A Genome-wide Short Hairpin RNA Screening of Jurkat T-cells for Human Proteins Contributing to Productive HIV-1 Replication
2009; Elsevier BV; Volume: 284; Issue: 29 Linguagem: Inglês
10.1074/jbc.m109.010033
ISSN1083-351X
AutoresMan Lung Yeung, Laurent Houzet, Venkat S. R. K. Yedavalli, Kuan‐Teh Jeang,
Tópico(s)RNA Interference and Gene Delivery
ResumoShort interfering RNAs (siRNAs) have been used to inhibit HIV-1 replication. The durable inhibition of HIV-1 replication by RNA interference has been impeded, however, by a high mutation rate when viral sequences are targeted and by cytotoxicity when cellular genes are knocked down. To identify cellular proteins that contribute to HIV-1 replication that can be chronically silenced without significant cytotoxicity, we employed a shRNA library that targets 54,509 human transcripts. We used this library to select a comprehensive population of Jurkat T-cell clones, each expressing a single discrete shRNA. The Jurkat clones were then infected with HIV-1. Clones that survived viral infection represent moieties silenced for a human mRNA needed for virus replication, but whose chronic knockdown did not cause cytotoxicity. Overall, 252 individual Jurkat mRNAs were identified. Twenty-two of these mRNAs were secondarily verified for their contributions to HIV-1 replication. Five mRNAs, NRF1, STXBP2, NCOA3, PRDM2, and EXOSC5, were studied for their effect on steps of the HIV-1 life cycle. We discuss the similarities and differences between our shRNA findings for HIV-1 using a spreading infection assay in human Jurkat T-cells and results from other investigators who used siRNA-based screenings in HeLa or 293T cells. Short interfering RNAs (siRNAs) have been used to inhibit HIV-1 replication. The durable inhibition of HIV-1 replication by RNA interference has been impeded, however, by a high mutation rate when viral sequences are targeted and by cytotoxicity when cellular genes are knocked down. To identify cellular proteins that contribute to HIV-1 replication that can be chronically silenced without significant cytotoxicity, we employed a shRNA library that targets 54,509 human transcripts. We used this library to select a comprehensive population of Jurkat T-cell clones, each expressing a single discrete shRNA. The Jurkat clones were then infected with HIV-1. Clones that survived viral infection represent moieties silenced for a human mRNA needed for virus replication, but whose chronic knockdown did not cause cytotoxicity. Overall, 252 individual Jurkat mRNAs were identified. Twenty-two of these mRNAs were secondarily verified for their contributions to HIV-1 replication. Five mRNAs, NRF1, STXBP2, NCOA3, PRDM2, and EXOSC5, were studied for their effect on steps of the HIV-1 life cycle. We discuss the similarities and differences between our shRNA findings for HIV-1 using a spreading infection assay in human Jurkat T-cells and results from other investigators who used siRNA-based screenings in HeLa or 293T cells. The use of RNA interference (RNAi) 2The abbreviations used are: RNAiRNA interferenceHIV-1human immunodeficiency virus, type 1siRNAshort interfering RNARTreverse transcriptasePBSphosphate-buffered salineGFPgreen fluorescent proteinVSV-Gvesicular stomatitis virus G. to silence genes holds potential applications for antiviral therapy (1.Dorsett Y. Tuschl T. Nat. Rev. Drug Discov. 2004; 3: 318-329Crossref PubMed Scopus (813) Google Scholar, 2.Fire A. Trends Genet. 1999; 15: 358-363Abstract Full Text Full Text PDF PubMed Scopus (494) Google Scholar). RNAi, directed to viral and/or host RNA sequences, has been employed to inhibit HIV-1 replication (3.Bennasser Y. Yeung M.L. Jeang K.T. BioDrugs. 