vectors.</a> Methods in Molecular Biology. , 377-388 (2017).</li><li>Blum, H., Beier, H., Gross, H. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+silver+staining+of+plant+proteins,+RNA+and+DNA+in+polyacrylamide+gels.">Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels.</a> ELECTROPHORESIS. 8, 93-99 (1987).</li></ol>

The efficiency by which the genetically introduced cysteines can be chemically modified is typically 80-99%, and certain variables influence this efficiency. First, it is paramount that the genetically introduced cysteines do not undergo premature oxidation. While being well-protected in the reducing environment of the producer cells, it is mandatory to provide a non-oxidative environment after releasing vector particles from the producer cells and during chemical modification. To this end, reducing reagents can be used ...

Adenoviruses (Ad), members of the family Adenoviridae, are non-enveloped DNA viruses of which more than 70 types so far have been identified (http://hadvwg.gmu.edu). Depending on hemaglutination properties, genome structure, and sequencing results, the 70 Ad types can be divided into seven species (human adenoviruses A to G)1,2. The human Ad genome is 38 kb in size and encapsulated by an icosahedral nucleocapsid3. Due to their abundance, the capsid protein hexon, penton base, and fiber are all referred to as major capsid proteins. The most abundant and largest capsid protein hexon forms 20 capsid facets, each consisting of 12 hexon homotrimers4,5. Penton, located on each icosahedral edge (vertex), consists of pentamers of a penton base and represents the base for the vertex spike that is built of glycosylated fiber trimers5,6. The native Ad cell entry is basically composed of two major steps. First, the fiber knob binds to the primary receptor. In Ad types from species A, C, E, and F, this is the coxsackie and adenovirus receptor (CAR). This interaction brings the virion into spatial proximity of the cell surface, thereby facilitating interactions between cellular integrins and RGD-motif in the penton base and consequently inducing cellular responses. Second, changes in the cytoskeleton lead to internalization of the virion and transport to the endosome7. Upon partial disassembly in the endosome, the virion is released to the cytoplasm und ultimately travels to the nucleus for replication.
While Ad can be delivered locally (e.g., for genetic vaccination), systemic delivery through the bloodstream as required for onco-virotherapy faces several barriers. While circulating in the bloodstream, injected virions encounter the defense system of the host&#39;s immune system, leading to fast neutralization of the virus-based vectors and rendering Ad-based vectors extremely inefficient in systemic applications. Furthermore, the natural hepatotropism of Ad interferes with systemic delivery and must be resolved to redirect Ad to its new target cells.
Germline-encoded natural IgM antibodies of the innate immune system rapidly recognize and bind highly repetitive structures on the surface of the virion8,9. These immune complexes then activate the classical and non-classical pathways of the complement system, leading to fast complement-mediated neutralization of a large portion of the virions8. A second pathway resulting in major removal of Ad virions is mediated by macrophages10&#160;and associated with acute toxic and haemodynamic side effects11,12. In the case of Ad in particular, Kupffer cells residing in the liver bind to and phagocytically take up the Ad virions via specific scavenger receptors, thereby eliminating them from the blood13,14,15. Specific scavenger receptors have also been identified on liver sinusoidal endothelial cells (LSE cells)16,and LSE cells also seem to contribute to vector elimination17, but to what extent still needs clarification. Furthermore, some Ad types and their&#160;derived vectors are efficiently sequestered by human erythrocytes18&#160;to which they bind via CAR or the complement receptor CR119.&#160;Of note, this sequestering mechanism cannot be studied in the mouse model system as in contrast to human erythrocytes, mouse erythrocytes do not express CAR.
Specific anti-Ad antibodies generated by the adaptive immune system after exposure to Ad either due to previous infections with Ad or after the first delivery in systemic applications raise a further barrier to effective use of Ad vectors, and they should be evaded in efficient systemic delivery.
Finally, the strong hepatotropism of some Ad types (including Ad5) severely hinders application of Ad in systemic therapy. This tropism resulting in hepatocyte transduction is due to the high affinity of the Ad virion to blood coagulation factor X (FX), mediated by the interaction of FX with the Ad hexon protein20,21,22. FX bridges the virion to heparin sulfate glycans (HSPGs) on the surface of hepatocytes20,23,24,25. A crucial factor for this interaction seems to be the specific extent of N- and O-sulfation of the HSPGs in liver cells24, which is distinct from HSPGs on other cell types. In addition to this FX-mediated pathway, recent studies suggest further pathways not yet identified that result in Ad transduction of hepatocytes26,27,28.
