Il lavoro è stato sostenuto in parte da Public Health Service concedere 1R01AI081568 dal NIAID a YW e dalle generose donazioni dei donatori e piloti del giro 2009 NYCDC Aids organizzato da M. Rosen e Day2 Inc.

1. Trasfezione di plasmidi per la produzione delle particelle lentivirali Rev-dipendente Set up: The Rev-dipendente GFP vettori lentivirali, PNL-GFP-RRE-SA, è stato descritto in precedenza 4,5,6. Per assemblare in una particella virale, il plasmide è stato contransfected in cellule HEK293 T con HIV-1 costruire imballaggi, pCMVΔ8.2 (gentilmente fornito dal Dr. Didier Trono), e un plasmide porta la glicoproteina VSV-G (pHCMV-G) . La trasfezione è stata effettuata utilizzando il metodo di fosfato di calcio. Preparazione di tamponi: 10 X HBS (Hepes Buffered Saline) è stata preparata sciogliendo 5 g di Hepes, 8 g di NaCl, 0,37 g di KCl, 1 g di destrosio, 0,103 g di Na 2 HPO 4 (anidro) in 100 ml di H 2 O. Aliquota the10 X tampone HBS in 1 ml aliquote e conservare a -20 ° C. Al momento della transfezione, convertire il X 10 HBS a 2 x HBS con H 2 O (1: 5 diluizione), e portare il pH compreso tra 7,05-7,12. (Per 10 ml 2 X HBS, che di solito richiede circa 50 ml di NaOH 1M). Filtro sterilizzare il tampone HBS 2X passando attraverso un filtro Millipore 0,22 mM. CaCl tampone 2 è stata preparata sciogliendo CaCl 2 in 10 mm ad un Hepes 2M concentrazione finale. Regolare il pH a 5,8, filtro sterilizzare il buffer e conservare a 4 ° C. Procedimento: <ol><li> Un giorno prima della transfezione, semi di 2 x 10 6 cellule HEK293T in un 100 mm Petri-piatto, e far crescere le cellule durante la notte in 10 ml di DMEM + 10% FBS a 37 ° C, 5% di CO 2. </li><li> Il giorno dopo, togliere surnatante dalle cellule e sostituirlo con 5 ml fresca DMEM + 10% FBS, continuamente le cellule di coltura per 4 ore. </li><li> In un tubo di polistirene da 5 ml, aggiungere 480 microlitri di buffer HBS 2X. </li><li> In un secondo tubo 5 ml in polistirolo, aggiungere 60 microlitri 2M CaCl 2 buffer, il DNA plasmidico e trasfezione di buffer TE (1 mM Tris, 25 mM EDTA, pH 8,0) per un volume totale di 480 microlitri. Per ogni Petri-piatto, plasmidi deve essere aggiunto nella proporzione di 10 mcg di PNL-GFP-RRE-SA, 7,5 mcg di pCMVΔR8.3, e 2,5 mg di pHCMV-G. </li><li> Aggiungere il plasmide DNA CaCl 2 miscela goccia a goccia nella provetta 2 X HBS, e incubare a temperatura ambiente per 30 minuti. Un precipitato bene si formerà. </li><li> Aggiungere il 960 microlitri della miscela goccia a goccia dalla pipetta per le cellule. Incubare a 37 ° C, 5% CO 2 durante la notte. </li><li> Il giorno successivo, rimuovere il supernatante e aggiungere 10 ml di fresca DMEM + 10% FBS, e continuamente incubare le cellule a 37 ° C CO, 5% 2 durante la notte. </li><li> A 48 ore dopo la transfezione, raccogliere il virus eliminando il supernatante e trasferirlo in 50 mL sterile. Aggiungere 10 ml fresca fresca FBS DMEM + 10% in ogni Petri-piatto e continuare a cultura durante la notte. Conservare il supernatante virus a 4 ° C. </li><li> Continuare a raccogliere a 72 ore dopo la trasfezione raccogliendo il sopranatante. Unire tutti i surnatanti, e centrifugare il surnatante a 500 xg per 15 minuti per far sedimentare e rimuovere i detriti cellulari. </li><li> Il supernatante sono stati raccolti e filtrata attraverso un filtro Millipore 0,22 mM. Il virus si è ulteriormente concentrata nella dimensione-esclusione colonne. </li></ol> 2. Concentrare le particelle virali e determinare titolo virale <ol><li> Particelle virali si sono concentrati