2007; 21: 17-22Crossref PubMed Scopus (24) Google Scholar, 4.Naito Y. Nohtomi K. Onogi T. Uenishi R. Ui-Tei K. Saigo K. Takebe Y. Retrovirology. 2007; 4: 80Crossref PubMed Scopus (47) Google Scholar, 5.Kumar A. Retrovirology. 2007; 4: 26Crossref PubMed Scopus (18) Google Scholar, 6.Berkhout B. Jeang K.T. J. Biol. Chem. 2007; 282: 26641-26645Abstract Full Text Full Text PDF PubMed Scopus (79) Google Scholar). These approaches are effective over the short term; however, over longer durations, they have elicited either a high rate of escape mutation when viral sequences are targeted or cytotoxicity when cellular genes are chronically suppressed (7.Das A.T. Brummelkamp T.R. Westerhout E.M. Vink M. Madiredjo M. Bernards R. Berkhout B. J. Virol. 2004; 78: 2601-2605Crossref PubMed Scopus (395) Google Scholar, 8.Michienzi A. Castanotto D. Lee N. Li S. Zaia J.A. Rossi J.J. Ann. N.Y. Acad. Sci. 2003; 1002: 63-71Crossref PubMed Scopus (64) Google Scholar, 9.Boden D. Pusch O. Lee F. Tucker L. Ramratnam B. J. Virol. 2003; 77: 11531-11535Crossref PubMed Scopus (373) Google Scholar, 10.Westerhout E.M. Ooms M. Vink M. Das A.T. Berkhout B. Nucleic Acids Res. 2005; 33: 796-804Crossref PubMed Scopus (352) Google Scholar). RNA interference human immunodeficiency virus, type 1 short interfering RNA reverse transcriptase phosphate-buffered saline green fluorescent protein vesicular stomatitis virus G. If cellular genes important for HIV-1 replication (11.Goff S.P. Nat. Rev. Microbiol. 2007; 5: 253-263Crossref PubMed Scopus (203) Google Scholar, 12.Lama J. Planelles V. Retrovirology. 2007; 4: 52Crossref PubMed Scopus (110) Google Scholar), but dispensable for host cell viability, could be identified, then silencing the RNAs from these genes may remedy the proclivity for HIV-1 mutational escapes when viral sequences are targeted. Toward this objective, Brass et al. (13.Brass A.L. Dykxhoorn D.M. Benita Y. Yan N. Engelman A. Xavier R.J. Lieberman J. Elledge S.J. Science. 2008; 319: 921-926Crossref PubMed Scopus (1183) Google Scholar), Konig et al. (14.König R. Zhou Y. Elleder D. Diamond T.L. Bonamy G.M. Irelan J.T. Chiang C.Y. Tu B.P. De Jesus P.D. Lilley C.E. Seidel S. Opaluch A.M. Caldwell J.S. Weitzman M.D. Kuhen K.L. Bandyopadhyay S. Ideker T. Orth A.P. Miraglia L.J. Bushman F.D. Young J.A. Chanda S.K. Cell. 2008; 135: 49-60Abstract Full Text Full Text PDF PubMed Scopus (796) Google Scholar), and Zhou et al. (15.Zhou H. Xu M. Huang Q. Gates A.T. Zhang X.D. Castle J.C. Stec E. Ferrer M. Strulovici B. Hazuda D.J. Espeseth A.S. Cell Host Microbe. 2008; 4: 495-504Abstract Full Text Full Text PDF PubMed Scopus (627) Google Scholar) have recently used libraries of presynthesized siRNA to knock down transiently HeLa/293T cell RNAs. They reported ∼272, 278, and 304 annotated gene candidates that contribute to steps in the HIV-1 life cycle. Intriguingly, the identities of the gene candidates discovered by Brass et al. (13.Brass A.L. Dykxhoorn D.M. Benita Y. Yan N. Engelman A. Xavier R.J. Lieberman J. Elledge S.J. Science. 2008; 319: 921-926Crossref PubMed Scopus (1183) Google Scholar), Konig et al. (14.König R. Zhou Y. Elleder D. Diamond T.L. Bonamy G.M. Irelan J.T. Chiang C.Y. Tu B.P. De Jesus P.D. Lilley C.E. Seidel S. Opaluch A.M. Caldwell J.S. Weitzman M.D. Kuhen K.L. Bandyopadhyay S. Ideker T. Orth A.P. Miraglia L.J. Bushman F.D. Young J.A. Chanda S.K. Cell. 2008; 135: 49-60Abstract Full Text Full Text PDF PubMed Scopus (796) Google Scholar), and Zhou et al. (15.Zhou H. Xu M. Huang Q. Gates A.T. Zhang X.D. Castle J.C. Stec E. Ferrer M. Strulovici B. Hazuda D.J. Espeseth A.S. Cell Host Microbe. 