Recently, it has been shown that FX is not only involved in hepatocyte transduction of Ad, but also by binding, the virion shields the virus particle against neutralization by the complement system26. Reduction of hepatocyte transduction by preventing FX binding, therefore, would create the unwanted side effect of increasing Ad neutralization via the innate immune system.
A profound knowledge of the complex interactions between vectors and host organisms is therefore necessary to develop more efficient vectors for systemic applications that circumvent the obstacles imposed by the host&#39;s organism.
One strategy that has been originally used for therapeutic proteins has been adapted for Ad vectors to at least partially overcome the above described barriers. Antigenicity and immunogenicity of therapeutic protein compounds could be reduced by coupling to polyethylene glycol (PEG)29,30. Hence, the covalent coupling of polymers such as PEG or poly[N-(2-hydroxypropyl)methacrylamid] (pHPMA) to the capsid surface shields the vector from unwanted vector-host interactions. Commonly, polymer coupling targets &#949;-amine groups from lysine side residues that are randomly distributed on the capsid surface. Vector particles in solution are, due to the hydrophilic nature of the attached polymers, surrounded by a stable water shell that reduces the risk of immune cell recognition or enzymatic degradation. Moreover, PEGylated Ad vectors were shown to evade neutralization by anti-hexon antibodies in vitro and in pre-immunized mice in vivo31. In contrast to genetic capsid modifications, chemical coupling of polymers is performed after production and purification, allowing not only for the use of conventional producer cells and production of high titer vector stocks, but also for simultaneous modification of thousands of amino acids on the capsid surface. However, amine-directed shielding occurs randomly throughout the whole capsid surface, resulting in high heterogeneities and not allowing for modification of specific capsomers. Furthermore, the large polymer moieties required for beneficial effects impair virus bioactivity32.
To overcome these limitations, Kreppel et al.33 introduced a geneti-chemical concept for vector re- and de-targeting. Cysteines were genetically introduced into the virus capsid at solvent-exposed positions like fiber HI-loop33, protein IX34, and hexon35,36. Although not naturally-occurring, cysteine-bearing Ad vectors can be produced at high titers in normal producer cells. Importantly, insertion of cysteines in certain capsomers and in different positions within a single capsomer allows for highly specific modifications of thiol group-reactive moieties. This geneti-chemical approach has been shown to overcome numerous obstacles in Ad vector design. The combination of amine-based PEGylation for detargeting and thiol-based coupling of transferrin to the fiber knob HI-loop has been proven to successfully retarget modified Ad vectors to CAR-deficient cells33. Since hexon is involved in most undesired interactions (neutralizing antibodies, blood coagulation factor FX), thiol-based modification strategies were also applied to hexon. Coupling small PEG moieties to HVR5 of hexon prevented Ad vector particles to transduce SKOV-3 cells in the presence of FX, whereas large PEG moieties increased hepatocyte transduction14,35. Ad vector particles carrying mutations in the fiber knob inhibiting CAR binding and in HVR7 inhibiting binding of FX (and bearing inserted cysteines in HVR1 for position-specific PEGylation) were shown to evade antibody- and complement-mediated neutralization, as well as scavenger receptor-mediated uptake without loss of infectivity. Interestingly, despite a lack of the natural FX shield, PEGylation again improved transduction of hepatocytes as a function of PEG size36. However, it was shown that covalent shielding does have an impact on intracellular trafficking processes. Prill et al. compared irreversible versus bioresponsive shields based on pHPMA and demonstrated that neither the mode of shielding nor co-polymer charge had an impact on cell entry but did affect particle trafficking to the nucleus. Employing a bioresponsive shield with positively charged pHPMA co-polymers allowed for particle trafficking to the nucleus, maintaining the high transduction efficiencies of Ad vectors in vitro and in vivo37.
In summary, these data indicate that, even under the assumption that all vector-host-interactions were known and considered, excessive capsid surface modifications are necessary to overcome the hurdles associated with systemic vector delivery.
Here we provide a protocol to perform site-specific chemical modifications of adenovirus vector capsids for shielding and/or retargeting of adenovirus vector particles and adenovirus-based oncolytic viruses. The concept of this technology is outlined in Figure 1. It allows the shielding of certain capsid regions from unwanted interactions by covalent attachment of synthetic polymers. At the same, it also provides a means to attach ligands and combine shielding and targeting. Using simple chemistry, experimenters will be able to covalently modify adenovirus vector surface with a wide variety of molecules including peptides/proteins, carbohydrates, lipids, and other small molecules. Furthermore, the protocol provides a general concept for the chemical modification of biologically active virus-derived vectors under maintenance of their biological integrity and activity.

