Name: silac based proteomic characterization of exosomes from hiv-1 infected cells
Uploaded: 2017-03-03T12:30:00
Description: Watch this Scientific Journal Video about SILAC Based Proteomic Characterization of Exosomes from HIV-1 Infected Cells at JoVE.com

This work was supported by an ARRA supplement to the Lifespan/Tufts/Brown CFAR, P30AI042853-13S1, NIH P20GM103421, P01AA019072, R01HD072693, and K24HD080539 to BR. This work was also supported by Lifespan Pilot Research Fund (#701- 5857), Rhode Island Foundation Medical Research Grant (#20133969), and NIH COBRE URI/RIH Pilot Research Grant (P20GM104317) to ML. We thank James Myall and Vy Dang for help with the manuscript and figure preparation.

1. Cell Culture and HIV-1 Infection
NOTE: Before starting experiments, it is recommended to check the cells&#39; viability through Trypan Blue staining11 and their proliferation through a MTT assay12. It is also critical to use newly prepared SILAC medium. Various cell lines can be used, as long as they are in an actively proliferative stage, and are susceptible to HIV-1 infection, or the test condition of choice. In this protocol, use H9 cell line...

<ol>
	<li>Kowal, J., 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=Proteomic+comparison+defines+novel+markers+to+characterize+heterogeneous+populations+of+extracellular+vesicle+subtypes.">Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes.</a> Proc Natl Acad Sci U S A. 113 (8), 968-977 (2016).</li><li>Schorey, J. S., Bhatnagar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exosome+function:+from+tumor+immunology+to+pathogen+biology.">Exosome function: from tumor immunology to pathogen biology.</a> Traffic. 9 (6), 871-881 (2008).</li><li>Thery, C., Ostrowski, M., Segura, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane+vesicles+as+conveyors+of+immune+responses.">Membrane vesicles as conveyors of immune responses.</a> Nat Rev Immunol. 9 (8), 581-593 (2009).</li><li>Booth, A. 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=Exosomes+and+HIV+Gag+bud+from+endosome-like+domains+of+the+T+cell+plasma+membrane.">Exosomes and HIV Gag bud from endosome-like domains of the T cell plasma membrane.</a> J Cell Biol. 172 (6), 923-935 (2006).</li><li>Van Engelenburg, S. 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=Distribution+of+ESCRT+machinery+at+HIV+assembly+sites+reveals+virus+scaffolding+of+ESCRT+subunits.">Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits.</a> Science. 343 (6171), 653-656 (2014).</li><li>Li, 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=Quantitative+proteomic+analysis+of+exosomes+from+HIV-1-infected+lymphocytic+cells.">Quantitative proteomic analysis of exosomes from HIV-1-infected lymphocytic cells.</a> Proteomics. 12 (13), 2203-2211 (2012).</li><li>Ong, S. E., 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=Stable+isotope+labeling+by+amino+acids+in+cell+culture,+SILAC,+as+a+simple+and+accurate+approach+to+expression+proteomics.">Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.</a> Mol Cell Proteomics. 1 (5), 376-386 (2002).</li><li>Ross, P. 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=Multiplexed+protein+quantitation+in+Saccharomyces+cerevisiae+using+amine-reactive+isobaric+tagging+reagents.">Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.</a> Mol Cell Proteomics. 3 (12), 1154-1169 (2004).</li><li>Anderson, L., Hunter, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+mass+spectrometric+multiple+reaction+monitoring+assays+for+major+plasma+proteins.">Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins.</a> Mol Cell Proteomics. 5 (4), 573-588 (2006).</li><li>Ong, S. E., Mann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stable+isotope+labeling+by+amino+acids+in+cell+culture+for+quantitative+proteomics.">Stable isotope labeling by amino acids in cell culture for quantitative proteomics.</a> Methods Mol Biol. 359, 37-52 (2007).</li><li>Strober, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Current Protocols in Immunology. , (2001).</li><li>Verma, 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=Evaluation+of+the+MTT+lymphocyte+proliferation+assay+for+the+diagnosis+of+neurocysticercosis.">Evaluation of the MTT lymphocyte proliferation assay for the diagnosis of neurocysticercosis.</a> J Microbiol Meth. 81 (2), 175-178 (2010).</li><li>Cepko, C., Pear, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retrovirus+infection+of+cells+in+vitro+and+in+vivo.">Retrovirus infection of cells in vitro and in vivo.</a> Curr Protoc Mol Biol. , (2001).</li><li>Lennette, E. T., Karpatkin, S., Levy, 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=Indirect+immunofluorescence+assay+for+antibodies+to+human+immunodeficiency+virus.">Indirect immunofluorescence assay for antibodies to human immunodeficiency virus.</a> J Clin Microbiol. 25 (2), 199-202 (1987).</li><li>Thery, C., Amigorena, S., Raposo, G., Clayton, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+characterization+of+exosomes+from+cell+culture+supernatants+and+biological+fluids.">Isolation and characterization of exosomes from cell culture supernatants and biological fluids.</a> Curr Protoc Cell Biol. , 22 (2006).</li><li>Olson, B. J. S. C., Markwell, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Current Protocols in Protein Science. , (2001).