A new design of a lentiviral shRNA vector with inducible co-expression of ARGONAUTE 2 for enhancing gene silencing efficiency
- Jiening He†1,
- Lian Huang†1,
- Huiling Qiu†1,
- Jiexuan Li1,
- Lan Luo1,
- Yanjiao Li1,
- Shengli Tian1Email author,
- Kang Kang2,
- Jun Luo3,
- Lin Liu4 and
- Deming Gou1Email author
© He et al. 2015
Received: 27 August 2015
Accepted: 19 November 2015
Published: 8 December 2015
RNA interference (RNAi) is a robust tool for inhibiting specific gene expression, but it is limited by the uncertain efficiency of siRNA or shRNA constructs. It has been shown that the overexpression of ARGONAUTE 2 (AGO2) protein increases silencing efficiency. However, the key elements required for AGO2-mediated enhancement of gene silencing in lentiviral vector has not been well studied.
To explore the application of AGO2-based shRNA system in mammalian cells, we designed shRNA vectors targeting the EGFP reporter gene and evaluated the effects of various factors on silencing efficiency including stem length, loop sequence, antisense location as well as the ratio between AGO2 and shRNA. We found that 19 ~ 21-bp stem and 6- or 9-nt loop structure in the sense-loop-antisense (S-L-AS) orientation was an optimal design in the AGO2-shRNA system. Then, we constructed a single lentiviral vector co-expressing shRNA and AGO2 and demonstrated that the simultaneous expression of shRNA and AGO2 can achieve robust silencing of exogenous DsRed2 and endogenous ID1 and P65 genes. However, the titers of packaged lentivirus from constitutive expression of AGO2 vector were extremely low, severely limiting its broad application. For the first time, we demonstrated that the problem can be significantly improved by using the inducible expression of AGO2 lentiviral system.
We reported a novel lentiviral vector with an optimal design of shRNA and inducible AGO2 overexpression which provides a new tool for RNAi research.
Over one and a half decades after RNA inference (RNAi) discovery in nematodes , RNAi-based technology (e.g. siRNA and shRNA) is now widely used for gene knockdown in basic scientific research and provides promise to new therapeutic strategies for a variety of diseases [2, 3]. With the development of siRNA or shRNA libraries, and high-throughput screening techniques, genome-wide RNAi screening is employed for broad and unbiased identification of genetic modifiers of various cell- or organism-based phenotypes [4, 5].
In principle, RNAi can be used to repress the expression of any genes. However, it is still much unknown about the siRNA biogenesis and action of mechanism. The application of RNAi technique is limited by the inconsistent efficiency of targeting sequences . The existing computational approaches for siRNA selection allow the identification of potential sequences, but they do not ensure that each selected siRNA has sufficient silencing efficiency. It has been observed that many designed siRNAs or shRNAs are not effective. On average, about 25 % of the selected siRNA/shRNA sequences are functional with a knockdown efficiency more than 75 %. As a result, it is recommended to screen highly potent siRNA/shRNA sequences from at least four potential sites of a given mRNA . Therefore, an approach to enhance RNAi efficiency is desired for its broad applications in gene-function analysis, drug-target discovery and validation, and developing therapeutic siRNA/shRNA for various diseases.
Several attempts have been made to improve RNAi efficacy. For example, modifications can be made to improve the stability of chemically synthesized siRNA, resulting in enhanced siRNA inhibition efficacy . For vector-based shRNA, improvements can be achieved through manipulating expression strategy, using different types of promoters, modifying shRNA structures, and simultaneously expressing multiple shRNAs in a single vector [9–13]. Another strategy was developed to enhance siRNA biogenesis using the small molecule, enoxacin. Importantly, this molecule has only minor effects on cellular gene or miRNA expression .
Over the last few years, a better understanding of RNAi mechanism facilitates the identification of key proteins involved in the RNAi pathway, including the members of the ARGONAUTE family, DICER, EXPORTIN-5 (XPO5) and trp RNA-binding attenuation protein (TRAP) [15, 16]. Several groups have demonstrated that co-expression of some key components with shRNAs increases the RNAi efficacy [6, 17–19]. For example, overexpression of XPO5, a factor required for nuclear export of both shRNAs and pre-miRNAs, enhances RNAi mediated by shRNAs . Similarly, overexpressing AGO2 also increases efficiency of siRNA or shRNA-mediated gene silencing in vitro and in vivo [6, 19–22]. In this study, we evaluated key elements required for AGO2-mediated enhancement of gene silencing and developed a novel lentiviral shRNA vector with inducible co-expression of AGO2.