2008; 4: 495-504Abstract Full Text Full Text PDF PubMed Scopus (627) Google Scholar) are highly divergent with very little overlap when the three studies are compared with each other (16.Goff S.P. Cell. 2008; 135: 417-420Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar). HeLa and 293T cells are highly efficient model cells for siRNA transfection. They are, however, poor representations of T-cells that are physiologically infected by HIV-1. In this respect, human T-cell lines, such as Jurkat, are better models, although the latter cells cannot be transfected efficiently with siRNAs. To perform a genome-wide RNAi screening in Jurkat T-cells, we decided to employ a shRNA library cloned in a retroviral vector. Our approach was to transduce Jurkat cells with the shRNA library and then select for cell clones that are individually integrated for single constitutively expressed shRNA. These shRNA clones are then infected with HIV-1. Because Jurkat T-cells are killed by HIV-1 infection, a cell would survive only if it harbored a shRNA that has knocked down sufficiently a gene required for lytic viral replication (Fig. 1A). Execution of the above strategy identified 252 human genes whose chronic knockdown in Jurkat cells apparently interrupted productive HIV-1 infection. These 252 Jurkat genes are mostly distinct from the HeLa and 293T candidates described by Brass et al. (13.Brass A.L. Dykxhoorn D.M. Benita Y. Yan N. Engelman A. Xavier R.J. Lieberman J. Elledge S.J. Science. 2008; 319: 921-926Crossref PubMed Scopus (1183) Google Scholar), Konig et al. (14.König R. Zhou Y. Elleder D. Diamond T.L. Bonamy G.M. Irelan J.T. Chiang C.Y. Tu B.P. De Jesus P.D. Lilley C.E. Seidel S. Opaluch A.M. Caldwell J.S. Weitzman M.D. Kuhen K.L. Bandyopadhyay S. Ideker T. Orth A.P. Miraglia L.J. Bushman F.D. Young J.A. Chanda S.K. Cell. 2008; 135: 49-60Abstract Full Text Full Text PDF PubMed Scopus (796) Google Scholar), and Zhou et al. (15.Zhou H. Xu M. Huang Q. Gates A.T. Zhang X.D. Castle J.C. Stec E. Ferrer M. Strulovici B. Hazuda D.J. Espeseth A.S. Cell Host Microbe. 2008; 4: 495-504Abstract Full Text Full Text PDF PubMed Scopus (627) Google Scholar). There were, however, many examples in our discovered genes that located to the same cellular signaling pathways as genes described by others. Jurkat and its derivative cell clones were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% (v/v) heat-inactivated fetal calf serum (HyClone), 100 units/ml penicillin, and 100 μg/ml streptomycin (Invitrogen). Cells were selected and maintained in the same medium as described above with the addition of 0.125 μg/ml puromycin. Feline immunodeficiency virus vector-based shRNA library was produced as described in the manufacturer's protocol from SBI with the following modifications. 293T cells were propagated in Dulbecco's modified Eagle's medium (Invitrogen) with 10% fetal calf serum and transfected with 10 μg of the pPACK packaging plasmid mixture and 2 μg of the shRNA library lentivector constructs (SBI) using Lipofectamine and Plus reagents according to the manufacturer's protocol (Invitrogen). 24 and 72 h after transfection, conditioned culture media were collected to harvest the packaged viruses. Viruses were quantified by reverse transcriptase (RT) (17.Willey R.L. Smith D.H. Lasky L.A. Theodore T.S. Earl P.L. Moss B. Capon D.J. Martin M.A. J. Virol. 1988; 62: 139-147Crossref PubMed Google Scholar). 