</li><li>Gauci, V. J., Padula, M. P., Coorssen, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coomassie+blue+staining+for+high+sensitivity+gel-based+proteomics.">Coomassie blue staining for high sensitivity gel-based proteomics.</a> J Proteom. 90, 96-106 (2013).</li><li>Soldi, M., Bonaldi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ChroP+approach+combines+ChIP+and+mass+spectrometry+to+dissect+locus-specific+proteomic+landscapes+of+chromatin.">The ChroP approach combines ChIP and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin.</a> J Vis Exp. (86), (2014).</li><li>Trompelt, K., Steinbeck, J., Terashima, M., Hippler, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+approach+for+the+comparative+analysis+of+multiprotein+complexes+based+on+15N+metabolic+labeling+and+quantitative+mass+spectrometry.">A new approach for the comparative analysis of multiprotein complexes based on 15N metabolic labeling and quantitative mass spectrometry.</a> J Vis Exp. (85), (2014).</li><li>Li, 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=Stem-loop+binding+protein+is+a+multifaceted+cellular+regulator+of+HIV-1+replication.">Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication.</a> J Clin Invest. 126 (8), 3117-3129 (2016).</li><li>Li, M., Ramratnam, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+Characterization+of+Exosomes+from+HIV-1-Infected+Cells.">Proteomic Characterization of Exosomes from HIV-1-Infected Cells.</a> Methods Mol Biol. 1354, 311-326 (2016).</li><li>Emmott, E., Goodfellow, I. <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+protein+interaction+partners+in+mammalian+cells+using+SILAC-immunoprecipitation+quantitative+proteomics.">Identification of protein interaction partners in mammalian cells using SILAC-immunoprecipitation quantitative proteomics.</a> J Vis Exp. (89), (2014).</li><li>Keerthikumar, 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=ExoCarta:+A+Web-Based+Compendium+of+Exosomal+Cargo.">ExoCarta: A Web-Based Compendium of Exosomal Cargo.</a> J Mol Biol. 428 (4), 688-692 (2016).</li><li>Kim, D. 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=EVpedia:+a+community+web+portal+for+extracellular+vesicles+research.">EVpedia: a community web portal for extracellular vesicles research.</a> Bioinformatics. 31 (6), 933-939 (2015).</li><li>Fu, W., 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+immunodeficiency+virus+type+1,+human+protein+interaction+database+at+NCBI.">Human immunodeficiency virus type 1, human protein interaction database at NCBI.</a> Nucleic Acids Res. 37, 417-422 (2009).</li><li>Pathan, 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=FunRich:+An+open+access+standalone+functional+enrichment+and+interaction+network+analysis+tool.">FunRich: An open access standalone functional enrichment and interaction network analysis tool.</a> Proteomics. 15 (15), 2597-2601 (2015).</li><li>Huang da, W., Sherman, B. T., Lempicki, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Systematic+and+integrative+analysis+of+large+gene+lists+using+DAVID+bioinformatics+resources.">Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.</a> Nat Protoc. 4 (1), 44-57 (2009).</li><li>Szklarczyk, 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=The+STRING+database+in+2011:+functional+interaction+networks+of+proteins,+globally+integrated+and+scored.">The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.</a> Nucleic Acids Res. 39, 561-568 (2011).</li><li>Thery, C., Amigorena, S., Raposo, G., Clayton, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+characterization+of+exosomes+from+cell+culture+supernatants+and+biological+fluids.">Isolation and characterization of exosomes from cell culture supernatants and biological fluids.</a> Curr Protoc Cell Biol. , (2006).</li><li>Lobb, R. J., 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=Optimized+exosome+isolation+protocol+for+cell+culture+supernatant+and+human+plasma.">Optimized exosome isolation protocol for cell culture supernatant and human plasma.</a> J Extracell Vesicles. 4, 27031 (2015).</li><li>Webber, J., Clayton, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+pure+are+your+vesicles.">How pure are your vesicles.</a> J Extracell Vesicles. 2, (2013).</li><li>Cantin, R., Diou, J., Belanger, D., Tremblay, A. M., Gilbert, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discrimination+between+exosomes+and+HIV-1:+purification+of+both+vesicles+from+cell-free+supernatants.">Discrimination between exosomes and HIV-1: purification of both vesicles from cell-free supernatants.</a> J Immunol Methods. 338 (1-2), 21-30 (2008).</li><li>Chertova, E., 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=Proteomic+and+biochemical+analysis+of+purified+human+immunodeficiency+virus+type+1+produced+from+infected+monocyte-derived+macrophages.">Proteomic and biochemical analysis of purified human immunodeficiency virus type 1 produced from infected monocyte-derived macrophages.</a> J Virol. 80 (18), 9039-9052 (2006).</li><li>Nikolov, M., Schmidt, C., Urlaub, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+mass+spectrometry-based+proteomics:+an+overview.">Quantitative mass spectrometry-based proteomics: an overview.</a> Methods Mol Biol. 893, 85-100 (2012).</li></ol>

