The work presented here was supported by the Canadian Institutes of Health Research (CIHR) (grants DCB-120266, PPP-133377 and HBF-348967 to A.G.).

1. Cells and Transfections
<ol>
	<li>Culture HEK 293T cells in Dulbecco&#39;s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Prepare a 2 x 105 cells/ml suspension in the cell culture medium. Add 500, 100 and 1,000 &#181;l of the cell suspension to each well of 24-well, 96-well and 12-well plates, for viral production, cell viability and immune activation assays, respectively (Figure 2A).</li>
	<li>Gently swirl the plates and incuba...

<ol>
	<li>Hoxie, J. A., June, C. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+cell+and+gene+therapies+for+HIV.">Novel cell and gene therapies for HIV.</a> Cold Spring Harb Perspect Med. 2, a007179 (2012).</li><li>Bobbin, M. L., Burnett, J. C., Rossi, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+interference+approaches+for+treatment+of+HIV-1+infection.">RNA interference approaches for treatment of HIV-1 infection.</a> Genome Med. 7, 50 (2015).</li><li>Allers, 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=Evidence+for+the+cure+of+HIV+infection+by+CCR5Delta32/Delta32+stem+cell+transplantation.">Evidence for the cure of HIV infection by CCR5Delta32/Delta32 stem cell transplantation.</a> Blood. 117, 2791-2799 (2011).</li><li>DiGiusto, D. 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=Development+of+hematopoietic+stem+cell+based+gene+therapy+for+HIV-1+infection:+considerations+for+proof+of+concept+studies+and+translation+to+standard+medical+practice.">Development of hematopoietic stem cell based gene therapy for HIV-1 infection: considerations for proof of concept studies and translation to standard medical practice.</a> Viruses. 5, 2898-2919 (2013).</li><li>Burke, B. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+Cellular+Resistance+to+HIV-1+Infection+In+Vivo+Using+a+Dual+Therapeutic+Lentiviral+Vector.">Engineering Cellular Resistance to HIV-1 Infection In Vivo Using a Dual Therapeutic Lentiviral Vector.</a> Mol Ther Nucleic Acids. 4, e236 (2015).</li><li>DiGiusto, D. 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=RNA-based+gene+therapy+for+HIV+with+lentiviral+vector-modified+CD34(+)+cells+in+patients+undergoing+transplantation+for+AIDS-related+lymphoma.">RNA-based gene therapy for HIV with lentiviral vector-modified CD34(+) cells in patients undergoing transplantation for AIDS-related lymphoma.</a> Sci Transl Med. 2, 36ra43 (2010).</li><li>Scarborough, R. J., Gatignol, 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+and+Ribozymes.">HIV and Ribozymes.</a> Adv Exp Med Biol. 848, 97-116 (2015).</li><li>Eekels, J. J., Berkhout, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+a+durable+treatment+of+HIV-1+infection+using+RNA+interference.">Toward a durable treatment of HIV-1 infection using RNA interference.</a> Prog Mol Biol Transl Sci. 102, 141-163 (2011).</li><li>Blazquez, L., Fortes, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=U1+interference+(U1i)+for+Antiviral+Approaches.">U1 interference (U1i) for Antiviral Approaches.</a> Adv Exp Med Biol. 848, 51-69 (2015).</li><li>McIntyre, G. 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=96+shRNAs+designed+for+maximal+coverage+of+HIV-1+variants.">96 shRNAs designed for maximal coverage of HIV-1 variants.</a> Retrovirology. 6, 55 (2009).</li><li>Sajic, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+modified+U1+snRNAs+to+inhibit+HIV-1+replication.">Use of modified U1 snRNAs to inhibit HIV-1 replication.</a> Nucleic Acids Res. 35, 247-255 (2007).</li><li>Low, J. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SHAPE-directed+discovery+of+potent+shRNA+inhibitors+of+HIV-1.">SHAPE-directed discovery of potent shRNA inhibitors of HIV-1.</a> Mol Ther. 20, 820-828 (2012).</li><li>Scarborough, 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=A+Conserved+Target+Site+in+HIV-1+Gag+RNA+is+Accessible+to+Inhibition+by+Both+an+HDV+Ribozyme+and+a+Short+Hairpin+RNA.">A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA.</a> Mol Ther Nucleic Acids. 