106–107 cpm of RT units were used to infect 8 × 106 Jurkat cells. After 8 h of exposure to virus, cells were washed two times with PBS and resuspended in RPMI 1640 medium (Invitrogen). One week after transduction, the cells were selected with 0.125 μg/ml puromycin containing growth medium for 3 weeks. For secondary validations, independent shRNA expressing vector constructs (Mission shRNA) were purchased from Sigma. These shRNA-packaged viruses were generated in 293T cells using ViraPowerTM Lentiviral Expression Systems (Invitrogen) according to the manufacturer's protocol. Selected Jurkat clones were split into two flasks and subjected to HIV-1 infection or mock infection. Four weeks after infection, small RNAs were harvested using the mirVanaTM small RNA isolation kit (Ambion). cDNA synthesis and labeling were performed as described in the manufacturer's protocol. Reverse transcription was performed using 5 μg of total RNA in the presence of the 10 μm cDNA synthesis GNF primer (ATTTATTGTATCTGTGGGAGCCTC), 100 mm dithiothreitol, 10 mm of each dNTP, 1× reverse transcriptase buffer, and 200 units × 4 of SuperScript® III Reverse Transcriptase (Invitrogen). The reaction mixtures were allowed to incubate at 42 °C for 1 h. The reaction was stopped by heat inactivation at 72 °C for 5 min. Half of the reaction mixture was then transferred to a tube containing 1× PCR buffer, 20 mm dNTP, 20 μm forward GNF primer (TGCATGTCGCTATGTGTTCTGGGA), and 20 μm reverse GNF primer (ACAAAGCACTGGAAGCTATCGAA) and Advantage® HF2 Taq polymerase (Clontech). PCR were performed under the following conditions: step 1, 94 °C for 4 min; step 2, 94 °C for 30 s and then 68 °C for 1 min; step 3, repeat step 2 for 20 cycles; and step 4, 68 °C for 3 min. An aliquot was made of 1 μl of the first round PCR into 4 new tubes, each containing 1× PCR buffer, 20 mm dNTP, 20 μm NRev GNF universal primer (AAAGAATGCTTATGGACGCTAGAA) and NFwd-Bio primer (Biotin-CTTCCTGTCAGA) and Advantage® HF2 Taq polymerase (Clontech). The PCR conditions were then as follows: step 1, 94 °C for 2 min, 50 °C for 2 min and then 68 °C for 1 min; step 2, 94 °C for 30 s and then 68 °C for 30 s; step 3, repeat step 2 for 18 cycles; and step 4, 68 °C for 3 min. The PCR products were then gel purified using the Qiagen QIAquick PCR purification kit as described in the manufacturer's protocol. After purification, the PCR product was treated with λ-exonuclease (New England Biolabs) at 37 °C for 2 h to remove the non-biotinylated strand. The digested products were purified as described above and then quantified. 10 μg of the purified products were hybridized on the GeneChip® Human Genome U133 +2 Array (Affymetrix) using the Affymetrix hybridization buffer and then stained with streptavidin-phycoerythrin (Molecular Probes). Following the standard Affymetrix protocol, the image of the processed chip was captured by a scanner controlled by Affymetrix GCOS software. Data were first normalized by the quantile normalization method, and the variances were calculated based on analysis of variance analysis. The signals were summarized for replicates with two or more replicate values above 100. The fold changes were determined based on the ratio of the signals between the mock and infected samples. Pathway analysis was done by using the Ingenuity program. 1 × 106 cells were stained with anti-CXCR4-PE/anti-CD4-APC or their isotype controls (BD Biosciences) for 30 min at 4 °C. The stained samples were washed two times with PBS containing 1% fetal calf serum. After washing, the cells were resuspended with the wash buffer containing 0.5% of paraformaldehyde. Flow cytometry analyses were performed using a FACSCalibur (BD Biosciences) equipped with CellQuest software (BD Biosciences). Live cell gating was first done by measuring the forward (FSC) and sideward (SSC) light scatter of unstained Jurkat cells. Background level settings were determined based on the signals detected in Jurkat cells stained with isotype controls IgG1κ-APC and IgG2aκ-PE. For monitoring of Jurkat cells killed by virus infection, Jurkat cells infected or mock-infected after 3 and 5 days with HIV-1 were harvested. Cells were washed twice with PBS, and the percentage of cell death was determined by the Annexin-V-FITC detection kit II (BD