In the procedures described in this paper, we demonstrated the application of the SILAC technique to investigate the effect of HIV-1 infection on the host exosomal proteome. Initially, uninfected and HIV-1 infected cells are differentially isotope-labeled. The differentially labeled exosomes are then purified before performing protein extraction. Next, liquid chromatography-tandem mass spectrometry is employed to analyze the exosomal proteome. Finally, the resulting mass spectrometry data and potential candidate proteins...

Many human diseases, including viral infections, are often associated with distinctive cellular processes that take place in and around the affected cells. Proteins, often acting as the ultimate cellular effectors, mediate these processes. Analysis of the proteins often can provide invaluable information as to the local environment of affected cells and help us to understand the underlying mechanism of disease pathogenesis. Among various protein analysis techniques, proteomics holds particularly great promise. As a powerful, large-scale tool, proteomics can provide a systemic understanding of cellular processes, particularly in the area of the function and interaction of proteins. Analyzing specific proteins is made simpler through the development of labeling techniques, which allow investigators to monitor the expression of cellular components, particularly proteins, in the site of investigation. Although many proteomic analyses have been performed at cellular proteome scale, proteomic characterizations on subcellular compartments have proved to be particularly informative1. This is exemplified well in the studies of HIV-1 infection.
Exosomes, 30-100 nm membrane vesicles secreted by a wide range of cell types2,3, are critical components of intercellular communication and molecular transport. They were previously discovered to play important roles in the HIV-1 budding process4,5. By combining proteomic analysis with functional dissection, we found that exosomes released from HIV-1 infected cells are composed of a unique and quantitatively different protein signature and harbor regulatory molecules that impact cellular properties on neighboring receptive cells, including cellular apoptosis and proliferation6. The methods are described in this protocol, namely SILAC (stable isotope labeling by amino acids in cell culture)7 based proteomic characterization of exosomes from HIV-1 infected cells. Similar approaches can be applied to better understand other subcellular compartments during pathogenesis by adjusting the experimental stress to the specific compartment or fraction of interest and making necessary changes to the described procedures.
Given the recent development of quantitative proteomic methods, there are many to choose from when selecting the most efficient method for a particular experiment. Among these are the chemical-based iTRAQ (isobaric tags for relative and absolute quantification)8 and the label-free MRM (multiple reaction monitoring)9 techniques. Both methods are powerful tools and are good choices for specific settings. For a typical laboratory mainly working with cell lines, however, these two methods have relatively higher costs and are more time-consuming when compared to the SILAC based method. SILAC is a metabolic based labeling technique that incorporates nonradioactive isotopic forms of amino acids from the culture media into cellular proteins. Typically, SILAC experiments start with two cell populations, for example, infected and uninfected. Each is differentially labeled in its specific isotopic environment until full labeling is achieved. The labeled exosomes of these cells are then subjected to protein extraction. Once extracted, the labeled exosomal proteins are analyzed using liquid chromatography tandem mass spectroscopy10. Finally, the mass spectrometry results and significantly labeled proteins are subjected to statistical and bioinformatics analyses as well as rigorous biochemical verification. Our previous investigative reports suggest that the SILAC/exosome procedures are more appropriate for cell lines than primary cells, as cell lines are usually in an active proliferating state for efficient isotopic labeling,

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		<tr height="21">
			<td height="21" style="height:21px;width:227px;">H9 cell line</td>
			<td style="width:121px;">ATCC</td>