<table>
	<tbody>
		<tr>
			<td>Vector purification and chemical modification</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Argon gas</td>
			<td>Air liquide</td>
			<td>local gas dealer</td>
			<td></td>
		</tr>
		<tr>
			<td>Liquid Nitrogen</td>
			<td>Air liquide</td>
			<td>local gas dealer</td>
			<td></td>
		</tr>
		<tr>
			<td>500 mL centrifuge tubes</td>
			<td>Corning</td>
			<td>431123</td>
			<td></td>
		</tr>
		<tr>
			<td>Stericup Express Plus 0.22 &#181;m</td>
			<td>Millipore</td>
			<td>SCGPU02RE</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris(2-carboxyethyl) phosphine (TCEP)</td>
			<td>Sigma-Aldrich</td>
			<td>C4706-10g</td>
			<td></td>
		</tr>
		<tr>
			<td>2 mL (3mL) Norm Ject (syringes)</td>
			<td>Henke Sass Wolf</td>
			<td>4020.000V0</td>
			<td></td>
		</tr>
		<tr>
			<td>Fine-Ject needles for single use (yellow 0.9 x 40 mm)</td>
			<td>Henke Sass Wolf</td>
			<td>4710009040</td>
			<td></td>
		</tr>
		<tr>
			<td>Caesium chloride 99.999% Ultra Quality</td>
			<td>Roth</td>
			<td>8627.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Silica gel beads</td>
			<td>Applichem</td>
			<td>A4569.2500</td>
			<td></td>
		</tr>
		<tr>
			<td>Methoxypolyethylene glycol maleimide - 750 (PEG mal-750)</td>
			<td>Iris Biotech</td>
			<td></td>
			<td>store in silica gel beads at -80 &#176;C</td>
		</tr>
		<tr>
			<td>13.2 mL Ultra Clear Ultracentrifuge Tubes</td>
			<td>Beckman Coulter</td>
			<td>344059</td>
			<td>only open in hood</td>
		</tr>
		<tr>
			<td>PD-10 size exclusion chromatography column</td>
			<td>GE Healthcare</td>
			<td>17-0851-01</td>
			<td>store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Hepes</td>
			<td>AppliChem</td>
			<td>A1069.1000</td>
			<td></td>
		</tr>
		<tr>
			<td>SDS Ultrapure</td>
			<td>AppliChem</td>
			<td>A1112,0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>AppliChem</td>
			<td>A1123.1000</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Material for cell-culture</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS</td>
			<td>PAN Biotech</td>
			<td>P04-36500</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>PAN Biotech</td>
			<td>P04-03590</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin/EDTA</td>
			<td>PAN Biotech</td>
			<td>P10-0231SP</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS Good</td>
			<td>PAN Biotech</td>
			<td>P40-37500</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin</td>
			<td>PAN Biotech</td>
			<td>P06-07100</td>
			<td></td>
		</tr>
		<tr>
			<td>Biosphere Filter Tips (various sizes)</td>
			<td>Sarstedt</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Serological Pipettes (various sizes)</td>
			<td>Sarstedt</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>reaction tubes (various sizes)</td>
			<td>Sarstedt</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>TC plates 15cm</td>
			<td>Sarstedt</td>
			<td>83.3903</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Material for silver staining protocol</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>J.T.Baker</td>
			<td>8045</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol absolute</td>
			<td>AppliChem</td>
			<td>1613,2500PE</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic Acid</td>
			<td>AppliChem</td>
			<td>A0820,2500PE</td>
			<td></td>
		</tr>
		<tr>
			<td>Formaldehyde 37%</td>
			<td>AppliChem</td>
			<td>A0877,0250</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol absolute</td>
			<td>AppliChem</td>
			<td>A1613,2500PE</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium thiosulfate</td>
			<td>AppliChem</td>
			<td>1,418,791,210</td>
			<td></td>
		</tr>
		<tr>
			<td>Silver nitrate</td>
			<td>AppliChem</td>
			<td>A3944.0025</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium carbonate</td>
			<td>AppliChem</td>
			<td>A3900,0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Special Lab Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Desiccator</td>
			<td>Nalgene</td>
			<td>5311-0250</td>
			<td></td>
		</tr>
		<tr>
			<td>Megafuge 40</td>
			<td>Heraeus</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Roter for Megafuge TX750 + Adapter andLlids for 500 mL tubes</td>
			<td>Heraeus</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Water bath</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ultracentrifuge e.g. Optima XPN-80</td>
			<td>Beckman Coulter</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>suitable Ultrazentrifuge Rotor e.g. SW41</td>
			<td>Beckman Coulter</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>pH -Meter</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Stand with clamps</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Goose neck lamp</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Over-head rotor</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Thermal Block</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Photometer (OD 260)</td>
			<td>Conventional</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

combined genetic and chemical capsid modifications of adenovirus-based gene transfer vectors for shielding and targeting