3, e178 (2014).</li><li>Lain&#233;, 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=In+vitro+and+in+vivo+cleavage+of+HIV-1+RNA+by+new+SOFA-HDV+ribozymes+and+their+potential+to+inhibit+viral+replication.">In vitro and in vivo cleavage of HIV-1 RNA by new SOFA-HDV ribozymes and their potential to inhibit viral replication.</a> RNA Biol. 8, 343-353 (2011).</li><li>Scarborough, R. J., L&#233;vesque, M. V., Perreault, J. P., Gatignol, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+Evaluation+of+Clinically+Relevant+SOFA-HDV+Ribozymes+Targeting+HIV+RNA.">Design and Evaluation of Clinically Relevant SOFA-HDV Ribozymes Targeting HIV RNA.</a> Methods Mol Biol. 1103, 31-43 (2014).</li><li>Scarborough, R. J., Adams, K. L., Daher, A., Gatignol, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effective+Inhibition+of+HIV-1+Production+by+Short+Hairpin+RNAs+and+Small+Interfering+RNAs+Targeting+a+Highly+Conserved+Site+in+HIV-1+Gag+RNA+Is+Optimized+by+Evaluating+Alternative+Length+Formats.">Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats.</a> Antimicrob Agents Chemother. 59, 5297-5305 (2015).</li><li>Sarzotti-Kelsoe, 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=Optimization+and+validation+of+the+TZM-bl+assay+for+standardized+assessments+of+neutralizing+antibodies+against+HIV-1.">Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1.</a> J Immunol Methods. 409, 131-146 (2014).</li><li>Campos, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long+lasting+control+of+viral+rebound+with+a+new+drug+ABX464+targeting+Rev+-+mediated+viral+RNA+biogenesis.">Long lasting control of viral rebound with a new drug ABX464 targeting Rev - mediated viral RNA biogenesis.</a> Retrovirology. 12, 1-15 (2015).</li><li>Zhu, 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=The+CRISPR/Cas9+system+inactivates+latent+HIV-1+proviral+DNA.">The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA.</a> Retrovirology. 12, 22 (2015).</li><li>Bounou, S., Leclerc, J. E., Tremblay, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Presence+of+host+ICAM-1+in+laboratory+and+clinical+strains+of+human+immunodeficiency+virus+type+1+increases+virus+infectivity+and+CD4(+)-T-cell+depletion+in+human+lymphoid+tissue,+a+major+site+of+replication+in+vivo.">Presence of host ICAM-1 in laboratory and clinical strains of human immunodeficiency virus type 1 increases virus infectivity and CD4(+)-T-cell depletion in human lymphoid tissue, a major site of replication in vivo.</a> J Virol. 76, 1004-1014 (2002).</li><li>Shan, 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=A+novel+PCR+assay+for+quantification+of+HIV-1+RNA.">A novel PCR assay for quantification of HIV-1 RNA.</a> J Virol. 87, 6521-6525 (2013).</li><li>Clerzius, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+PKR+activator,+PACT,+becomes+a+PKR+inhibitor+during+HIV-1+replication.">The PKR activator, PACT, becomes a PKR inhibitor during HIV-1 replication.</a> Retrovirology. 10, 96 (2013).</li><li>Bradford, M. 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+rapid+and+sensitive+method+for+the+quantitation+of+microgram+quantities+of+protein+utilizing+the+principle+of+protein-dye+binding.">A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.</a> Anal Biochem. 72, 248-254 (1976).</li><li>Stoscheck, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitation+of+protein.">Quantitation of protein.</a> Methods Enzymol. 182, 50-68 (1990).</li><li>Battisti, 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=Additive+activity+between+the+trans-activation+response+RNA-binding+protein,+TRBP2,+and+cyclin+T1+on+HIV+type+1+expression+and+viral+production+in+murine+cells.">Additive activity between the trans-activation response RNA-binding protein, TRBP2, and cyclin T1 on HIV type 1 expression and viral production in murine cells.</a> AIDS Res Hum Retroviruses. 19, 767-778 (2003).</li><li>Bannwarth, 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=Cell-specific+regulation+of+TRBP1+promoter+by+NF-Y+transcription+factor+in+lymphocytes+and+astrocytes.">Cell-specific regulation of TRBP1 promoter by NF-Y transcription factor in lymphocytes and astrocytes.