			<td style="width:111px;">HTB-176</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">Trypan Blue</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">15250061</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">MTT assay kit</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">V13154</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:26px;width:227px;">Dialyzed fetal bovine serum (FBS)</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">26400044</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">SILAC Protein Quantitation Kit &#8211; RPMI 1640</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">89982</td>
			<td style="width:168px;">DMEM version (89983)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">L-Arginine-HCl, 13C6, 15N4 for SILAC</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">88434</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">L-Lysine-2HCl, 13C6 for SILAC</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">88431</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">HIV-1NL4-3&#160;&#160;</td>
			<td style="width:121px;">NIH AIDS Reagent Program</td>
			<td style="width:111px;">2480</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Alliance HIV-1 p24 Antigen ELISA kit</td>
			<td style="width:121px;">PerkinElmer</td>
			<td style="width:111px;">NEK050001KT</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Refrigerated super-speed centrifuge</td>
			<td style="width:121px;">Eppendorf</td>
			<td style="width:111px;">22628045</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Refrigerated ultracentrifuge</td>
			<td style="width:121px;">Beckman Coulter</td>
			<td style="width:111px;">363118</td>
			<td style="width:168px;">Should be able to reach 100,000g</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">50mL Conical Centrifuge Tubes</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">14-432-22</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">Ultracentrifuge Tubes</td>
			<td style="width:121px;">Beckman Coulter</td>
			<td style="width:111px;">326823</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">SW 32 Ti Rotor</td>
			<td style="width:121px;">Beckman Coulter</td>
			<td style="width:111px;">369694</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">RIPA buffer</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">89900</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">Protease Inhibitor Cocktails</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">&#160;78430</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">ThermoMixer&#160;</td>
			<td style="width:121px;">Eppendorf</td>
			<td style="width:111px;">5384000020</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">BCA Protein Assay Kit&#160;</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">23250</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">Spectrophotometer</td>
			<td style="width:121px;">Biorad</td>
			<td style="width:111px;">1702525</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">SDS PAGE Gel apparatus</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">EI0001</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Novex 4-20% Tris-Glycine Mini Gels</td>
			<td style="width:121px;">Novex</td>
			<td style="width:111px;">XV04200PK20</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">Gel staining reagent</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td style="width:111px;">G1041</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Sequencing Grade Modified Trypsin</td>
			<td style="width:121px;">Promega</td>
			<td style="width:111px;">V5111</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">SpeedVac Concentrator</td>
			<td style="width:121px;">Thermo Fisher</td>
			<td style="width:111px;">SPD131DDA</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:227px;">Antibody to human annexin A5</td>
			<td style="width:121px;">Abcam</td>
			<td style="width:111px;">ab14196</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Antibody to human lactate dehydrogenase B chain</td>
			<td style="width:121px;">Abcam</td>
			<td style="width:111px;">ab53292</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="28">
			<td height="28" style="height:28px;width:227px;">Graphing and Statistical Software</td>
			<td style="width:121px;">Systat&#160;</td>
			<td style="width:111px;">SigmaPlot&#160;</td>
			<td style="width:168px;">Or GraphPad Prism</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:227px;">Quantitative proteomics software suite</td>
			<td style="width:121px;">Max Planck Institue of Biochemistry</td>
			<td style="width:111px;">Maxquant&#160;</td>
			<td style="width:168px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:227px;">Software and databases</td>
			<td style="width:121px;">Various vendors</td>
			<td style="width:111px;"></td>
			<td style="width:168px;">Refer to main text for details</td>
		</tr>
	</tbody>
</table>