da una dimensione di esclusione colonna (100.000 MW tagliati fuori, Centricoin). Surnatante virale è stato caricato in colonna, e centrifugati a 6.000 xga 4 ° C per 15 minuti. </li><li> Surnatante concentrato virale è stato raccolto, frazionare e conservati a -80 ° C. </li><li> Il titolo virale è stata determinata da infezione di un TNF-trattati, l&#39;HIV-1 positivi linea cellulare Jacket, J1.1 7. Le cellule sono state coltivate in una piastra da 96 pozzetti a 2,5 x 10 5 cellule per ml (100 ml in totale), e infettati con 100 ml di diluito serialmente VNL-GFP-RRE-SA per una settimana. Il titolo (TCID50) della particella è stata stimata contando i pozzi GFP positivo seguendo il metodo di Reed e Muench 8. </li></ol> 3. Marcatura di HIV-1 Cellule positive con la particella lentivirali, VNL-GFP-RRE-SA Set up: un essere umano linea di cellule T CD4, CEM-SS, per la prima volta infettati con HIV-1. A 48 ore dopo l&#39;infezione, le cellule sono state superinfezione con le particelle lentivirali, VNL-GFP-RRE-SA. A seguito di una superinfezione per altri due giorni, GFP-positive cellule sono state analizzate mediante citometria di flusso. Come controllo, l&#39;HIV-1 non infette CEM-SS cellule sono state infettate con identico VNL-GFP-RRE-SA. Solo l&#39;HIV-1-infetti le cellule CEM-SS ha dato luogo a cellule GFP positive ma non l&#39;HIV-1 non infette CEM-SS cellule. Procedimento: <ol><li> Due ore prima dell&#39;infezione, aggiungere polybrane ad una concentrazione finale di 4 mg / ml. Contare le celle e prendere 2 x 10 5 cellule per ogni infezione. Infettare le cellule con 200 ng (p24) del virus HIV-1 NL4-3 per 2 ore. </li><li> Lavaggio cellule centrifugare a 300 xg per 10 minuti, risospenderecellule in 2 x 10 5 cellule / ml, e la cultura a 37 ° C per 48 ore. </li><li> Contare le celle e prendere 2 x 10 5 cellule per infezione da VNL-GFP-RRE-SA. Aggiungere 100 ml di VNL-GFP-RRE-SA e incubare a 37 ° C durante la notte. Lavare le cellule e risospendere in 2 x 10 5 cellule / ml. </li><li> Effettuare analisi di citometria a flusso a 48 dopo una superinfezione ore. Cellule infette sono state pellettato e risospese in 500 ml paraformaldehede 1%, incubate a temperatura ambiente per 20 minuti, e poi analizzati in un analizzatore FACScan (Becton Dickinson). </li></ol> 4. Rappresentante Risultati Se gli esperimenti vengono eseguiti con successo, una popolazione consistente GFP sarà rilevata in HIV-1-infetti le cellule CEM-SS dal citometro a flusso, mentre, nel controllo, le cellule GFP positive non verranno rilevati in HIV-1 non infette CEM-SS cellule. Se gli esperimenti vengono eseguiti con successo, il Rev-dipendente vettori lentivirali, VNL-GFP-RRE-SA, permetterà la rilevazione altamente specifici di replicazione HIV in popolazioni di cellule viventi, attraverso la misurazione della proteina verde fluorescente (GFP) espressione. In questo esempio, raccolte CEM-SS cellule sono state colorate con un PE-anticorpo marcato topo topo monoclonale contro CD24, HSA, e quindi analizzati su un citometro di flusso sia per HSA e di espressione della GFP. <img src="/files/ftp_upload/2198/2198fig1.jpg" alt="Figura 1" /> Figura 1. Come si vede qui, una popolazione GFP consistente è stata rilevata in HIV-1-cellule infettate con superinfezione VNL-GFP-RRE-SA (Figura 1c). Al contrario, le cellule GFP positive non sono state rilevate in entrambi i non infetti da HIV-1 CEM-SS cellule senza superinfezione lentivirali (figura 1a) o di HIV-1 le cellule non infette con superinfezione lentivirali (Figura 1b).