</a> J Mol Biol. 355, 898-910 (2006).</li><li>Clerzius, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ADAR1+interacts+with+PKR+during+human+immunodeficiency+virus+infection+of+lymphocytes+and+contributes+to+viral+replication.">ADAR1 interacts with PKR during human immunodeficiency virus infection of lymphocytes and contributes to viral replication.</a> J Virol. 83, 10119-10128 (2009).</li><li>Burugu, S., Daher, A., Meurs, E. F., Gatignol, 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+translation+and+its+regulation+by+cellular+factors+PKR+and+PACT.">HIV-1 translation and its regulation by cellular factors PKR and PACT.</a> Virus Res. 193, 65-77 (2014).</li><li>ter Brake, O., Konstantinova, P., Ceylan, M., Berkhout, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silencing+of+HIV-1+with+RNA+interference:+a+multiple+shRNA+approach.">Silencing of HIV-1 with RNA interference: a multiple shRNA approach.</a> Mol Ther. 14, 883-892 (2006).</li><li>Naito, Y., 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=Optimal+design+and+validation+of+antiviral+siRNA+for+targeting+HIV-1.">Optimal design and validation of antiviral siRNA for targeting HIV-1.</a> Retrovirology. 4, 80 (2007).</li><li>Mandal, D., Feng, Z., Stoltzfus, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Excessive+RNA+splicing+and+inhibition+of+HIV-1+replication+induced+by+modified+U1+small+nuclear+RNAs.">Excessive RNA splicing and inhibition of HIV-1 replication induced by modified U1 small nuclear RNAs.</a> J Virol. 84, 12790-12800 (2010).</li><li>Chang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhanced+expression+and+HIV-1+inhibition+of+chimeric+tRNA(Lys3)-ribozymes+under+dual+U6+snRNA+and+tRNA+promoters.">Enhanced expression and HIV-1 inhibition of chimeric tRNA(Lys3)-ribozymes under dual U6 snRNA and tRNA promoters.</a> Mol Ther. 6, 481-489 (2002).</li><li>Chang, L. J., Liu, X., He, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lentiviral+siRNAs+targeting+multiple+highly+conserved+RNA+sequences+of+human+immunodeficiency+virus+type+1.">Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1.</a> Gene Ther. 12, 1133-1144 (2005).</li><li>Daniels, S. 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=HIV-1+RRE+RNA+acts+as+an+RNA+silencing+suppressor+by+competing+with+TRBP-bound+siRNAs.">HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs.</a> RNA Biol. 12, 123-135 (2015).</li><li>Castanotto, 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=Combinatorial+delivery+of+small+interfering+RNAs+reduces+RNAi+efficacy+by+selective+incorporation+into+RISC.">Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC.</a> Nucleic Acids Res. 35, 5154-5164 (2007).</li><li>Vickers, T. A., Sabripour, M., Crooke, S. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=U1+adaptors+result+in+reduction+of+multiple+pre-mRNA+species+principally+by+sequestering+U1snRNP.">U1 adaptors result in reduction of multiple pre-mRNA species principally by sequestering U1snRNP.</a> Nucleic Acids Res. 39, e71 (2011).</li><li>Tai, C. J., Li, C. L., Tai, C. J., Wang, C. K., Lin, L. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Early+Viral+Entry+Assays+for+the+Identification+and+Evaluation+of+Antiviral+Compounds.">Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds.</a> J Vis Exp. , (2015).</li><li>Riss, T. L., et al., Sittampalam, G. 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=.">.</a> Assay Guidance Manual. , (2004).</li><li>Reynolds, 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=Induction+of+the+interferon+response+by+siRNA+is+cell+type-+and+duplex+length-dependent.">Induction of the interferon response by siRNA is cell type- and duplex length-dependent.</a> Rna. 12, 988-993 (2006).</li><li>Whitehead, K. A., Dahlman, J. E., Langer, R. S., Anderson, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silencing+or+stimulation?+siRNA+delivery+and+the+immune+system.">Silencing or stimulation? siRNA delivery and the immune system.</a> Annu Rev Chem Biomol Eng. 2, 77-96 (2011).</li></ol>