silac based proteomic characterization of exosomes from hiv-1 infected cells

Proteomics is the large-scale analysis of proteins. Proteomic techniques, such as liquid chromatography tandem mass spectroscopy (LC-MS/MS), can characterize thousands of proteins at a time. These powerful techniques allow us to have a systemic understanding of cellular changes, especially when cells are subjected to various stimuli, such as infections, stresses, and specific test conditions. Even with recent developments, analyzing the exosomal proteome is time-consuming and often involves complex methodologies. In addition, the resultant large dataset often needs robust and streamlined analysis in order for researchers to perform further downstream studies. Here, we describe a SILAC-based protocol for characterizing the exosomal proteome when cells are infected with HIV-1. The method is based on simple isotope labeling, isolation of exosomes from differentially labeled cells, and mass spectrometry analysis. This is followed by detailed data mining and bioinformatics analysis of the proteomic hits. The resultant datasets and candidates are easy to understand and often offer a wealth of information that is useful for downstream analysis. This protocol is applicable to other subcellular compartments and a wide range of test conditions.

Figure 1A is a flowchart outlining the SILAC labeling procedure21. In order to purify the exosomes, the samples must be spun down via centrifuge. Figure 1B shows the steps of exosome purification by serial ultracentrifugation21. Once purified, the exosomes are subject to experimental proteomic analysis as outlined in the procedure.&#160;
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Watch this Scientific Journal Video about SILAC Based Proteomic Characterization of Exosomes from HIV-1 Infected Cells at JoVE.com

SILAC Based Proteomic Characterization of Exosomes from HIV-1 Infected Cells

Here, we describe a quantitative proteomics method using the technique of stable isotope labeling by amino acids in cell culture (SILAC) to analyze the effects of HIV-1 infection on host exosomal proteomes. This protocol can be easily adapted to cells under different stress or infection conditions.

Proteomics is the large-scale analysis of proteins. Proteomic techniques, such as liquid chromatography tandem mass spectroscopy (LC-MS/MS), can ...