<ol>
	<li>Garcia, J. A., Wu, F. K., Mitsuyasu, R., Gaynor, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interactions+of+cellular+proteins+involved+in+the+transcriptional+regulation+of+the+human+immunodeficiency+virus.">Interactions of cellular proteins involved in the transcriptional regulation of the human immunodeficiency virus.</a> EMBO Journal. 6, 3761-3770 (1987).</li><li>Merzouki, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HIV-1+gp120/160+expressing+cells+upregulate+HIV-1+LTR+directed+gene+expression+in+a+cell+line+transfected+with+HIV-1+LTR-reporter+gene+constructs.">HIV-1 gp120/160 expressing cells upregulate HIV-1 LTR directed gene expression in a cell line transfected with HIV-1 LTR-reporter gene constructs.</a> Cell Mol Biol (Noisy-le-grand. 41, 445-452 (1995).</li><li>Aguilar-Cordova, E., Chinen, J., Donehower, L., Lewis, D. E., Belmont, J. 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+sensitive+reporter+cell+line+for+HIV-1+tat+activity,+HIV-1+inhibitors,+and+T+cell+activation+effects.">A sensitive reporter cell line for HIV-1 tat activity, HIV-1 inhibitors, and T cell activation effects.</a> AIDS Res Hum Retroviruses. 10, 295-301 (1994).</li><li>Wu, Y., Beddall, M. H., Marsh, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rev-dependent+lentiviral+expression+vector.">Rev-dependent lentiviral expression vector.</a> Retrovirology. 4, 12-12 (2007).</li><li>Wu, Y., Beddall, M. H., Marsh, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rev-dependent+indicator+T+cell+line.">Rev-dependent indicator T cell line.</a> Current HIV Research. 5, 395-403 (2007).</li><li>Young, J., Tang, Z., Yu, Q., Yu, D., Wu, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+killing+of+HIV-1-positive+macrophages+and+T+Cells+by+the+Rev-dependent+lentivirus+carrying+anthrolysin+O+from+Bacillus+anthracis.">Selective killing of HIV-1-positive macrophages and T Cells by the Rev-dependent lentivirus carrying anthrolysin O from Bacillus anthracis.</a> Retrovirology. 5, 36-36 (2008).</li><li>Perez, V. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+HIV-1-infected+T+cell+clone+defective+in+IL-2+production+and+Ca2++mobilization+after+CD3+stimulation.">An HIV-1-infected T cell clone defective in IL-2 production and Ca2+ mobilization after CD3 stimulation.</a> Journal of Immunology. 147, 3145-3148 (1991).</li><li>Reed, L. J., Muench, 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+simple+method+of+estimating+fifty+percent+endpoints.">A simple method of estimating fifty percent endpoints.</a> American Journal of Hygiene. 27, 493-497 (1938).</li></ol>

Nessun conflitto di interessi dichiarati.

Come per il precedente sviluppato Tat-dipendente vettori di espressione, il sistema Rev qui descritto è uno sfruttamento di un processo evoluto HIV. L&#39;inclusione di Rev-dipendenza rende l&#39;LTR-based vettore di espressione altamente dipendente dalla presenza di replicazione dell&#39;HIV. L&#39;applicazione di questo vettore come riportato qui, un dipendente del virus HIV-reporter, offre un approccio nuovo romanzo di identificare le cellule HIV-positive. Il vettore consente di esame delle cellule viventi, può esprimere qualsiasi gene per la sperimentazione clinica o di base, e come uno pseudo-digitato lentivirus ha accesso alla maggior parte dei tipi di cellule e tessuti.