Adenovirus vectors are potent tools for genetic vaccination and oncolytic virotherapy. However, they are prone to multiple undesired vector-host interactions, especially after in vivo delivery. It is a consensus that the limitations imposed by undesired vector-host interactions can only be overcome if defined modifications of the vector surface are performed. These modifications include shielding of the particles from unwanted interactions and targeting by the introduction of new ligands. The goal of the protocol presented here is to enable the reader to generate shielded and, if desired, retargeted human adenovirus gene transfer vectors or oncolytic viruses. The protocol will enable researchers to modify the surface of adenovirus vector capsids by specific chemical attachment of synthetic polymers, carbohydrates, lipids, or other biological or chemical moieties. It describes the cutting-edge technology of combined genetic and chemical capsid modifications, which have been shown to facilitate the understanding and overcoming of barriers for in vivo delivery of adenovirus vectors. A detailed and commented description of the crucial steps for performing specific chemical reactions with biologically active viruses or virus-derived vectors is provided. The technology described in the protocol is based on the genetic introduction of (naturally absent) cysteine residues into solvent-exposed loops of adenovirus-derived vectors. These cysteine residues provide a specific chemical reactivity that can, after production of the vectors to high titers, be exploited for highly specific and efficient covalent chemical coupling of molecules from a wide variety of substance classes to the vector particles. Importantly, this protocol can easily be adapted to perform a broad variety of different (non-thiol-based) chemical modifications of adenovirus vector capsids. Finally, it is likely that non-enveloped virus-based gene transfer vectors other than adenovirus can be modified from the basis of this protocol.

Figure 2 shows examples of the cytopathic effect (CPE) on 293 (HEK 293) cells that indicates successful vector production. Cells should show morphology (Figure 2C) 40-48 hours after inoculation with the virus vector. The right timepoint for harvesting is crucial for not losing virus particles by cell lysis and preventing oxidation of the genetically introduced thiol groups. If vector particles are released into the medium by cell...

Watch this Scientific Journal Video about Combined Genetic and Chemical Capsid Modifications of Adenovirus-Based Gene Transfer Vectors for Shielding and Targeting at JoVE.com

Combined Genetic and Chemical Capsid Modifications of Adenovirus-Based Gene Transfer Vectors for Shielding and Targeting

The protocol described here enables researchers to specifically modify adenovirus capsids at selected sites by simple chemistry. Shielded adenovirus vectors particles and retargeted gene transfer vectors can be generated, and vector host interactions can be studied.

Adenovirus vectors are potent tools for genetic vaccination and oncolytic virotherapy. However, they are prone to multiple undesired vector-host ...