The overall goal of this procedure is to characterize the exosomal proteome from HIV-1 infected cells. This method can help answer the key question in the exosome biology field such as the effect of external stresses on the composition of the exosome proteome. The main advantage of this technique is that it can be learned even with a limited background in proteomics and exosome biology.Though this method can provide insight into HIV infection, it can also be applied to other disease studies such as bacterial infections. The H9 cell line is used in this experiment although various cell lines can be used as long as they are in actively proliferating stage and are susceptible to the test condition of choice. Seed two times 10 to the sixth stage nine cells into each of two cell culture flasks.Grow one population in 10 milliliters of labeled medium containing 10%stylized FBS, 100 milligrams per liter C13-labeled L-lysine, and 100 milligrams per liter C13 and N15-labeled L-arginine. Grow the other population in 10 milliliters of unlabeled medium with 10%stylized FBS, L-lysine, and L-arginine. Grow the cells for six doublings at which point the proteins of the cells in the labeled medium are more than 99%labeled with heavy amino acids.Add fresh media or change media at regular time intervals depending on the type of cells. At the end of labeling, increase the culture volume to 30 milliliters to accommodate the growth of more cells. Infect the labeled cells with the NL4-3 strain of HIV-1 using a standard HIV-1 infection protocol.Add an appropriate amount of virus to the cells and incubate for 48 hours while the unlabeled cells continue to grow in unlabeled medium without HIV-1 infection. At the end of HIV-1 infection, the supernatants from both cell populations are harvested for exosome isolation. Collect the supernatants of the cultures in 50-milliliter conical tubes avoiding the cells.Centrifuge for 10 minutes at 300 times g and four degrees Celsius to remove remaining cells. Collect the supernatants in new 50-milliliter conical tubes and centrifuge for 10 minutes at 2, 000 times g to remove dead cells. Transfer the resulting supernatants to commercial rotor-compatible tubes that are able to withstand ultracentrifugation.Be sure to balance the ultracentrifuge tubes. Centrifuge the tubes for 30 minutes at 10, 000 times g to remove cell debris. Collect the supernatants in new ultracentrifuge tubes.Centrifuge for 70 minutes at 100, 000 times g. Discard the supernatant. Resuspend each exosome-rich pellet in five milliliters of fresh PBS and transfer the solution to a fresh ultracentrifuge tube.Centrifuge again for 70 minutes at 100, 000 times g. After the final spin, discard the supernatant. The cell pellets are now ready for protein extraction.To begin this procedure, dissolve each isolated exosomal pellet in 100 to 200 microliters of fer-pa-lai-ses and extraction buffer with added protease inhibitors that can inhibit a full range of proteases. Centrifuge the dissolved solutions for 10 minutes at 13, 000 times g and four degrees Celsius. Transfer the cleared supernatants to new 1.5-milliliter microcentrifuge tubes.After quantifying the protein concentration of each sample by standard assays, mix equal amounts of proteins from the labeled and unlabeled samples. Run the equal mixture on a four to 20%SDS-PAGE gel for 30 minutes. Stain the gel with Coomassie blue followed by destaining.Using a razor blade, cut the sample lane from the gel, then cut the gel lane into 10 to 15 equal pieces. Put each piece into a fresh 1.5-milliliter microcentrifuge tube for a total of 10 to 15 tubes, and continue with the protein extraction procedure as described in the text protocol. The procedures for proteomic data analysis will not be demonstrated but are summarized in this flowchart.The extracted proteins are first analyzed by liquid chromatography, tandem mass spectroscopy, and the quality of the data is assessed. Next, the data is pretreated by removing proteins that have less than two quantified peptides. Significantly upregulated and downregulated proteins are then identified.Finally, the replicates of the significant candidates are compared to achieve consistency, and the data from all replicates are merged. To begin the characterization of the identified proteins, use their GenBank accession numbers or UniProt IDs to search against current exosome databases. ExoCarta will be used in this demonstration.Click query and input either the gene or protein name or accession number. Any evidence in exosomes verifies that the candidate proteins have been previously found in exosomes and it adds a layer of confidence that the candidates are indeed in exosomes. Next, search the candidates against the HIV-1 and human protein interaction database.On the protein domain name entry, enter the candidate's names or accession numbers, and click search. The search results can provide insight into the interactions between HIV-1 and the protein candidates, and suggest which of the candidates might be truly HIV-1-associated. The third step is to gain global insight on the candidates using a gene ontology or GO analysis software such as fun-brich.Under enrichment analysis, click add dataset and upload the GenBank accession numbers or UniProt IDs of the candidates, then select the chart type to visualize the GO analysis. GO analysis result are visualized in the form of pie charts that provide information about the candidate proteins in the areas of biological process, cellular component, and molecular function. The next step is to identify statistically overrepresented GO terms via DAVID analysis.Click the functional annotation tool, enter the candidate list, and select the identifier of the gene such as the UniProt ID.Select gene list and search. When the search is complete, click the annotation summary results page under the gene ontology category to view the enriched GO terms, p-values, and other parameters. Finally, investigate potential protein-protein interactions and possible biochemical pathways using the openly accessible STRING database.Input the protein ID or sequence into the designated search box and select the correct species for analysis. Click search. The results will give information on both direct and indirect associations.The top 10 known matches for the exosomal candidate displayed in the results should be considered for a significant candidate selection. Representative results from a DAVID analysis of a set of 14 proteins are shown. The biological process enrichment indicated that cell death-related processes are significantly enriched.The cellular component enrichment shows many proteins with an intracellular origin, and the molecular function enrichment identified a role in protein binding for most of the candidates. L-lactate dehydrogenase B chain or LDHB was selected as the most significant candidate, and STRING analysis identified the top 10 interacting partners of LDHB. The majority of LDHB partners were also functionally and locationally related to exosomes in HIV-1.Once mastered, this technique can be done in one week if it is performed properly. While attempting this procedure, it is important to remember to perform each step at the right temperature and condition. Following this procedure, other methods such as affinity isolation can be performed in order to confirm the predictions of bioinformatic analysis.After its development, this technique paved the way for researches in the exosomal field to explore the changes in the exosomal proteome associated with HIV-1 infections in biology. After watching this video, you should have a good understanding of how to isolate exosome from cell culture, analyze their proteomes, and investigate their association with HIV. Don't forget, work with HIV or other infectious agent can be extremely hazardous and precautions such as wearing personal protective equipment should always be taken while performing this procedure.