Co-expression of AGO2 protein strongly enhances shRNA silencing activities
To test whether the increase in protein levels of some crucial components in RNAi machinery would facilitate the silencing effect, we co-transfectd AGO1, AGO2, Dicer or XPO5 with shRNA vector into HEK293 cells and examined silencing efficiency. The results showed that AGO2 overexpression significantly enhanced the silencing activities of shEGFP417 from 84 % ± 2.1 to 96 % ± 1.8 and shEGFP450 from 12 % ± 9.2 to 70 % ± 4.4, respectively (Fig. 1b, c, d). However, overexpression of XPO5 showed merely a limited improvement of silencing activities compared to that of AGO2 (Fig. 1b, c). Overexpression of AGO1 and DICER did not show any enhancement in gene silencing.
Evidence from a large-scale study has indicated that miR-30a-based shRNAmiR30 vector produced a more effective silencing activity . Therefore, we further examined the effects of these RNAi components on shRNAmiR30-based gene silencing by co-transfecting pSM2c-shEGFP417miR30 vector, EGFP/DsRed2-expressing plasmids and a vector overexpressing each RNAi component. Similar to the results using the U6-shRNA system, overexpression of AGO2 also showed the most significant improvement of silencing efficacy with the miR-30a-based shRNA vector (Fig. 1e). These data also suggested that AGO2 was a dominant factor facilitating miR-30a-based shRNA activities and likely to be a limiting factor for the efficient knockdown.
Effects of stem length, loop size, and antisense strand location on the efficacy of AGO2-shRNA
To further improve the AGO2/shRNA system, we constructed several variants of shEGFP417 with different loop sizes (Fig. 3c). As shown in Fig. 3d, 19 bp stem length of shEGFP417 with 4-nt (TTCG), 6-nt (CTCGAG) or 9-nt (TTCAAGAGA) loop sequences exhibited different knockdown efficiency. We observed that the silencing efficiency of the shEGFP417 with 6-nt CTCGAG loop was comparable to that with the 9-nt TTCAAGAGA loop (>75 %). However, shEGFP417 with 4-nt loop sequence showed much less inhibition (~30 %). When AGO2 protein was co-expressed, the silencing efficiency of shEGFP417 with 4-, 6- or 9-nt loop were all improved dramatically.
According to the previous reports, silencing efficiency of shRNA was also influenced by the position of antisense sequences [25, 26]. We therefore constructed 19 bp stem length of shEGFP417 with three different sizes of loop at the orientation of antisense-loop-sense (AS-L-S) or sense-loop-antisense (S-L-AS) structures (Fig. 3c). When vectors expressing these shRNAs, EGFP/DsRed2 and AGO2 were co-transfected into HEK293 cells, we found that the silencing activities of shEGFP with 6- or 9-nt loop sequences in AS-L-S orientation were lower than the corresponding shRNA in S-L-AS orientation (Fig. 3d). Co-expression of AGO2 protein improved the silencing activities of AS-L-S shRNAs, but the efficiency was still lower than the respective AGO2-co-expressed traditional S-L-AS shRNA constructs. Overall, the results provide us a general guideline that 19–21-bp stem and 6- or 9-nt loop structure in the S-L-AS orientation should be used for the new AGO2-shRNA system.
Effects of a single lentiviral vector co-expressing shRNA and AGO2 on silencing efficiency
Functionally, we examined the effect of ID1 knockdown on cell proliferation and observed that all shID1-AGO2 infected HeLa cells had a lower cell proliferation rate compared to each corresponding shID1 without AGO2 co-expression (Fig. 5c).
P65 was selected as another target for the shRNA-AGO2 system and three shRNAs were chosen (Fig. 5a). As shown in Fig. 5d, without AGO2 co-expression, shP65-380 and shP65-1069 exhibited a moderate silencing efficiency while shP65-1622 was less effective. However, the co-expression of AGO2 significantly improved the knockdown efficiency, further supporting that AGO2 plays an essential role in shRNA-mediated gene silencing.