This method can help to answer key questions in the field of Gene Therapy, Oncolysis and Genetic Vaccination. It facilitates understanding and modulating of vector hosts interactions of adenovirus gene transfer vectors, the most frequently used vector type in clinical trials up to date. The main advantage of this technique is that adenovirus capsulates can be specifically modified in a highly defined manner at selected positions and to variable extent by using simple chemistry.The implications of this technique extends towards therapy because vector host modification cannot only be analyzed but also modulated in a patient oriented way. Though this method provides insight into specific vector host interactions, it may also be used for labeling and tracking of virus particles in living organisms, such as mice. Generally, individuals new to this method will struggle with the unique combination of Virology and Organic Cchemistry that requires practical knowledge from both fields.Special demonstration of this technique is critical because here methods from Organic Chemistry meet methods from Cell Biology and Virology, including field-specific handling tricks. To begin this procedure prepare all buffers as outlined in the text protocol. Weigh one milliliter of each gradient buffer to check its density.After sterilizing all the buffers, sparge the buffers containing TCEP with argon gas for about 30 seconds to prevent oxidation of the TCEP. Store the vials containing the solid powdered coupling moiety in larger tubes, each filled with a cushion of silica gel beads, to prevent the build up of condensing water when thawing the vials. Place these tubes into a desiccator.Remove the air in the desiccator and replace it with argon gas. Then close each tube tightly and transfer it into a bigger container with silica gel beads. Once all the tubes have been transferred, close the container.Store the container at 80 degrees Celsius until ready to use. When ready to thaw, place the container into a layer of silica beads in a desiccator. Allow the container to slowly warm to room temperature and then open the container.When cells reach the optimal cytopathic affect, collect them by scraping the plates and transferring the supernatant to centrifuge tubes. Spin the cell suspension at 400 times G for 10 minutes. Next, re-suspend the cell pellet in four milliliters of Ad buffer containing 10 millimolar TCEP and transfer the resulting solution to a sterile 50 milliliter tube.Freeze the solution in liquid nitrogen, and then thaw it in a water bath at 37 degrees Celsius. Repeat this freeze thaw cycle three times to rescue the vector. Centrifuge at 5000 G and four degrees Celsius for ten minutes.While centrifuging set out two ultra centrifuge tubes to begin preparing two equal Cesium chloride step gradients. Add three milliliters of the lower phase to each of these tubes. Mark the level of the lower phase on the tube before loading the upper phase.Then carefully stack five milliliters of the upper phase unto the lower phase, pipetting it very slowly down along the walls of the tube. When the gradients are prepared and centrifugation is complete load the supernatant from the sample equally over the two gradients. Fill the remaining space in each gradient tube with Ad-buffer containing ten millimolar TCEP making sure to fill the tubes all the way to the top.Adjust the weight of the opposite tubes to a zero weight difference. And alter centrifuge for 176000 times G and 4 degrees Celsius for two hours. After this, use a clamp to fix one ultra centrifugation tubes to a stand.Making sure to leave the area around the lower phase level marked accessible. Place the goose-necked lamp above the tube. Around the mark, at the border between the lower and upper phases, a distinct band should be visible.Puncture the tube with a needle, and aspirate the vector band into a syringe to collect the vector. Transfer collected vector virons to a 15 milliliter tube and calculate the amount of coupling substrate needed as outlined in the text protocol. Then, transfer the vector solution to a tube of appropriate size.And the calculated amount of coupling compounds stock solution. Gently mix by overhead rotation for one hour at room temperature. Next, adjust the total volume of the vector solution to six milliliters by adding Ad buffer.Purify the vector from the unreacted coupling moiety using a second Cesium chloride binding step as outlined in the text protocol. Puncture the tube with a needle and aspirate the vector band into a syringe. Transfer the collected vectors to a 15 milliliter tube.If the combined from both gradient tubes is less than 2.5 milliliters, adjust the volume to 2.5 milliliters by adding Ad buffer. Load the combined virons unto an equal upgraded Pd column and discard the flow through. Then add three milliliters of Ad buffer to the column and collect the flow through.Add 333 microliters of glycerol to the collected flow through to obtain the final concentration of ten percent. Divide these into suitable aliquots. Making sure to include an aliquot of 20 microliters for tighter determination by OD 260 measurement.Store the vector solution at 80 degrees Celsius until ready to use. Representative results of the effects on 293 cells indicate that vector production is successful. Cells should show morphology 40-48 hours after being inoculated with the virus vector.Silver stained SDS phage is then used to assessed coupling efficiency. Vectors with Cysteins introduced into the capsomere pentone base both with the hexon modified and unmodified are run. The Hexon bands exhibit a shift indicating successful modification of over 90 percent of the monomers per capsid.While attempting this procedure it is important to ensure a reducing environment for unmodofied vector particle. After modification, a regular atmosphere is suitable. Precise documentary calculations have to ensure quantitative modification of all vector particles.The development of this technique helps research in the field of Gene Therapy to further explore safe and deficient strategies for vector delivery. Following this procedure other methods like coupling of ligands for targeting or fluorescent dyes for labeling can be performed in order to answer additional questions like receptor usage and bio distribution. Please make sure to obey your local GMO and Working Safety Regulations.

