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

Este trabalho foi apoiado por um suplemento de ARRA ao tempo de vida / Tufts / Brown CFAR, P30AI042853-13S1, NIH P20GM103421, P01AA019072, R01HD072693 e K24HD080539 a BR. Este trabalho também foi apoiado por expectativa de vida Fundo Pilot Research (# 701- 5857), Rhode Island Medical Foundation Grant Research (# 20.133.969) e NIH COBRE URI / RIH Pilot Research Grant (P20GM104317) para ML. Agradecemos James Myall e Vy Dang para obter ajuda com a preparação do manuscrito e figura.

1. Cultura celular e infecção HIV-1 NOTA: Antes de iniciar experimentos, recomenda-se verificar a viabilidade das células através de coloração com Trypan Blue 11 e sua proliferação através de um ensaio de MTT 12. Também é fundamental para usar o meio SILAC recém-preparado. Várias linhas de células podem ser utilizados, desde que eles se encontram numa fase activamente prolif erativa, e são susceptíveis a infecção por HIV-1, ou a...

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Nos procedimentos descritos no presente documento, demonstramos a aplicação da técnica SILAC para investigar o efeito de infecção por HIV-1 no proteoma exosomal hospedeiro. Inicialmente, as células infectadas e não infectadas com HIV-1 são diferencialmente marcado com isótopo. Os exossomas marcados diferencialmente são então purificados antes de realizar a extracção de proteínas. Em seguida, a espectrometria de massa em tandem com cromatograf ia líquida é utilizada para analisar o proteoma exosomal. Fina...

Muitas doenças humanas, incluindo infecções virais, estão muitas vezes associados com os processos celulares distintos que ocorrem e em torno das células afectadas. Proteínas, muitas vezes agindo como os efetores celulares finais, mediar estes processos. Análise das proteínas muitas vezes pode fornecer informações valiosas quanto ao ambiente local das células afetadas e ajudar-nos a compreender o mecanismo subjacente da patogênese da doença. Entre as várias técnicas de análise de proteínas, proteômica detém particularmente grande promessa. Como uma ferramenta poderosa, em larga escala, proteómica pode fornecer uma compreensão sistémica de processos celulares, particularmente na área da função e da interacção de proteínas. A análise de proteínas específicas é simplificada através do desenvolvimento de técnicas de marcação, que permitem que os investigadores para monitorar a expressão de componentes celulares, particularmente proteínas, no local da investigação. Embora muitas análises proteomic foram realizados em celularescala proteoma, caracterizações proteômicas em compartimentos subcelulares provaram ser particularmente informativa 1. Isto é exemplificado bem nos estudos de infecção por HIV-1. Exossomos, 30-100 vesículas de membrana nm secretadas por uma ampla gama de tipos de células 2, 3, são componentes essenciais da comunicação intercelular e de transporte molecular. Eles foram previamente descoberto para desempenhar papéis importantes no processo de VIH-1 de brotamento 4, 5. Ao combinar a análise proteômica com dissecção funcional, descobrimos que exossomos libertados de HIV-1 células infectadas são compostos de uma única e quantitativamente diferentes assinatura proteína e porto moléculas regulatórias que afetam propriedades celulares em células receptoras, incluindo apoptose e proliferação celular 6 vizinho. Os métodos são descritos neste protocolo,nomeadamente SILAC (rotulagem isótopo estável por aminoácidos de cultura de células) 7 com base caracterização proteomic de exossomas a partir do HIV-1 de células infectadas. Abordagens semelhantes podem ser aplicados para entender melhor outros compartimentos subcelulares durante patogênese ajustando o esforço experimental para o compartimento ou fracção de interesse específico e fazer as mudanças necessárias para os procedimentos descritos. Dado o recente desenvolvimento de métodos de proteômica quantitativos, há muitos a escolher de ao selecionar o método mais eficiente para uma experiência particular. Entre eles estão os iTRAQ com base química (marcas isobáricos para a quantificação relativa e absoluta) 8 eo MRM livre-label (monitoramento de reações múltiplas) 9 técnicas. Ambos os métodos são ferramentas poderosas e são boas opções para configurações específicas. Para um laboratório típico trabalhando principalmente com linhas celulares, no entanto, estes dois métodos têm relativelY custos mais elevados e são mais demorado quando comparado com o método baseado SILAC. SILAC é uma técnica de marcação metabólica com base que incorpora formas isotópicas de aminoácidos não radioactivos de meios de cultura para as proteínas celulares. Tipicamente, as experiências SILAC começar com duas populações de células, por exemplo, infectados e não infectados. Cada um está marcado diferencialmente em seu ambiente isotópica específica até rotulagem completa seja alcançada. Os exossomas marcados destas células são então submetidas a extracção de proteínas. Uma vez extraído, as proteínas marcadas são exosomal analisadas utilizando espectrometria de massa em tandem com cromatograf ia líquida 10. Finalmente, os resultados de espectrometria de massa e as proteínas marcadas são significativamente submetido a análise estatística e bioinformática, bem como para a verificação bioquímica rigorosa. Nossos relatórios de investigação anteriores sugerem que os procedimentos SILAC / exossomo são mais apropriadas para linhas de células do que as células primárias, como linhas celulares são geralmente em umestado de proliferação ativa de marcação isotópica eficiente,

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			<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.

Figura 1A é um fluxograma descrevendo o procedimento de marcação SILAC 21. A fim de purificar os exossomos, as amostras devem ser girado para baixo através de centrifugação. A Figura 1B mostra os passos de purificação exossomo por ultracentrifugação de série 21. Uma vez purificado, os exossomas estão sujeitas a análise proteomic experimental tal como descrito no procedimento. <p class="jove...

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

Aqui, nós descrevemos um método proteómica quantitativa utilizando a técnica de marcação por isótopos estáveis ​​aminoácidos em cultura de células (SILAC) para analisar os efeitos da infecção por HIV-1 em proteomas exosomal hospedeiro. Este protocolo pode ser facilmente adaptado a diferentes células sob condições de stress ou infecções.

SILAC Based proteômica Caracterização de exossomas de HIV-1 células infectadas

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

Research

JoVE Journal

Immunology and Infection

Specific Marking of HIV-1 Positive Cells using a Rev-dependent Lentiviral Vector Expressing the Green Fluorescent Protein

Marcação específica de HIV-1 células positivas utilizando um Vector Rev-dependente Lentivirus Expressando a Proteína Verde Fluorescente

Most of HIV-responsive expression vectors are based on the HIV promoter, the long terminal repeat (LTR). While responsive to an early HIV protein, Tat, ...

Imunologia e Infecção

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

Inferência genotípica do HIV-1 Tropismo Usando de base populacional de Seqüenciamento 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

Preparação e Uso de HIV-1 infectados CD4 + T-Primária células como as células-alvo em Ensaios Natural Killer Celular citotóxicos

 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

Amplificar e Quantificação do HIV-1 RNA no indivíduos infectados pelo HIV com carga viral abaixo do limite de detecção pela Standard Ensaios Clínicos

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

Em desencapsulamento vitro do 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

Novas ferramentas para expandir as células T reguladoras de indivíduos HIV-1-infected

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.

Avaliando a inata Sensing de HIV-1 CD4 Infected<sup&gt; +</sup&gt; As células T por células dendríticas plasmocitóides Usando um<em&gt; Ex vivo</em&gt; Co-cultura do sistema.

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

Avaliação conformacional do HIV-1 trimérico glicoproteínas do envelope Usando um ELISA Ensaio Celular

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

Isolamento de exossomas a partir do plasma de indivíduos HIV-1 positivos

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. ...