Biosciences) following the manufacturer's protocol. Total RNAs were isolated using the mirVana miRNA isolation kit (Ambion). The RNAs were first quantified by NanoDrop® Spectrophotometer (ND-1000; Grace Scientific, LLC). Real-time PCR was then performed using 1 μg of the total RNA and TaqMan® EZ RT-PCR Core Reagents (ABI Biosystems) and TaqMan Tamra Probes (TaqMan Gene Expression Assays, inventoried for the corresponding genes; ABI Biosystems) according to the manufacturer's protocol. Briefly, the RT step was done at 50 °C for 10 min, and the amplification was performed under the condition of 15 s at 95 °C and 1 min at 60 °C for 55 cycles in a 7300 Real Time PCR System (Applied Biosystems). Virus stock was prepared by transfecting 293T cells. Supernatant virus was quantified by RT (17.Willey R.L. Smith D.H. Lasky L.A. Theodore T.S. Earl P.L. Moss B. Capon D.J. Martin M.A. J. Virol. 1988; 62: 139-147Crossref PubMed Google Scholar) and/or the p24 Antigen enzyme-linked immunosorbent assay (RETRO-TEK; ZeptoMetrix Corp.); typically, 106–107 cpm of RT units were used to infect 5 × 106 Jurkat cells. After 8 h of exposure to virus, cells were washed two times with PBS and resuspended into RPMI. After 24 h, cellular DNA and RNA were isolated using DNAzol® Reagent (Invitrogen) and TRI® Reagent (Sigma), respectively, and quantified by the Nanodrop Spectrophotometer. HIV proviral DNA was detected by quantitative PCR on 50 ng of genomic DNA using the primers TCAGCATTATCAGAAGGAGCCACC (forward) TCATCCATCCTATTTGTTCCTGAAG (reverse). For HIV RNA quantification, reverse transcription was performed on 0.5 μg of cellular RNA with oligo(dT) as the RT primer, and quantitative PCR for HIV RNA was performed with 5% of the RT reaction using the same primers. A standard curve from 101 to 106 copies of pNL4.3 was used for quantification, and the glyceraldehyde-3-phosphate dehydrogenase gene and mRNA quantification was performed for normalization (forward, GCTCACTGGCATGGCCTTCCGTGT and reverse, TGGAGGAGTGGGTGTCGCTGTTGA). p24 Antigen enzyme-linked immunosorbent assay was carried out according to the manufacturer's protocol. Briefly, the conditioned supernatant was first diluted in PBS and then lysed in the lysis buffer. Samples together with the standards made of HIV-1 p24 (from concentrations of 0 to 125 pg/ml) were loaded on a pre-washed 96-well plate. The plate was then incubated overnight at 37 °C. The HIV-1 p24 Detector Antibody was then applied and incubated at 37 °C for 1 h after washing. Next, unhybridized antibody was washed away before the application of streptavidin-peroxidase working solution. The solution was incubated at 37 °C for 30 min. Color development was done by administration of the substrate working solution and incubation at 25 °C for 30 min. Stop solution was then applied to stop the reaction. The optical density (450 nm) was then acquired by a microplate reader (Mithras LB 940; Berthold Technologies). Cell proliferation was determined using a modified 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay employing the Cell Counting kit 8 (CCK-8; Dojindo) according to the manufacturer's protocol. 10 μl of CCK-8 solution (2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodium salt; Dojindo) was added to 100 μl of cells (around 5 × 103 cells/well) in a 96-well plate. The cell viability was determined by reading the optical density at 450 nm. The data were collected from three independents experiments. Results are presented as the mean ± S.E. from at least three independent experiments. Jurkat parental cells and clones were transfected with either GFP-Gag or GFP plasmid individually. Seventy-two hours after transfection, cells were allowed to settle on a chambered coverglass (Lab-Tek) for 3 h prior to imaging. Live