A shRNA lentiviral vector with inducible AGO2 expression
RNAi-based siRNA/shRNA has been developed as a robust tool for the inhibition of gene expression in vitro and in vivo. Nevertheless, the uncertainty of RNAi silencing efficiency is still a restriction of its application. As a key component of the RNA-induced silencing complex (RISC), AGO2 is responsible for the endonuclease cleavage of target mRNAs . The process of RNAi cannot be accomplished without AGO2. Several studies have shown that the overexpression of AGO2 significantly improves shRNA-mediated gene silencing. Diederichs et al. co-transfected HEK293 cells with vectors expressing AGO2 and shEGFP and showed that AGO2 overexpression significantly enhanced the silencing efficiency of shEGFP . Chen et al. found co-expression of AGO2 enhanced shRNA-induced RNAi in Xenopus CNS Neurons in vivo . Similarly, Grimm et al. demonstrated that AGO2 obviously enhanced the inhibition efficiency and extended the inhibition time of shRNAs in mice. It also reduced the liver toxicity caused by shRNA . Recently, the distinctive AGO2 property has been further exploited by constructing an Adeno-associated viral vector co-expressing AGO2 and shRNA . They also showed that AGO2-overexpressing cell lines generated through lentiviral transduction yielded a better siRNA inhibition outcome and improved RNAi phenotypes. But they did not demonstrate the successful application of a single lentiviral vector co-expressing shRNA and AGO2.
In this study, we found that the overexpression of AGO2 strongly increased silencing efficiency of shRNAs. This effect was observed not only in U6-driven traditional shRNAs, but also in miR-30a-based shRNAmir30. In contrast, overexpression of AGO1, DICER or XPO5 did not exhibit significant improvement of RNAi activities even though they are essential in transporting or processing precursor dsRNAs.
As the knockdown efficiency of shRNAs is affected by the length of stem, the loop sequences and the location of antisense strand in shRNA structure [7, 27], we evaluated the effects of these factors in the new designed AGO2/shRNA co-expression system. Similar to traditional shRNAs, a hairpin ranging from 19–21 bp with 6–9 nt loop produces a better knockdown activity in the AGO2/shRNA system. In contrast to the previous report showing that the artificially synthesized AS-L-S shRNA outshined S-L-AS shRNA in gene silencing , our data indicate that S-L-AS shRNA was much more efficient than AS-L-S shRNA in gene silencing. This is also the case when the shRNA structures were co-expressed with AGO2, even though silencing efficiencies of both shRNA structures were dramatically increased by the overexpression of AGO2. The detailed mechanism of the different inhibition efficiencies driven by these two types of shRNA remains unclear. But, the discrepancy could be due to different genes that are targeted.
Based on the evaluation of shRNAs targeting either exogenous DsRed2 or endogenous ID1 and P65 genes, we demonstrate that the co-expression of shRNA and AGO2 in a single vector achieved a robust gene silencing outcome. Vector-based shRNA has its limitation due to the low transfection efficiency in many types of cells, poor integration ability, and insufficient expression level. Lentiviral vectors are a promising tool for both in vivo and ex vivo gene therapy as well as their extensively application in basic biomedical research because of their ability to incorporate into genomic DNA with high efficiency, especially in cells that are not actively dividing. The approach of lentivirus-based shRNA/AGO2 makes it possible in improving the shRNA-mediated silencing of the target mRNA, which provides a promising tool for RNAi application. Similar strategy should be also useful for miRNA overexpression in mammalian cells.
When we packaged lentivirus in 293T cells using a lentiviral vector with U6-driven shRNA and CMV-driven AGO2 expression cassettes, we observed that the lentivirus titer was extremely low. Initially, we thought that the low titer might be caused by the over-limited size of AGO2 insert in the lentiviral vector. However, when we removed the PGK-Puro expression cassette, we did not observe any improvements in virus titer. This suggests that the low virus titer is probably due to constitutive expression of AGO2. Indeed, the virus titer from inducible AGO2-shRNA vector was increased by over 1000 fold. This new inducible AGO2-shRNA lentiviral expression vector contains the TETO6-mini promoter-driven AGO2, Ubc promoter-driven rtTA3 and U6-shRNA expression cassette. When AGO2 was induced by the addition of Dox, the RNAi efficiency was significantly improved. The modified strategy of constitutive expression of shRNA and inducible expression of AGO2 in a single lentiviral-vector has advantages of a low toxicity and prolonged efficacy.
We reported a novel lentiviral vector with an optimal design of shRNA and inducible AGO2 overexpression which has a robust silencing of exogenous and endogenous targets in mammalian cells and provides a powerful tool for RNAi application.