The HIV-1 production assay described was performed using HEK293T cells (Figure 2) and is similar to assays used to screen HIV-1 RNA for effective ribozyme13, shRNA10,29, siRNA30, and U1i RNA11,31 target sites. Using different methods to quantify HIV-1 production, most studies have measured viral production 48 hr after co-transfection of an HIV-1 expression plasmid with candidate RNAs. Following the production of HIV-1, immature virions undergo proteolytic cleav...

A limitation of current HIV-1 treatments is that they must be chronically administered to prevent disease progression. Transplant of HIV-1 resistant T lymphocyte, or hematopoietic stem cells, has the potential to provide long term control of HIV-1 replication in the absence of drug therapy1,2 and may also be an effective approach to attain an HIV-1 cure3. One way to render cells resistant to HIV-1 replication is to insert one or more genes coding for anti-HIV-1 RNAs or peptides into an infected individual&#39;s cells during an autologous transplant4. Several candidate anti-HIV-1 genes have been designed with some entering clinical trials in combinations of two5 or three6, to prevent the development of HIV-1 resistance to any single gene.
Anti-HIV-1 RNAs are among the top candidates for combination gene therapy due to their low potential to elicit immune responses and because they are transcribed from very short gene sequences. Some anti-HIV-1 RNAs have been designed to target viral entry and integration. However, most anti-HIV-1 RNAs target post-integration steps in the viral life cycle (Figure 1). Post-integration inhibitors include decoy RNAs, targeting the HIV-1 regulatory proteins Tat or Rev1, and antisense-based RNAs, targeting different sites in HIV-1 RNA, such as ribozymes7, shRNAs8 and U1i RNAs9. Methods that have been used to compare the efficacy of anti-HIV-1 RNAs include monitoring viral replication in cells transduced with genes coding for candidate RNAs and measuring viral production in cells transiently transfected with plasmids expressing candidate RNAs and an HIV-1 expression plasmid10-13. We have previously used an HIV-1 production assay to screen HIV-1 RNA for new ribozyme target sites13-15. These methods have since been refined to optimize the format of an RNA interference molecule expressed from plasmid DNA as an shRNA or delivered as a synthetic siRNA16. The assay measures the production of mature viruses from human embryonic kidney (HEK) 293T cells, and can be used to compare the effects of inhibitors that target post-integration steps in the HIV-1 replication cycle (Figure 1). For inhibitors that target pre-integration steps, alternative assays such as a TZM-bl cell infectivity assay17 are needed to evaluate antiviral efficacy.
Major safety concerns for the delivery of anti-HIV-1 RNAs in the clinic include potential off-target effects on human RNAs or proteins, and activation of innate immune sensors. To evaluate the toxicity of anti-HIV-1 siRNAs, we have used a cell viability assay in different cell lines16. We also measured activation of the double stranded RNA immune sensors, RNA activated protein kinase R (PKR) and Toll like receptor 3 (TLR3), as well as expression of the interferon stimulated gene, ADAR1 p150. These assays can be used to confirm that the efficacy of anti-HIV-1 RNAs is not due to indirect effects on cell viability or immune sensor activation. They are also useful in excluding candidate RNAs with potential toxicities from further development.
In the following protocols, procedures to identify new therapeutic RNAs and optimize the format of existing ones are described. The methods are useful for screening RNA based post-integration inhibitors of HIV-1 replication and could be adapted to screen other post-integration inhibitors, such as small molecules targeting Rev mediated export of viral RNA18 or CRISPR/Cas systems designed to target integrated HIV-1 DNA19.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>DMEM HyClone</td>