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Biosafety Cabinet</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>37&deg;C 5%CO2 incubator</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Flow cytometer</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>FACSCalibur</td>
<td>&nbsp;</td>
<tr>
<td>Centrifuge</td>
<td>&nbsp;</td>
<td>Beckman</td>
<td>Allega&trade;6KR</td>
<td>&nbsp;</td>
<tr>
<td>4&deg;C regrigerator</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>-20&deg;C refrigerator</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td> -80&deg;C refrigerator</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Cell counter</td>
<td>&nbsp;</td>
<td>Nexcelom</td>
<td>Cellometer&trade; AutoT4</td>
<td>&nbsp;</td>
<tr>
<td>HEK293T cell line</td>
<td>&nbsp;</td>
<td>NIH</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>CEM-SS cell line</td>
<td>&nbsp;</td>
<td>NIH</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Jurkat cell line J1.1</td>
<td>&nbsp;</td>
<td>NIH</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>DMEM</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>11965-118</td>
<td>&nbsp;</td>
<tr>
<td>RPMI 1640</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>21870</td>
<td>&nbsp;</td>
<tr>
<td>HI FBS</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>10438-018</td>
<td>&nbsp;</td>
<tr>
<td>HIV-1NL4-3</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>prepared by tranfsection of HeLa cells with cloned proviral DNA</td>
</tr>
<tr>
<td>pNL-GFP-RRE</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>copmlete deletion of all HIV ORFs of pNL4-3</td>
</tr>
<tr>
<td>pNL-GFP-RRE-SA</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>Insert HIV-1 A5 and D4 into pNL-GFP-RRE</td>
</tr>
<tr>
<td>pCMV&Delta;8.2</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>provided by Dr. Dider Trono</td>
</tr>
<tr>
<td>pHCMV-G</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>10 x HBS (Hepes Buffered Saline)</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>11344-041</td>
<td>&nbsp;</td>
<tr>
<td>2M CaCl2 buffer</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>S-013-154-10</td>
<td>&nbsp;</td>
<tr>
<td>1% paraformaldehy</td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>158127</td>
<td>&nbsp;</td>
<tr>
<td>Bleach</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>50ml Falcon tubes</td>
<td>&nbsp;</td>
<td>BD Bioscience</td>
<td>358206</td>
<td>&nbsp;</td>
<tr>
<td>5ml round bottom tubes</td>
<td>&nbsp;</td>
<td>BD Bioscience</td>
<td>352063</td>
<td>&nbsp;</td>
<tr>
<td>0.45&mu;M Millipore filter</td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>SLHA033SS</td>
<td>&nbsp;</td>
<tr>
<td>0.20&mu;M Millipore filter</td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>SLFG85000</td>
<td>&nbsp;</td>
<tr>
<td>100mm Petri-dish</td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>CLS430588</td>
<td>&nbsp;</td>
<tr>
<td>Size-exclusion column (100,000MW cut off)</td>
<td>&nbsp;</td>
<td>SartoriuStedim biotech</td>
<td>VS2041</td>
<td>&nbsp;</td>
<tr>
<td>2ml frozen tube</td>
<td>&nbsp;</td>
<td>Axygen</td>
<td>SCT-200</td>
<td>&nbsp;</td>
<tr>
<td>96-well plate</td>
<td>&nbsp;</td>
<td>BD Bioscience</td>
<td>353227</td>
<td>&nbsp;</td>
<tr>
<td>1.7mL Microcentrifuge Tube</td>
<td>&nbsp;</td>
<td>Axygen</td>
<td>MCT- 175-C</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

specific marking of hiv-1 positive cells using a rev-dependent lentiviral vector expressing the green fluorescent protein

La maggior parte di HIV-reattiva vettori di espressione sono basati sul promotore di HIV, la ripetizione terminale lunga (LTR). Mentre risponde ad una proteina HIV in fase precoce, Tat, la LTR è anche sensibile agli stati di attivazione cellulare e per l&#39;attività di cromatina locale dove l&#39;integrazione è avvenuta. Questo può portare ad alta HIV-indipendente attività, e ha limitato l&#39;utilità di LTR-reporter per marcare le cellule HIV positivi 1,2,3. Qui, abbiamo costruito un vettore di espressione lentivirali che possiede, oltre alla Tat-reattiva LTR, numerose sequenze di DNA dell&#39;HIV che includono l&#39;Ap-risposta elemento e dei siti di splicing HIV 4,5,6. Il vettore è stato incorporato in un virus giornalista lentivirale, consentendo il rilevamento altamente specifici di replicare l&#39;HIV in popolazioni di cellule viventi. L&#39;attività del vettore è stata misurata l&#39;espressione della proteina fluorescente verde (GFP). L&#39;applicazione di questo vettore come riportato qui offre un nuovo approccio alternativa ai metodi esistenti, come la PCR in situ o colorazione dell&#39;antigene HIV, di identificare le cellule HIV-positive. Il vettore può anche esprimere geni terapeutici per la sperimentazione clinica o di base per indirizzare le cellule HIV-positive.