images were captured by Leica TCS-NT (Leica Microsystem). To identify genes in human T-cells important to HIV-1 replication that can be knocked down without cytotoxicity, we used a puromycin-marked feline immunodeficiency virus-based lentivector shRNA library that targets 54,509 human transcripts, including ESTs. This library has 3 to 5 shRNAs designed for each of the 54,509 human transcripts, and all the shRNAs are "bar-coded" for rapid identification using the GeneChip® Human Genome U133 +2 Array. Starting with the feline immunodeficiency virus-based shRNA lentivector library, we produced a corresponding VSV-G packaged shRNA virus library. We used the VSV-G shRNA virus to transduce Jurkat T-cells, a T-cell model commonly used in many HIV-1 studies due to its similar transcriptional profile when compared with that of CD4+ T cells (18.Lewinski M.K. Bisgrove D. Shinn P. Chen H. Hoffmann C. Hannenhalli S. Verdin E. Berry C.C. Ecker J.R. Bushman F.D. J. Virol. 2005; 79: 6610-6619Crossref PubMed Scopus (220) Google Scholar). After transduction, puromycin was applied to select for cells that have integrated shRNAs. The selected cells were then challenged with a high titer stock of HIV-1 NL4-3 at a multiplicity of infection of 1. In the above protocol, cells with a shRNA that knocks down an mRNA whose loss triggers cytotoxicity would be culled during puromycin selection. Because Jurkat cells die when infected by HIV-1 (under our infection conditions 92 and 96% of Jurkat cells showed Annexin V death profile at days 3 and 5 after infection, data not shown), we anticipated that cells knocked down for an mRNA irrelevant to virus replication would succumb rapidly to virus infection. By contrast, a Jurkat shRNA clone silenced for a human mRNA needed for lytic HIV-1 replication would be expected to survive the infection. The shRNA in the survival cell can then be amplified by RT-PCR and identified via microarray bar-coding to reveal the targeted host mRNA (Fig. 1A). To verify the proper execution of this strategy, we monitored each step for the anticipated outcome. We first optimized the experimental conditions for achieving a highly efficient (∼72%) dose-dependent VSV-G virus transduction of Jurkat cells (supplemental Fig. S1). Next, Jurkat cells were transduced with the VSV-G-shRNA virus library, and the representativeness of the shRNA-transduced clones was verified. RNAs from two independently transduced cell populations were collected a few days after shRNA virus library transduction and were RT-PCR amplified and hybridized to the Human Genome U133 +2 Array (Fig. 1B, Transductions 1 and 2). Based on the array data, the concordance between two populations was determined to approximately 85.68–87.70%, supporting the reproducibility of the transductions. To determine the shRNA coverage within the shRNA-transduced cells, two separate hybridizations using the starting shRNA vector library (Fig. 1B, Libraries 1 and 2) were compared with the two shRNA transduction (Transductions 1 and 2). In this analysis, the complexity of the shRNA-transduced cells encompassed on average 84.34% of the total targeted mRNAs in the shRNA vector library. We note that the array patterns in the transduced cells (Fig. 1B, Transductions 1 and 2) are distinctly different from background hybridization visualized using RT-PCR of RNA from a mock-transduced Jurkat cell sample (Fig. 1B, Bottom, Background neg Control). Taken together, the results support that the shRNA virus transductions achieved robust (∼85%), albeit not 100% representation, of the initial shRNA vector library. The transduced cells were selected next with puromycin. After 3 weeks of selection, 9,357 independent shRNA Jurkat clones remained, whereas 45,052 shRNA clones became