			<td>GE Healthcare</td>
			<td>SH30243.01</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS HyClone</td>
			<td>GE Healthcare</td>
			<td>SH30396.03</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin Gibco</td>
			<td>Thermo Fisher</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture plates, 96 well, 24 well, 6 well.</td>
			<td>Corning</td>
			<td>353075, 353047, 353043</td>
			<td></td>
		</tr>
		<tr>
			<td>Micro tubes Axygen</td>
			<td>Corning</td>
			<td>311-08-051</td>
			<td></td>
		</tr>
		<tr>
			<td>Low molecular weight Poly I:C</td>
			<td>InvivoGen</td>
			<td>3182-29-6</td>
			<td></td>
		</tr>
		<tr>
			<td>DharmaFECT-1</td>
			<td>Dharmacon</td>
			<td>T-2001-01</td>
			<td>transfection reagent for synthetic RNAs</td>
		</tr>
		<tr>
			<td>TransIT-LT1</td>
			<td>Mirus</td>
			<td>MIR 2300</td>
			<td>transfection reagent for RNA expression plasmids</td>
		</tr>
		<tr>
			<td>Nonidet P40 (NP-40)</td>
			<td>USB</td>
			<td>19628</td>
			<td></td>
		</tr>
		<tr>
			<td>[32P]dTTP</td>
			<td>Perkin Elmer</td>
			<td>BLU505H</td>
			<td></td>
		</tr>
		<tr>
			<td>poly(A) RNA template&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>10108626001</td>
			<td></td>
		</tr>
		<tr>
			<td>oligo(dT)12-18 DNA primer</td>
			<td>Thermo Fisher</td>
			<td>18418-012</td>
			<td></td>
		</tr>
		<tr>
			<td>DEAE filtermat paper&#160;</td>
			<td>Perkin Elmer</td>
			<td>1450-522</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate scintillation counter</td>
			<td>Perkin Elmer</td>
			<td>1450-024</td>
			<td></td>
		</tr>
		<tr>
			<td>MTT</td>
			<td>Sigma-Aldrich</td>
			<td>M-2128</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS HyClone</td>
			<td>GE Healthcare</td>
			<td>SH30028.02</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate spectrophotometer</td>
			<td>Bio-rad</td>
			<td>1706930</td>
			<td></td>
		</tr>
		<tr>
			<td>Lysis buffer tablets</td>
			<td>Roche</td>
			<td>4693159001, 4906837001</td>
			<td>protease and phosphatase inhibitors</td>
		</tr>
		<tr>
			<td>Microcentrifuge</td>
			<td>Eppendorf</td>
			<td>5415R</td>
			<td></td>
		</tr>
		<tr>
			<td>Bradford reagent</td>
			<td>Bio-rad</td>
			<td>500-0006</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel running chamber</td>
			<td>Hoefer</td>
			<td>SE600</td>
			<td></td>
		</tr>
		<tr>
			<td>Semi-dry transfer cell</td>
			<td>Bio-rad</td>
			<td>1703940</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein ladder EZ-Run</td>
			<td>Thermo Fisher</td>
			<td>BP3603-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Nitrocellulose membrane</td>
			<td>Bio-rad</td>
			<td>162-0094</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Sigma-Aldrich</td>
			<td>A9647-1006</td>
			<td></td>
		</tr>
		<tr>
			<td>Antibody stripping solution</td>
			<td>Millipore</td>
			<td>2504</td>
			<td></td>
		</tr>
		<tr>
			<td>ECL - Pierce</td>
			<td>Thermo Fisher&#160;</td>
			<td>PI32106</td>
			<td></td>
		</tr>
		<tr>
			<td>ADAR1 antibody</td>
			<td></td>
			<td></td>
			<td>from Dr. B.L. Bass</td>
		</tr>
		<tr>
			<td>phospho-T446-PKR antibody</td>
			<td>Abcam</td>
			<td>ab32036</td>
			<td></td>
		</tr>
		<tr>
			<td>phospho-S396-IRF3 antibody</td>
			<td>Cell Signaling</td>
			<td>4947</td>
			<td></td>
		</tr>
		<tr>
			<td>PKR antibody</td>
			<td></td>
			<td></td>
			<td>from Dr. A. Hovanessian</td>
		</tr>
		<tr>
			<td>IRF3 antibody</td>
			<td>Cell Signaling</td>
			<td>11904</td>
			<td></td>
		</tr>
		<tr>
			<td>Actin antibody</td>
			<td>Millipore</td>
			<td>MAB1501</td>
			<td></td>
		</tr>
		<tr>
			<td>Peroxidase-labeled goat anti-rabbit</td>
			<td>KPL</td>
			<td>474-1506</td>
			<td></td>
		</tr>
		<tr>
			<td>Peroxidase-labeled goat anti-mouse</td>
			<td>KPL</td>
			<td>474-1806</td>
			<td></td>
		</tr>
		<tr>
			<td>Ponceau S&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>6226-79-5</td>
			<td></td>
		</tr>
	</tbody>
</table>