Watch this Scientific Journal Video about Specific Marking of HIV-1 Positive Cells using a Rev-dependent Lentiviral Vector Expressing the Green Fluorescent Protein at JoVE.com

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

Abbiamo sviluppato un vettore lentivirale che possiede, oltre alla Tat-reattiva LTR, l&#39;Ap-risposta elemento (RRE) che possono regolare l&#39;espressione genica giornalista in modo da HIV-1 Tat e Rev-dipendente. Il vettore consente l&#39;individuazione specifica di replicare l&#39;HIV nelle cellule viventi attraverso l&#39;espressione di GFP.

Marcatura specifica di HIV-1 Cellule positive con un Rev-dipendente Vector lentivirali Esprimendo la proteina fluorescente verde

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, ...

specific-marking-hiv-1-positive-cells-using-rev-dependent-lentiviral

Nanyang Technological University

Research

JoVE Journal

Immunology and Infection

12.9K Views.  George Mason University. Abbiamo sviluppato un vettore lentivirale che possiede, oltre alla Tat-reattiva LTR, l'Ap-risposta elemento (RRE) che possono regolare l'espressione genica giornalista in modo da HIV-1 Tat e Rev-dipendente. Il vettore consente l'individuazione specifica di replicare l'HIV nelle cellule viventi attraverso l'espressione di GFP.

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

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 viral population uses the CCR5 coreceptor for cellular entry, and not an alternative coreceptor. One approach to tropism testing is to examine the sequence of the V3 region of the HIV envelope, which interacts with the coreceptor.
Methods: Viral RNA is extracted from blood plasma. The V3 region is amplified in triplicate with nested reverse transcriptase-PCR. The amplifications are then sequenced and analyzed using the software, RE_Call. Sequences are then submitted to a bioinformatic algorithm such as geno2pheno to infer viral tropism from the V3 region. Sequences are inferred to be non-R5 if their geno2pheno false positive rate falls below 5.75%. If any one of the three sequences from a sample is inferred to be non-R5, the patient is unlikely to respond to a CCR5-antagonist.

HIV tropism can be inferred from the V3 region of the viral envelope. V3 is PCR amplified in triplicate using nested RT-PCR, sequenced, and interpreted using bioinformatic software. Samples with with 1 or more sequence(s) with low g2P scores are classified as non-R5 virus.

Inferenza genotipica del virus HIV-1 Tropismo utilizzo basati sulla popolazione sequenziamento del 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 ...

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Immunologia e infezioni

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

Maraviroc (MVC) is the first licensed antiretroviral drug from the class of coreceptor antagonists. It binds to the host coreceptor CCR5, which is used by the majority of HIV strains in order to infect the human immune cells (Fig. 1). Other HIV isolates use a different coreceptor, the CXCR4. Which receptor is used, is determined in the virus by the Env protein (Fig. 2). Depending on the coreceptor used, the viruses are classified as R5 or X4, respectively. MVC binds to the CCR5 receptor inhibiting the entry of R5 viruses into the target cell. During the course of disease, X4 viruses may emerge and outgrow the R5 viruses. Determination of coreceptor usage (also called tropism) is therefore mandatory prior to administration of MVC, as demanded by EMA and FDA. 
The studies for MVC efficiency MOTIVATE, MERIT and 1029 have been performed with the Trofile assay from Monogram, San Francisco, U.S.A. This is a high quality assay based on sophisticated recombinant tests. The acceptance for this test for daily routine is rather low outside of the U.S.A., since the European physicians rather tend to work with decentralized expert laboratories, which also provide concomitant resistance testing. These laboratories have undergone several quality assurance evaluations, the last one being presented in 20111.
For several years now, we have performed tropism determinations based on sequence analysis from the HIV env-V3 gene region (V3)2. This region carries enough information to perform a reliable prediction. 
The genotypic determination of coreceptor usage presents advantages such as: shorter turnover time (equivalent to resistance testing), lower costs, possibility to adapt the results to the patients' needs and possibility of analysing clinical samples with very low or even undetectable viral load (VL), particularly since the number of samples analysed with VL&lt;1000 copies/&mu;l roughly increased in the last years (Fig. 3).
The main steps for tropism testing (Fig. 4) demonstrated in this video: 
1. Collection of a blood sample 
 2. Isolation of the HIV RNA from the plasma and/or HIV proviral DNA from blood mononuclear cells 
 3. Amplification of the env region 
 4. Amplification of the V3 region 
 5. Sequence reaction of the V3 amplicon 
 6. Purification of the sequencing samples 
 7. Sequencing the purified samples 
 8. Sequence editing 
 9. Sequencing data interpretation and tropism prediction

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

The prediction of the coreceptor usage of HIV-1 is required for the administration of a new class of antiretroviral drugs, i.e. coreceptor antagonists. It can be performed by sequence analysis of the env gene and subsequent interpretation through an internet based interpretation system (geno2pheno[coreceptor]).