combined-genetic-chemical-capsid-modifications-adenovirus-based-gene

Research

Education

JoVE Journal

JoVE Core

Molecular Biology

Biology

Unit 1

DNA, Cells, and Evolution

SCIENTISTS IN ACTION

Culture of myeloid dendritic cells from bone marrow precursors

Myeloid dendritic cells (DCs) are frequently used to study the interactions between innate and adaptive immune mechanisms and the early response to infection. Because these are the most potent antigen presenting cells, DCs are being increasingly used as a vaccine vector to study the induction of antigen-specific immune responses. In this video, we demonstrate the procedure for harvesting tibias and femurs from a donor mouse, processing the bone marrow and differentiating DCs in vitro. The properties of DCs change following stimulation: immature dendritic cells are potent phagocytes, whereas mature DCs are capable of antigen presentation and interaction with CD4+ and CD8+ T cells. This change in functional activity corresponds with the upregulation of cell surface markers and cytokine production. Many agents can be used to mature DCs, including cytokines and toll-like receptor ligands. In this video, we demonstrate flow cytometric comparisons of expression of two co-stimulatory molecules, CD86 and CD40, and the cytokine, IL-12, following overnight stimulation with CpG or mock treatment. After differentiation, DCs can be further manipulated for use as a vaccine vector or to generate antigen-specific immune responses by in vitro pulsing using peptides or proteins, or transduced using recombinant viral vectors. 

This video demonstrates the procedure for differentiating myeloid dendritic cells from mouse bone marrow. Isolation of mouse tibia and femur, and processing of bone marrow are demonstrated. Pictures demonstrating cell morphology before and after differentiation, and figures depicting cell phenotype and IL-12 production following maturation using CpG are shown.

Myeloid dendritic cells (DCs) are frequently used to study the interactions between innate and adaptive immune mechanisms and the early response to ...

Method for Culture of Early Chick Embryos ex vivo (New Culture)

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  the formation and patterning of brain, neural tube, somite and heart primordia. Applications of chick embryo culture include electroporation of DNA or RNA constructs in order to analyze gene function, grafts of growth factor coated beads such as FGFs and BMPs , as well as whole mount in situ hybridization and immunohistochemistry. This video demonstrates the different steps in chick embryo culture; First, the embryo is explanted in saline. Then, the embryo is centered on a glass ring. The membranes surrounding the embryo are lifted along the walls of the ring. The ring is then placed in a culture dish containing a pool of albumine. The culture dish is sealed and placed in a humid chamber, where the embryo is cultured for up to 24 hrs. Finally, the embryo is removed from the ring, fixed and processed for further applications. A troubleshooting guide is also presented.

Method for Culture of Early Chick Embryos ex vivo New Culture

This video demonstrates New culture, a method by which chick embryos are cultured outside the egg for up to 24 hr. This method enables one to study early development (primitive streak to 14 som.), a period corresponding to E7-9 in mouse. Applications of this technique include electroporation, in situ hybridization and immunohistochemistry.

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

Double Whole Mount in situ Hybridization of Early Chick Embryos

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  gene expression in brain, neural tube, somite and heart primordia formation. This video demonstrates the different steps in 2-color whole mount in situ hybridization; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, the embryo is processed for prehybridization. The embryo is then hybridized with two different probes, one coupled to DIG, and one coupled to FITC.  Following overnight hybridization, the embryo is incubated with DIG coupled antibody. Color reaction for DIG substrate is performed, and the region of interest appears blue. The embryo is then incubated with FITC coupled antibody. The embryo is processed for color reaction with FITC, and the region of interest appears red. Finally, the embryo is fixed and processed for phtograph and sectioning. A troubleshooting guide is also presented.

This video demonstrates 2-color whole mount in situ hybridization, a method by which the spatial and temporal expression pattern of 2 different genes can be visualized in young chick embryos. This method was originally introduced by David Wilkinson, Domingos Henrique, Phil Ingham and David Ish -Horowicz.

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

The number of significant genetic associations with common complex traits is constantly increasing. However, most of these associations have not been understood at molecular level. One of the mechanisms mediating the effect of DNA variants on phenotypes is gene expression, which has been shown to be particularly relevant for complex traits1.
This method tests in a cellular context the effect of specific DNA sequences on gene expression. The principle is to measure the relative abundance of transcripts arising from the two alleles of a gene, analysing cells which carry one copy of the DNA sequences associated with disease (the risk variants)2,3. Therefore, the cells used for this method should meet two fundamental genotypic requirements: they have to be heterozygous both for DNA risk variants and for DNA markers, typically coding polymorphisms, which can distinguish transcripts based on their chromosomal origin (Figure 1). DNA risk variants and DNA markers do not need to have the same allele frequency but the phase (haplotypic) relationship of the genetic markers needs to be understood. It is also important to choose cell types which express the gene of interest. This protocol refers specifically to the procedure adopted to extract nucleic acids from fibroblasts but the method is equally applicable to other cells types including primary cells.
DNA and RNA are extracted from the selected cell lines and cDNA is generated. DNA and cDNA are analysed with a primer extension assay, designed to target the coding DNA markers4. The primer extension assay is carried out using the MassARRAY (Sequenom)5 platform according to the manufacturer's specifications. Primer extension products are then analysed by matrix-assisted laser desorption/ionization time of-flight mass spectrometry (MALDI-TOF/MS). Because the selected markers are heterozygous they will generate two peaks on the MS profiles. The area of each peak is proportional to the transcript abundance and can be measured with a function of the MassARRAY Typer software to generate an allelic ratio (allele 1: allele 2) calculation. The allelic ratio obtained for cDNA is normalized using that measured from genomic DNA, where the allelic ratio is expected to be 1:1 to correct for technical artifacts. Markers with a normalised allelic ratio significantly different to 1 indicate that the amount of transcript generated from the two chromosomes in the same cell is different, suggesting that the DNA variants associated with the phenotype have an effect on gene expression. Experimental controls should be used to confirm the results.