undetectable. The shRNA clones that were no longer detected could arise in part from the following two reasons. First, a shRNA clone that has knocked down an mRNA whose loss is cytotoxic to the cell would be eliminated during puromycin selection. Second, some of the undetected 45,152 clones were relatively enfeebled, although not absolutely cytotoxic, and during the course of more than 3 weeks of tissue culture selection, these relatively enfeebled cells were outcompeted in proliferation by the more rapidly dividing cells that harbored the 9,357 detected shRNAs. Regardless of the two explanations, the results showed that 18.2% (or 9,357) of the starting 54,509 mRNAs could be tolerably knocked down without affecting Jurkat viability in tissue culture. In the 9,357 shRNA clones, we found 1,365 moieties that were targeted by more than one discrete shRNA. This number is higher than that expected by random (1309.02, Z* = −1.61, standard error = 9.15, p value = 4.67 × 10−10), suggesting that the knock down of some genes could confer a slight growth advantage to cells. We next asked how many of the above 9,357 shRNA Jurkat clones could survive HIV-1 infection. The shRNA Jurkat clones were infected with HIV-1 NL4-3. After 4 weeks of infection, RNA from the survival cells was isolated, amplified by RT-PCR, and analyzed by microarray. The microarray hybridization revealed 252 distinct mRNAs that were enriched by at least 2–22-fold over control background (supplemental Fig. S2). Gene ontology analyses showed that these genes segregated into several functional classes (supplemental Fig. S3). These genes represented candidate factors that potentially contribute positively to HIV-1 replication in cultured Jurkat cells. Next, we selected at random 22 of the 252 gene candidates for additional investigation. For each of the 22 selected genes, we employed 5 discrete shRNAs that targeted independent sequences within the mRNA. Transduction of 22 × 5 shRNAs resulted in the generation of 110 shRNA clones. These clones were confirmed for integration of the expected shRNAs (data not shown), and each was then challenged with infection by HIV-1. Based on the empirical experience in the literature, we expected that not all shRNAs designed to mRNAs will be successful in target knock down inside cells. In RT assays measuring supernatant virus production from these shRNA clones, consistent with the initial shRNA library screening results, 63 of 110 clones were able to restrict HIV-1 replication by slightly less than 50% to >90% when compared with HIV-1 infection of control Jurkat cells (Fig. 2A). To demonstrate that the effect of HIV-1 restriction is due to knock down of the intended mRNAs, we quantified in 25 selected cell clones without HIV-1 infection the shRNA-targeted mRNAs by RT-PCR (Fig. 2B). Fig. 2B shows that in these 25 shRNA clones, the ambient level of the mRNA targeted by the respective shRNA was reduced by ∼85–90% (the level of the corresponding mRNA in control cells was set as 1). To verify further the above results, we performed two additional "control" experiments. First, a trivial explanation for reduced HIV-1 replication could be that the tested cells were nonspecifically reduced for cell surface CD4 and could no longer be infected by HIV-1. To exclude this possibility, we picked 9 cell clones and analyzed each by flow cytometry staining; none was found to be significantly different from parental Jurkat for CD4 (Fig. 3). Second, a reduction in HIV-1 replication could be a nonspecific result of shRNA-induced cytotoxicity. We deemed this explanation unlikely because all the cell clones were already selected for over 3 weeks in puromycin, prior to a second 4 weeks of HIV-1 infection. Nonetheless, 18 shRNA cell