Pronostico di HIV-1 Uso corecettore (tropismo) mediante analisi della sequenza utilizzando un approccio genotipica

Maraviroc (MVC) is the first licensed antiretroviral drug from the class of coreceptor antagonists. It binds to the host coreceptor CCR5, which is used by ...

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 composed of CA protein arranged as a lattice of hexagon. The capsid is closed by 7 pentamers at the broad end and 5 at the narrow end of the cone1, 2. Encased in this capsid shell is the viral ribonucleoprotein complex, and together they comprise the core.
Following fusion of the viral membrane with the target cell membrane, the HIV-1 is released into the cytoplasm. The capsid then disassembles releasing free CA in the soluble form3 in a process referred to as uncoating. The intracellular location and timing of HIV-1 uncoating are poorly understood. Single amino-acid substitutions in CA that alter the stability of the capsid also impair the ability of HIV-1 to infect cells4. This indicates that the stability of the capsid is critical for HIV-1 infection.
HIV-1 uncoating has been difficult to study due to lack of availability of sensitive and reliable assays for this process. Here we describe a quantitative method for studying uncoating in vitro using cores isolated from infectious HIV-1 particles. The approach involves isolation of cores by sedimentation of concentrated virions through a layer of detergent and into a linear sucrose gradient, in the cold. To quantify uncoating, the isolated cores are incubated at 37&deg;C for various timed intervals and subsequently pelleted by ultracentrifugation. The extent of uncoating is analyzed by quantifying the fraction of CA in the supernatant. This approach has been employed to analyze effects of viral mutations on HIV-1 capsid stability4, 5, 6. It should also be useful for studying the role of cellular factors in HIV-1 uncoating.

In vitro Uncoating of HIV-1 Cores

Uncoating is an essential step in the early phase of the HIV-1 life cycle and is defined as the disassembly of the capsid shell and the release of the viral ribonucleoprotein complex (vRNP). Here, we demonstrate techniques for isolating intact cores from HIV-1 virions and for quantifying their uncoating in vitro.

In uncoating vitro di 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 measurable increases in antigen-specific T cell responses in vaccine settings for cancer and infectious pathogens. However, their role in HIV-1 immuno-pathogenesis remains controversial, as they could either serve to suppress deleterious HIV-1-associated immune activation and thus slow HIV-1 disease progression or alternatively suppress HIV-1-specific immunity and thereby promote virus spread. Understanding and modulating Treg function in the context of HIV-1 could lead to potential new strategies for immunotherapy or HIV vaccines. However, important open questions remain on their role in the context of HIV-1 infection, which needs to be carefully studied.
Representing roughly 5% of human CD4+ T cells in the peripheral blood, studying the Treg population has proven to be difficult, especially in HIV-1 infected individuals where HIV-1-associated CD4 T cell and with that Treg depletion occurs. The characterization of regulatory T cells in individuals with advanced HIV-1 disease or tissue samples, for which only very small biological samples can be obtained, is therefore extremely challenging. We propose a technical solution to overcome these limitations using isolation and expansion of Tregs from HIV-1-positive individuals.
Here we describe an easy and robust method to successfully expand Tregs isolated from HIV-1-infected individuals in vitro. Flow-sorted CD3+CD4+CD25+CD127low Tregs were stimulated with anti-CD3/anti-CD28 coated beads and cultured in the presence of IL-2. The expanded Tregs expressed high levels of FOXP3, CTLA4 and HELIOS compared to conventional T cells and were shown to be highly suppressive. Easier access to large numbers of Tregs will allow researchers to address important questions concerning their role in HIV-1 immunopathogenesis. We believe answering these questions may provide useful insight for the development of an effective HIV-1 vaccine.