Genetic associations often remain unexplained at a functional level. This method aims to assess the effect of phenotype-associated genetic markers on gene expression by analyzing cells heterozygous for transcribed SNPs. The technology allows accurate measurement by MALDI-TOF mass spectrometry to quantify allele-specific primer extension products.

The number of significant genetic associations with common complex traits is constantly increasing. However, most of these associations have not been ...

Induction and Testing of Hypoxia in Cell Culture

Hypoxia is defined as the reduction or lack of oxygen in organs, tissues, or cells. This decrease of oxygen tension can be due to a reduced supply in oxygen (causes include insufficient blood vessel network, defective blood vessel, and anemia) or to an increased consumption of oxygen relative to the supply (caused by a sudden higher cell proliferation rate). Hypoxia can be physiologic or pathologic such as in solid cancers 1-3, rheumatoid arthritis, atherosclerosis etc&#x2026; Each tissues and cells have a different ability to adapt to this new condition. During hypoxia, hypoxia inducible factor alpha (HIF) is stabilized and regulates various genes such as those involved in angiogenesis or transport of oxygen 4. The stabilization of this protein is a hallmark of hypoxia, therefore detecting HIF is routinely used to screen for hypoxia 5-7. 
In this article, we propose two simple methods to induce hypoxia in mammalian cell cultures and simple tests to evaluate the hypoxic status of these cells.

Here we propose simple methods to induce hypoxia in cell cultures and simple tests to evaluate the hypoxic status of the cultures.

Hypoxia is defined as the reduction or lack of oxygen in organs, tissues, or cells.  This decrease of oxygen tension can be due to a reduced supply in ...

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Given the ever expanding number of model plant species for which complete genome sequences are available and the abundance of bio-resources such as knockout mutants, wild accessions and advanced breeding populations, there is a rising burden for gene functional annotation. In this protocol, annotation of plant gene function using combined co-expression gene analysis, metabolomics and informatics is provided (Figure 1). This approach is based on the theory of using target genes of known function to allow the identification of non-annotated genes likely to be involved in a certain metabolic process, with the identification of target compounds via metabolomics. Strategies are put forward for applying this information on populations generated by both forward and reverse genetics approaches in spite of none of these are effortless. By corollary this approach can also be used as an approach to characterise unknown peaks representing new or specific secondary metabolites in the limited tissues, plant species or stress treatment, which is currently the important trial to understanding plant metabolism.

Combination of genomics, co-expression gene analysis and the identification of target compounds via metabolism give gene functional annotation.

Given the ever expanding number of model plant species for which complete genome sequences are available and the abundance of bio-resources such as ...

Gene Transfer into Older Chicken Embryos by ex ovo Electroporation

The chicken embryo provides an excellent model system for studying gene function and regulation during embryonic development. In ovo electroporation is a powerful method to over-express exogenous genes or down-regulate endogenous genes in vivo in chicken embryos1. Different structures such as DNA plasmids encoding genes2-4, small interfering RNA (siRNA) plasmids5, small synthetic RNA oligos6, and morpholino antisense oligonucleotides7 can be easily transfected into chicken embryos by electroporation. However, the application of in ovo electroporation is limited to embryos at early incubation stages (younger than stage HH20 - according to Hamburg and Hamilton)8 and there are some disadvantages for its application in embryos at later stages (older than stage HH22 - approximately 3.5 days of development). For example, the vitelline membrane at later stages is usually stuck to the shall membrane and opening a window in the shell causes rupture of the vessels, resulting in death of the embryos; older embryos are covered by vitelline and allantoic vessels, where it is difficult to access and manipulate the embryos; older embryos move vigorously and is difficult to control the orientation through a relatively small window in the shell.
In this protocol we demonstrate an ex ovo electroporation method for gene transfer into chicken embryos at late stages (older than stage HH22). For ex ovo electroporation, embryos are cultured in Petri dishes9 and the vitelline and allantoic vessels are widely spread. Under these conditions, the older chicken embryos are easily accessed and manipulated. Therefore, this method overcomes the disadvantages of in ovo electroporation applied to the older chicken embryos. Using this method, plasmids can be easily transfected into different parts of the older chicken embryos10-12.