clones were chosen and compared head-to-head to parental Jurkat cells for relative proliferation rates in a CCK-8 metabolic assay. Cell growth rates, as reflected in the CCK-8 assay over a period of 4 days, were slightly variable as expected, but all were substantially robust and were little different from Jurkat control cells (Fig. 4).FIGURE 4CCK-8 measurement of the proliferation of Jurkat and shRNA Jurkat clones. The CCK-8 assay measures the dehydrogenase metabolic activity of proliferating cells. The 450 nm absorbance increases proportionally with the number of dividing cells. The indicated shRNA Jurkat clones (EXOSC5, CAPN3, HTR4, BTF3, PRMT3, GALC, PVALB, FGF7, STXBP2, CLDN3, ACT6LB, SNX10, PRDM2, CTBP1, NRF1, CREBP3, and NR2F1) showed CCK-8 profiles similar to that from control Jurkat cells (boxed).View Large Image Figure ViewerDownload Hi-res image Download (PPT) All 252 candidate genes will need to be carefully studied to check if and how each might influence HIV-1 replication. Several HIV-1 relevant assays are available that can be used to address how candidate proteins affect cell surface co-receptor, reverse transcription, transcription, and Gag trafficking (Fig. 5). As a first step, we investigated 7 gene candidates. They were variously tested for their effects on cell surface CXCR4 expression (Fig. 5A), HIV-1 reverse transcription (Fig. 5B), HIV-1 transcription (Fig. 5C), and GFP-Gag trafficking (Fig. 5D). Detailed studies remain ongoing, but illustrative results are shown. Thus, knockdown of NRF1 affected cell surface CXCR4 expression, whereas knockdown of EXOSC5, GALC, NCOA3, PRDM2, PRMT3, and STXBP2 did not (Fig. 5A). On the other hand, knockdown of STXBP2 reduced the amount of reverse transcribed viral DNA (Fig. 5B); knockdown of PRDM2 and NCOA3 reduced HIV-1 transcription (Fig. 5C); and knockdown of EXOSC5 affected GFP-Gag trafficking (Fig. 5D) in Jurkat cells. The knockdown of GALC showed no effect in these assays. The published literature is in part consistent with the above findings. There is evidence for a role played by NRF1 in regulating the expression of CXCR4 (19.Moriuchi M. Moriuchi H. Fauci A.S. AIDS Res. Hum. Retroviruses. 1999; 15: 821-827Crossref PubMed Scopus (16) Google Scholar). NCOA3 and PRDM2 have been reported to be transcriptional co-activators (20.Arimura A. van Peer M. Schröder A.J. Rothman P.B. J. Biol. Chem. 2004; 279: 31105-31112Abstract Full Text Full Text PDF PubMed Scopus (49) Google Scholar, 21.Steele-Perkins G. Fang W. Yang X.H. Van Gele M. Carling T. Gu J. Buyse I.M. Fletcher J.A. Liu J. Bronson R. Chadwick R.B. de la Chapelle A. Zhang X. Speleman F. Huang S. Genes Dev. 2001; 15: 2250-2262Crossref PubMed Scopus (184) Google Scholar), and Munier et al. (22.Munier S. Delcroix-Genête D. Carthagéna L. Gumez A. Hazan U. Retrovirology. 2005; 2: 73Crossref PubMed Scopus (22) Google Scholar) have suggested that NCOA3 can interact with the HIV-1 LTR. STXBP2 is an interactor of SYNTAXIN 3, which acts on the membrane function and processes of the cell (23.Riento K. Kauppi M. Keranen S. Olkkonen V.M. J. Biol. Chem. 2000; 275: 13476-13483Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar); however, it is unclear how knockdown of STXBP2 (directly or indirectly) affects the amount of reverse transcribed HIV-1 proviral DNA. EXOSC5 has been reported to be involved in RNA processing (24.Brouwer R. Allmang C. Raijmakers R. van Aarssen Y. Egberts W.V. Petfalski E. van Venrooij W.J. Tollervey D. Pruijn G.J. J. Biol. Chem. 2001; 276: 6177-6184Abstract Full Text Full Text PDF PubMed Scopus (94) Google Scholar). Intriguingly, detailed proteomic data show that this protein interacts with nucleoporin (NUP210), a compone
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