CD4+ Regulatory T cells are potent immune-modulators and serve important functions in immune homeostasis. The paucity of these cells in peripheral blood makes functional studies challenging, specifically in the context of HIV-1-infection. We here describe a method to isolate and expand functional CD4+ Tregs from peripheral blood from HIV-1-infected individuals.

Nuovi strumenti per espandere cellule T regolatorie di individui HIV-1-infetti

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.

HIV-1 innate sensing requires direct contact of infected CD4+ T cells with plasmacytoid dendritic cells (pDCs). In order to study this process, the protocols described here use freshly isolated human peripheral blood mononuclear cells (PBMCs) or plasmacytoid dendritic cells (pDCs) to sense infections in either T cell line (MT4) or heterologous primary CD4+ T cells. In order to ensure proper sensing, it is essential that PBMC are isolated immediately after blood collection and that optimal percentage of infected T cells are used. Furthermore, multi-parametric flow cytometric staining can be used to confirm that PBMC samples contain the different cell lineages at physiological ratios. A number of controls can also be included to evaluate viability and functionality of pDCs. These include, the presence of specific surface markers, assessing cellular responses to known agonist of Toll-Like Receptors (TLR) pathways, and confirming a lack of spontaneous type-I interferon (IFN) production. In this system, freshly isolated PBMCs or pDCs are co-cultured with HIV-1 infected cells in 96 well plates for 18-22 hr. Supernatants from these co-cultures are then used to determine the levels of bioactive type-I IFNs by monitoring the activation of the ISGF3 pathway in HEK-Blue IFN-&#945;/&#946; cells. Prior and during co-culture conditions, target cells can be subjected to flow cytometric analysis to determine a number of parameters, including the percentage of infected cells, levels of specific surface markers, and differential killing of infected cells. Although, these protocols were initially developed to follow type-I IFN production, they could potentially be used to study other imuno-modulatory molecules released from pDCs and to gain further insight into the molecular mechanisms governing HIV-1 innate sensing.

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

Unlike cell-free HIV-1 particles, infected CD4+ T cells are effectively sensed by plasmacytoid dendritic cells (pDCs). This manuscript describes a method where peripheral blood mononuclear cells (PBMCs) or isolated pDCs are co-cultured with HIV-1 infected T cells to evaluate innate sensing by pDCs as assessed by release of type-I IFN.

Valutare l&#39;innato rilevamento dell&#39;infezione da HIV-1 CD4 infetti<sup&gt; +</sup&gt; Cellule T dalle cellule dendritiche plasmacitoidi Utilizzando un<em&gt; Ex vivo</em&gt; Sistema di co-coltura.

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 are able to fuel the fusion process through their conformational changes could lead to the design of better, more effective immunogens for vaccine strategies. Here we describe a cell-based ELISA assay that allows studying the recognition of trimeric HIV-1 Env by monoclonal antibodies. Following expression of HIV-1 trimeric Env at the surface of transfected cells, conformation specific anti-Env antibodies are incubated with the cells. A horseradish peroxidase-conjugated secondary antibody and a simple chemiluminescence reaction are then used to detect bound antibodies. This system is highly flexible and can detect Env conformational changes induced by soluble CD4 or cellular proteins. It requires minimal amount of material and no highly-specialized equipment or know-how. Thus, this technique can be established for medium to high throughput screening of antigens and antibodies, such as newly-isolated antibodies.

Understanding viral surface antigens conformations is required to evaluate antibody neutralization and guide the design of effective vaccine immunogens. Here we describe a cell-based ELISA assay that allows the study of the recognition of trimeric HIV-1 Env expressed at the surface of transfected cells by specific anti-Env antibodies.

Valutazione conformazionale di HIV-1 trimeric busta glicoproteine ​​Utilizzando una base di Cell-ELISA Saggio

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. They are found in a number of biological fluids and are known to carry a variety of proteins, lipids, and nucleic acid molecules. Originally thought to be little more than reservoirs for cellular debris, the roles of exosomes regulating biological processes and in diseases are increasingly appreciated.
Several methods have been described for isolating exosomes from cellular culture media and biological fluids. Due to their small size and low density, differential ultracentrifugation and/or ultrafiltration are the most commonly used techniques for exosome isolation. However, plasma of HIV-1 infected individuals contains both exosomes and HIV viral particles, which are similar in size and density. Thus, efficient separation of exosomes from HIV viral particles in human plasma has been a challenge.
To address this limitation, we developed a procedure modified from Cantin et. al., 2008 for purification of exosomes from HIV particles in human plasma. Iodixanol velocity gradients were used to separate exosomes from HIV-1 particles in the plasma of HIV-1 positive individuals. Virus particles were identified by p24 ELISA. Exosomes were identified on the basis of exosome markers acetylcholinesterase (AChE), and the CD9, CD63, and CD45 antigens. Our gradient procedure yielded exosome preparations free of virus particles. The efficient purification of exosomes from human plasma enabled us to examine the content of plasma-derived exosomes and to investigate their immune modulatory potential and other biological functions.