evaluation of the efficacy and toxicity of rnas targeting hiv-1 production for use in gene or drug therapy

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

A general schematic of the procedures is shown in Figure 2 with an example transfection plan for three test RNAs and a control RNA provided in Figure 2B. For viral production and cell viability assays, the read-out for each test construct is normalized to a negative control. Replicates are transfected in sets, so that each test RNA is normalized to its adjacent negative control. This is done to avoid inaccurate data related to the time between complexing ...

Watch this Scientific Journal Video about Evaluation of the Efficacy And Toxicity of RNAs Targeting HIV-1 Production for Use in Gene or Drug Therapy at JoVE.com

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

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

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

The overall goal of this procedure is to compare the efficacy and toxicity of new RNAs targeting HIV-1 production. This method can help identify new RNA molecules for using HIV-1 gene or drug therapy, such as short hairpin or small interfering RNAs, ribozymes, and RNA decoys. The main advantage of this technique is that several new RNA designs can be screened simultaneously with a quick turnaround time.Although this method was designed to evaluate new RNA drug or gene therapy for HIV, it can also be applied to other systems, such as small molecules or CRISPR tasks. We first had the idea for this method when we were setting up experiments to screen a large number of ribozymes for anti-HIV effects. To begin, prepare a suspension of human embryonic kidney 293T cells at two times 10 to the fifth cells per milliliter in DMEM with 10%FPS and 1%penicillin streptomycin.Add 500, 100 and 1, 000 microliters of the cell suspension to each of the wells of 24, 96, and 12-well plates for viral production, cell viability, and immune activation assays, respectively. Gently swirl the plates and incubate them overnight at 37 degrees Celsius with 5%carbon dioxide to 50%to 70%confluency. For the viral production assay, prepare a 10 nanogram per microliter dilution of an HIV-1 expression plasmid and add 10 microliters to each assay tube.Next, prepare five micromolar dilutions of test RNAs and a negative control RNA. Then add 2.5 microliters or 10 microliters of each test RNA and negative control dilution to the corresponding tubes for 25 nanomolar or 100 nanomolar final concentrations. For the cell viability assay, prepare five micromolar dilutions of test RNAs and a 10 milligram per milliliter dilution of the positive control RNA, low molecular weight poly(I:C)Add two microliters of the test RNA or the positive control RNA dilutions to the corresponding tubes for 100 nanomolar or 200 micrograms per milliliter final concentrations, respectively.For the immune activation assay, add 20 microliters of test RNA or positive control RNA dilutions, as prepared for the cell viability assay, to the corresponding tubes for 100 nanomolar or 200 micrograms per milliliter final concentrations, respectively. Then add 50, 25, or 75 microliters of DMEM to each transfection tube for viral production, cell viability, and immune activation assays, respectively. For viral production assays, bring cells and prepared transfection tubes to a biosafety level three, or BSL-3, laboratory before the next step.Add two microliters of the transfection reagent sequentially to the transfection tubes, and incubate 15 to 20 minutes to allow complexes to form. Add the entire transfection mixture from each microtube drop-wise to the corresponding positions in the cell culture plates. Gently swirl, and incubate the plates for 48 hours at 37 degrees Celsius and 5%carbon dioxide.To carry out the viral production assay, after removing the 24-well cell culture plates from the incubator, transfer them to the BSL-3 cell culture hood. Gently swirl the plates and then transfer 150 microliters of the supernatant from each well to a corresponding well in a 96-well flat-bottom plate to be used to quantify HIV-1 production. Transfer five microliters of supernatant to the corresponding wells in a 96-well plate containing 25 microliters of a viral disruption cocktail.After incubating the mixture for five minutes at room temperature, transfer the plate to a radioactivity work station. Next, prepare a radioactive cocktail, and add 25 microliters to each well of viral supernatant and disruption cocktail. Incubate the plates at 37 degrees Celsius for two hours.Spot five microliters of the reaction mixture onto corresponding squares in a glass fiber/DEAE filter mat paper, and allow the spots to dry for 10 minutes. Use 2x SSC buffer to wash the papers five times for five minutes each, followed by two one-minute washes with 95%ethanol. Allow the papers to dry before sealing them in sample bags.Clip sample bags containing the filter mat paper into a cassette, and insert the cassette into a microplate scintillation counter. Then start the counter. For any viral quantification method, divide the values obtained for each test RNA by the adjacent negative control and multiply this value by 100 to get the percent inhibition of HIV-1 production for each replicate of the test RNAs.To carry out a cell viability assay, after removing the 96-well plates from the incubator, add 20 microliters of five milligrams per milliliter MTT