Gene Transfer into Older Chicken Embryos by ex ovo Electroporation

A method of gene transfer into chicken embryos at later incubation stages (older than Hamburger and Hamilton stage (HH) 22) is described. This method overcomes disadvantages of in ovo electroporation applied to older chicken embryos and is a useful technique to study gene function and regulation at older developmental stages.

The chicken embryo provides an  excellent model system for studying gene function and regulation during  embryonic development. In ovo electroporation is ...

Subcloning Plus Insertion (SPI) - A Novel Recombineering Method for the Rapid Construction of Gene Targeting Vectors

Gene targeting refers to the precise modification of a genetic locus using homologous recombination. The generation of novel cell lines and transgenic mouse models using this method necessitates the construction of a &#8216;targeting&#8217; vector, which contains homologous DNA sequences to the target gene, and has for many years been a limiting step in the process. Vector construction can be performed in vivo in Escherichia coli cells using homologous recombination mediated by phage recombinases using a technique termed recombineering. Recombineering is the preferred technique to subclone the long homology sequences (>4kb) and various targeting elements including selection markers that are required to mediate efficient allelic exchange between a targeting vector and its cognate genomic locus. Typical recombineering protocols follow an iterative scheme of step-wise integration of the targeting elements and require intermediate purification and transformation steps. Here, we present a novel recombineering methodology of vector assembly using a multiplex approach. Plasmid gap repair is performed by the simultaneous capture of genomic sequence from mouse Bacterial Artificial Chromosome libraries and the insertion of dual bacterial and mammalian selection markers. This subcloning plus insertion method is highly efficient and yields a majority of correct recombinants. We present data for the construction of different types of conditional gene knockout, or knock-in, vectors and BAC reporter vectors that have been constructed using this method. SPI vector construction greatly extends the repertoire of the recombineering toolbox and provides a simple, rapid and cost-effective method of constructing these highly complex vectors.

Subcloning Plus Insertion SPI - A Novel Recombineering Method for the Rapid Construction of Gene Targeting Vectors

Gene targeting methodologies can be used to generate transgenic mice with knockout, knock-in and tagged alleles. Here, we describe an improved method of recombineering in E. coli, that we term &#8216;subcloning plus insertion&#8217;, which can be used to generate custom gene targeting vectors rapidly.

Gene targeting refers to the precise modification of a genetic locus using homologous recombination. The generation of novel cell lines and transgenic ...

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described.

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Here we present a cost-effective method for defining chemical-genetic interactions in budding yeast. The approach is built on fundamental techniques in yeast molecular biology and is well suited for the mechanistic interrogation of small to medium collections of chemicals and other media environments.

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. ...

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP

The identification of molecules associated with specific genomic regions of interest is required to understand the mechanisms of regulation of the functions of these regions. To enable the non-biased identification of molecules interacting with a specific genomic region of interest, we recently developed the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technique. Here, we describe how to use enChIP to isolate specific genomic regions and identify the associated proteins and RNAs. First, a genomic region of interest is tagged with a transcription activator-like (TAL) protein or a clustered regularly interspaced short palindromic repeats (CRISPR) complex consisting of a catalytically inactive form of Cas9 and a guide RNA. Subsequently, the chromatin is crosslinked and fragmented by sonication. The tagged locus is then immunoprecipitated and the crosslinking is reversed. Finally, the proteins or RNAs that are associated with the isolated chromatin are subjected to mass spectrometric or RNA sequencing analyses, respectively. This approach allows the successful identification of proteins and RNAs associated with a genomic region of interest.

The identification of molecules associated with specific genomic regions of interest is required to understand the mechanisms of regulation of the functions of these regions. This protocol describes procedures to perform engineered DNA-binding molecule-mediated chromatin imunoprecipitation (enChIP) for identification of proteins and RNAs associated with a specific genomic region.