Plasmids and vector construction
pIRESneo-FLAG/HA-AGO1, pIRESneo-FLAG/HA-AGO2, pDEST-myc-Dicer, and pkmyc-XPO5, overexpressing human AGO1, AGO2, DICER or EXPORTIN-5 (XPO5) were purchased from Addgene. pIRESneo-FLAG/HA-Control generated from pIRESneo-FLAG/HA-AGO2 by removing the AGO2 sequence was used as a negative control for AGO2 experiment. The codon-optimized human AGO2 with FLAG/HA tags in pCAhU6 vector was kindly provided by Dr. Dirk Grimm (University of Heidelberg). pDsRed2-c1 vector expressing red florescence protein was purchased from Clontech. pENTR/CMV-EGFP vector expressing enhanced green florescence protein (EGFP) was generated as previously described .
Human U6 promoter-driven shRNAs were constructed using linearized BLOCK-iT™ U6 RNAi Entry Vector (Invitrogen). Two siRNA sequences with different silencing activities against EGFP coding region at position of 417-437 (5′-GCA CAA GCT GGA GTA CAA CTA-3′) and 450-470 (5′-CGT CTA TAT CAT GGC CGA CAA-3′) were selected for constructing EGFP silencing vectors, named pENTR/U6-shEGFP417 and pENTR/U6-shEGFP450. pSM2c-shEGFP417miR30 (Openbiosystem) was a miR-30-based shEGFP417 vector targeting EGFP at the same position of 417-437.
To construct lentiviral vectors co-expressing shRNAs and AGO2, the pLVX-puro vector (Clontech) was selected as a backbone plasmid. Since there are two BsmBI sites located in PGK promoter and puromycin resistant selection gene in the pLVX-puro vector, we removed both BsmBI sites via mutagenesis using overlap PCR strategy. The BsmBI site in the PGK promoter was changed to CGCCTC, which did not affect the promoter activity (data not shown). The BsmBI site in the puromycin resistant selection gene was changed to CGTGTC without affecting the encoded amino acid. The modified pLVX-puro was then digested with ClaI and XbaI and used for cloning U6 and CMV-AGO2 expression cassettes with Gibson Assembly kit (New England Biolab). Briefly, U6 promoter was PCR-amplified with the forward primer (5′-GCA GAG ATC CAG TTT ATC GAA CAA TCG ATA AGG TCG GGC AGG A-3′) and reverse primer (5′-CAA TGT CAA CGC GTA AAA AAG AGA CGC GTC TCA CGG TGT TTC GTC CTT TC-3′). Two BsmBI sites (underlined) in the reverse primer were included for cloning shRNA inserts. CMV-FLAG/HA/AGO2 fragment was amplified with the forward primer (5′-TTT TTT ACG CGT TGA CAT TGA TTA TTG ACT AGT TAT TAA TAG-3′) and reverse primer (5′-CTA CCC GGT AGA ATT ATA TAG CGA TCC ACT GAA TTC-3′) using a codon-optimized AGO2 vector of pCAnU6 as a template. We inserted a ccdB fragment with corresponding BsmBI site into the assembled vector, named pLVX/U6-ccdB-CMV-AGO2, which can be further digested by BsmBI, leaving five overhangs of 5′-CGGT and 5′-TTTT for the ligation of an annealed shRNA insert with 5′ overhangs of 5′-ACCG and 5′-AAAA.
To construct an inducible AGO2 lentiviral vector, the TurboRFP fragment in pTRIPz control vector (Openbiosystems) was first digested with AgeI, blunt-end with Klenows in the presence of dNTP, and then digested with EcoRI. The insert of AGO2 with FLAG/HA tag at the N-terminus was released from the pCAhU6 vector by Acc65I digestion, blunt-end with Klenows, and then digested with EcoR1. The new construct of pTAIPz consists of 6 repeats of a 19 bp tet operator sequence, followed by a minimal CMV promoter (miniP) and FLAG/HA/AGO2 insert. The co-expression rtTA3 transactivator and IRES-based puromycin is controlled by the human ubiquitin C (Ubc) promoter.
To generate a single lentiviral vector co-expressing shRNA and inducible AGO2, the U6-shRNA expression cassette released from pLVX-U6-shRNA-CMV-AGO2 was subcloned into the pTAIPz vector through EcoRI-MluI sites, resulting in a pTAIPz-shRNA construct.