and DPBS to each well. Then incubate the plates for three hours at 37 degrees Celsius. Add 150 microliters of acidified isopropanol with detergent to each well, and incubate the plates at room temperature for two hours.Then use a microplate spectrophotometer to determine the absorbance at 570 nanometers. Calculate the relative MTT metabolism for each positive control and test RNA by dividing the value obtained for each sample by its adjacent transfection control. For the immune activation assay, after removing the 12-well plates from the incubator, aspirate the culture medium and use DPBS to gently wash the cells twice.Then add 70 microliters of cold lysis buffer containing protease and phosphotase inhibitors to each well, and incubate the plates on ice for 10 minutes. Transfer cell lysates to microtubes, and fast freeze them by immersing the tubes in liquid nitrogen. After allowing the samples to thaw, freeze-thaw them two more times, for a total of three freeze-thaw cycles.Next, centrifuge the lysates at 15, 700 times g and 4 degrees Celsius for 15 minutes to pellet the cell debris. Then, following electrophoresis and transfer to a membrane, reveal protein bands by incubating the membrane in Ponceau S for one minute. Then wash it with double-distilled water.Use the bands and protein ladder as a guide to cut the membrane at 80 and 55 kilodaltons. Now, use TBS with 0.05%TWEEN 20 or TBST to wash out the Ponceau S staining. Add TBST with 5%non-fat milk to completely cover the membranes, and incubate them at room temperature with agitation for one hour.Transfer the membranes into TBST with 3%BSA and antibodies diluted 1:1, 000 for ADAR, phosphor-PKR, and phosphor-IRF3 for the top, middle, and bottom pieces of the membrane, respectively. Incubate at 4 degrees Celsius with agitation overnight. The following morning, use TBST to wash the membranes five times for five minutes each, before transferring to TBST with 5%non-fat milk and 1:5, 000 peroxidase labeled goat anti-rabbit secondary antibodies for one hour.After visualizing the protein bands on films, use a stripping solution to wash the middle and bottom pieces of the membrane for 10 minutes, before incubating the middle piece of the membrane in PKR antibodies and the bottom piece in IRF3 antibodies. As a positive control, probe the bottom membrane with antibodies to Actin according to the text protocol. A general schematic of the assays is shown here with an example transfection plan for three test RNAs and a control RNA.For viral production and cell viability assays, the readout for each test construct is normalized to a negative control. Using the HIV-1 production assay in cells transfected with a plasmid expressing HIV-1 strain NL4-3, the percent of RT activity in cells co-transfected with one of the siRNAs shown here, compared to cells transfected with a long Dicer substrate nonsense siRNA, was calculated to identify the optimal length of RNA interference molecules targeting a conserved site in HIV-1 RNA. Using the most effective siRNAs identified, the percent metabolism of MTT was determined for transfected cells.Along double-stranded RNA, poly(I:C)reduced cell viability only at the highest dose. No significant reduction in cell viability was observed for siRNAs targeting the 1498 site in HIV-1 RNA, regardless of their length. As demonstrated here by Western blot, the same set of RNAs was evaluated in the immune activation assay.Under conditions where poly(I:C)activated the expression of ADAR1-p150 and induced phosphorilation of PKR and IRF3, no significant effect on any inactivation markers could be observed for any of the test RNAs. Once mastered, this technique can be done in seven days, if it's performed properly. While attempting this procedure, it is important to use high quality preparations of both RNA and DNA for transfection.Furthermore, to include the proper negative and positive controls. Following this procedure, other methods like HIV infection of transduced cells, can be used to evaluate the long-term efficacy and toxicity of potential anti-HIV candidates. After its development, this technique allowed us to identify an accessible and conserved target site in HIV RNA and optimize the formats of ribozymes, shRNAs and siRNAs targeting it.After watching this video, you should have a good understanding of how to quickly screen new RNA candidates targeting HIV production for efficacy using the viral production assay, and potential toxicity using the immune activation and cell viability assays. Don't forget that working with HIV and radiolabeled nucleotides can be extremely hazardous. Precautions such as using certified biosafety and radioactivity laboratories should always be taken while performing this procedure.

evaluation-efficacy-toxicity-rnas-targeting-hiv-1-production-for-use

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JoVE Journal

Immunology and Infection

7.7K vistas.  Lady Davis Institute for Medical Research. The overall goal of this procedure is to compare the efficacy and toxicity of new RNAs targeting HIV-1 production. This method can help identify new RNA molecules for using HIV-1 gene or drug therapy, such as short hairpin or small interfering RNAs, ribozymes, and RNA decoys. The main advantage of this technique is that several new RNA designs can be screened simultaneously with a quick turnaround time.Although this method was designed to evaluate new RNA drug or gene therapy for HIV, ...