Research

JoVE Journal

Immunology and Infection

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Background: Prior to receiving a drug from CCR5-antagonist class in HIV therapy, a patient must undergo an HIV tropism test to confirm that his or her ...

Preparation and Use of HIV-1 Infected Primary CD4+ T-Cells as Target Cells in Natural Killer Cell Cytotoxic Assays

 Natural killer (NK) cells are a vital component of the innate immune response to virus-infected cells. It is important to understand the ability of NK ...

Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays

Amplifying viral genes and quantifying HIV-1 RNA in HIV-1 infected individuals with viral loads below the limit of detection by standard assays (below ...

In vitro Uncoating of HIV-1 Cores

In vitro Uncoating of HIV-1 Cores

The genome of the retroviruses is encased in a capsid surrounded by a lipid envelope. For lentiviruses, such as HIV-1, the conical capsid shell is ...

New Tools to Expand Regulatory T Cells from HIV-1-infected Individuals

CD4+ Regulatory T cells (Tregs) are potent immune modulators and serve an important function in human immune homeostasis. Depletion of Tregs has led to ...

Assessing the Innate Sensing of HIV-1 Infected CD4+ T Cells by Plasmacytoid Dendritic Cells Using an Ex vivo Co-culture System.

Assessing the Innate Sensing of HIV-1 Infected CD4+ T Cells by Plasmacytoid Dendritic Cells Using an Ex vivo Co-culture System.

HIV-1 innate sensing requires direct contact of infected CD4+ T cells with plasmacytoid dendritic cells (pDCs). In order to study this process, the ...

Conformational Evaluation of HIV-1 Trimeric Envelope Glycoproteins Using a Cell-based ELISA Assay

HIV-1 envelope glycoproteins (Env) mediate viral entry into target cells and are essential to the infectious cycle. Understanding how those glycoproteins ...

Isolation of Exosomes from the Plasma of HIV-1 Positive Individuals

Exosomes are small vesicles ranging in size from 30 nm to 100 nm that are released both constitutively and upon stimulation from a variety of cell types. ...

Phagosome Migration and Velocity Measured in Live Primary Human Macrophages Infected with HIV-1

Macrophages are phagocytic cells that play a major role at the crossroads between innate and specific immunity. They can be infected by the human ...

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

HIV-1 envelope proteins engage cognate receptors on the target cell surface, which leads to viral-cell membrane fusion followed by the release of the ...