Mammalian cell culture and fluorescence reporter assays
HEK293, HeLa, and A549 cells were obtained from American Type Culture Collection (ATCC) and were grown in DMEM medium with 10 % fetal bovine serum (FBS). The fluorescence reporter assays were performed in 24-well plates. In brief, cells were seeded at a density of 6 × 104 cells per well. After overnight incubation, the cells were co-transfected with different combinations of plasmids using linear polyethylenimine (PEI) transfection reagent. Six h after transfection, the cells were changed to fresh DMEM medium containing 10 % FBS and incubated for additional 48 h. The fluorescence of cells were first observed and photographed under an inverted fluorescence microscope, then trypsinized, and collected for flow cytometry analysis. The averaged green to red (G/R) or red to green (R/G) fluorescence ratio was used as an index for RNAi efficiency of EGFP or DsRed2 knockdown.
Lentivirus package and transduction
Lentiviral particles were packaged in 293T cells by transfection of three individual plasmids at a ratio of 3:1:3: (1) psPAX2 encoding HIV Gag-Pol (Addgene, 12260), (2) pVSVg (Addgene, 8454) encoding VSV-G glycoprotein, and (3) a lentiviral vector. Briefly, 293T cells were seeded on 10 cm culture dishes at a density of 4 × 106 cells per dish. After 24 h incubation, the cells were transfected with lentiviral vector (6.9 µg) and packing plasmids (17.1 µg) using PEI reagents. Cell-free supernatants were harvested 48 and 72 h after transfection and used for subsequent cell infection in the presence of 8 ng/ml polybrene. The infected cells were selected by supplementing culture medium with 1–2 µg/ml puromycin after 48 h infection.
Cell proliferation assay
A lentivirus expressing shRNA against ID1 or an un-related control shRNA with or without AGO2 co-expression were used to infect HeLa cells in the presence of polybrene. After 48 h infection, the infected cells were selected by supplementing culture medium with 1.5 µg/ml puromycin. Cell proliferation was then determined using the CellTiter 96 Aqueous One Solution proliferation assay (Promega).
Western blot analysis
Cells were lysed with ice-cold RIPA buffer (50 mM Tris–HCl, pH 7.5; 150 mM NaCl; 1 % NP-40; 0.25 % sodium deoxycholate, 1 mM EDTA), supplemented with a protease inhibitor cocktail (Roche). Protein concentration was determined using Bradford protein assay kit (Bio-Rad). Equal amounts of extracts were then electrophoresed on SDS–polyacrylamide gel and electro-blotted to nitrocellulose filter membranes (Millipore). Membranes were immersed in blocking buffer (5 % degreased milk powder) for 1 h and incubated with primary antibodies. The primary antibodies used are as follows: rabbit monoclonal anti-ID1, -ID2 (Cat #MA201, #MA229, CalBioreagents, San Mateo, CA, USA; 1:1000 dilutions); rabbit polyclonal anti-P65 (Cat #SC-372, Santa Cruz, Santa Cruz, CA, USA, 1:800 dilutions), rabbit polyclonal anti-Fus, anti-PALLD, anti-beta-actin and anti-HA (Proteintech Group, 1:2000 dilutions). After rinsing, membranes were incubated with horseradish peroxidase-conjugated secondary antibody at dilutions of 1:10,000 for 1 h at room temperature. Immunoreactive bands were detected by exposing to X-ray film.
All data shown are mean values of at least four experiments, each performed in triplicate, with standard deviation (SD). Statistically significant differences between groups were evaluated using the SPSS software. One asterisk, double asterisk, and three asterisks represent a significant difference between experimental pairs of p < 0.05, 0.01, and 0.001, respectively.
DG and ST designed experiments and analyzed data; JH, LH, JL, LL, and HQ performed experiments; DM and LL wrote the manuscript; KK, YL and JL edited the manuscripts; DG and ST supervised the project. All authors read and approved the final manuscript.
This study was supported in part by National Natural Science Foundation of China 81170047, 81370151 and 81570046 to D. Gou, and 31571199 to K. Kang, National Basic Research Program of China 973 Program 2012CB124701; Nanshan High-tech Development Project KC2013JSJS0020A to D. G.; Shenzhen Municipal Basic Research Program JC201006010725A to D. Gou, Shenzhen Overseas High-Level Talents Innovation Program YFZZ20111009 to D. Gou, Shenzhen High-tech Development Project CXZZ20140828163951592 to D. Gou, Transgenic project from the Ministry of Agriculture 2014ZX08009-051B to J. Luo, and Shenzhen Municipal Basic Research Program JCYJ20130329120507746 to K.Kang.
The authors declare that they have no competing interests.
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