Techniques describing a gradient procedure to separate exosomes from human immunodeficiency virus (HIV) particles are described. This procedure was used to isolate exosomes away from HIV particles in human plasma from HIV-infected individuals. The isolated exosomes were analyzed for cytokine/chemokine content.

Isolamento di esosomi dal plasma di HIV-1 individui positivi

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. ...

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.

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.

SILAC Based proteomica Caratterizzazione di Esosomi da HIV-1 le cellule infette

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

Dextran Enhances the Lentiviral Transduction Efficiency of Murine and Human Primary NK Cells

The efficient transduction of specific genes into natural killer (NK) cells has been a major challenge. Successful transductions are critical to defining the role of the gene of interest in the development, differentiation, and function of NK cells. Recent advances related to chimeric antigen receptors (CARs) in cancer immunotherapy accentuate the need for an efficient method to deliver exogenous genes to effector lymphocytes. The efficiencies of lentiviral-mediated gene transductions into primary human or mouse NK cells remain significantly low, which is a major limiting factor. Recent advances using cationic polymers, such as polybrene, show an improved gene transduction efficiency in T cells. However, these products failed to improve the transduction efficiencies of NK cells. This work shows that dextran, a branched glucan polysaccharide, significantly improves the transduction efficiency of human and mouse primary NK cells. This highly reproducible transduction methodology provides a competent tool for transducing human primary NK cells, which can vastly improve clinical gene delivery applications and thus NK cell-based cancer immunotherapy.

The goal of this study was to formulate technologies that allow for successful gene transduction in primary natural killer (NK) cells. The dextran-mediated lentiviral transduction of human or mouse primary NK cells results in higher gene expression efficiencies. This method of gene transduction will vastly improve NK cell genetic manipulation.

Destrano migliora l'efficienza di trasduzione lentivirale di cellule NK primarie Murine ed umane

The efficient transduction of specific genes into natural killer (NK) cells has been a major challenge. Successful transductions are critical to defining ...

Using Enhanced Green Fluorescence Protein-expressing Escherichia Coli to Assess Mouse Peritoneal Macrophage Phagocytosis

This manuscript describes a simple and reproducible method to perform a phagocytosis assay. The first part of this method involves building a pET-SUMO-EGFP vector (SUMO = small ubiquitin-like modifier) and expressing enhanced green fluorescence protein (EGFP) in Escherichia coli (BL21DE). EGFP-expressing E. coli is coincubated with macrophages for 1 h at 37 &#176;C; the negative control group is incubated on ice for the same amount of time. Then, the macrophages are ready for assessment. The advantages of this technique include its simple and straightforward steps, and phagocytosis can be measured by both flow cytometer and fluorescence microscope. The EGFP-expressing E. coli are stable and display a strong fluorescence signal even after the macrophages are fixed with paraformaldehyde. This method is not only suitable for the assessment of macrophage cell lines or primary macrophages in vitro but also suitable for the evaluation of granulocyte and monocyte phagocytosis in peripheral blood mononuclear cells. The results show that the phagocytic capability of peritoneal macrophages from young (eight-week-old) mice is higher than that of macrophages from aged (16-month-old) mice. In summary, this method measures macrophage phagocytosis and is suitable for studying the innate immune system function.

Using Enhanced Green Fluorescence Protein-expressing Escherichia Coli to Assess Mouse Peritoneal Macrophage Phagocytosis

Here, we present a protocol to assess mouse peritoneal macrophage phagocytosis using enhanced green fluorescence protein-expressing Escherichia coli.

Utilizzando Enhanced fluorescenza verde che esprimono proteine Escherichia Coli per valutare la fagocitosi dei macrofagi peritoneali del Mouse