Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition

Abstract

Human immunodeficiency virus type 1 (HIV-1) replication in T cells can be inhibited by RNA interference (RNAi) through short hairpin RNA (shRNA) expression from a lentiviral vector. However, for the development of a durable RNAi-based gene therapy against HIV-1, multiple shRNAs need to be expressed simultaneously in order to avoid viral escape. In this study, we tested a multiple shRNA expression strategy for different shRNAs using repeated promoters in a lentiviral vector. Although highly effective in co-transfection experiments, a markedly reduced activity of each expressed shRNA was observed in transduced cells. We found that this reduced activity was due to recombination of the expression cassette repeat sequences during the transduction of the lentiviral vector, which resulted in deletions of one or multiple cassettes. To avoid recombination, we tested different promoters for multiple shRNA expression. We compared the activity of the human polymerase III promoters U6, H1, and 7SK and the polymerase II U1 promoter. Activities of these promoters were similar, irrespective of which shRNA was expressed. We showed that these four expression cassettes can be combined in a single lentiviral vector without causing recombination. Moreover, whereas HIV-1 could escape from a single shRNA, we now show that HIV-1 escape can be prevented when four shRNAs are simultaneously expressed in a cell.

Figure 1

Reduced reporter knock-down in multi-short hairpin RNA (shRNA)-transduced cells. (a) Conserved shRNA target sequences in the human immunodeficiency virus type 1 (HIV-1) genome used in this study. (b) Lentiviral vector constructs used in this experiment. Single (shRNA1: Gag-5, Pol-1, or Pol-47), double (shRNA2), and triple shRNA (shRNA3) expression cassettes were cloned in the multiple cloning site (mcs) of JS1, the lentiviral vector construct. The lentiviral vector is a third generation self-inactivating vector, which contains an enhanced green fluorescent protein (eGFP) expression cassette that allows live sorting. Primers used to amplify across the mcs are indicated (fw1 and rev1). (c) A Luciferase reporter for Pol-47 was co-transfected in 293T cells with the empty control vector (JS1) or vectors expressing a single shRNA against HIV-1 (Gag-5, Pol-1, Pol-47), and vectors with a double and triple shRNA cassette (shRNA2 or shRNA3) and relative Luciferase expression was measured. (d) 293T cells were transduced with the indicated lentiviral vectors at a multiplicity of infection of 0.15 and selected with live fluorescence-activated cell sorting for GFP. Cells were transfected with the Luciferase reporter for Pol-47 and relative luciferase expression was measured. Averages and SDs in c and d represent three independent transfections, the average activity of the JS1 control was set at 1.0. LTR, long-terminal repeat; RLU, relative light units; RRE, rev-responsive element; RSV, Rous sarcoma virus promoter.

Figure 2

Triple short hairpin RNA (shRNA)-transduced cell lines contain cassette deletions. (a) Schematic representation of repeat sequences present in the shRNA3 lentiviral vector construct. The different shRNA expression cassettes for Pol-1, Pol-47, and Gag-5 are marked with A, B and C. The H1 promoter repeat sequence is 230 nucleotide (nt) in size, the sequence containing the pol III termination signal is 28 nt (terminator). The difference between the three cassettes is the shRNA encoding sequence, stem–loop–stem (gray, A; blocked, B; black, C). (b) 293T cells were transduced with shRNA3 at a multiplicity of infection of 0.15 and cell clones were selected with live fluorescence-activated cell sorting. A polymerase chain reaction (PCR) was performed across the cassette insertion. Control PCRs for 293T and shRNA1 clones were included, as well as an empty control (–) and input plasmids (shRNA1, 2, and 3). Differently sized PCR products were observed in the cell clones corresponding in size to either a single, double, or triple cassette insert. (c) Overview of sequence analysis of the shRNA3 293T cell clones. All possible deletions are shown. The number of cell clones with those deletions are shown in the first column. In total, we analyzed 22 sequences, the total number of clones in which a cassette was present is shown at the bottom of the deletion columns.

Figure 3

Similar levels of inhibition with different promoters and short hairpin RNA (shRNAs). (a) Different promoters used for shRNA expression. Three human polymerase III promoters, H1, U6, and 7SK, and the U1 human polymerase II promoter were used for shRNA expression. All expression cassettes have well-defined transcription start and termination sites. (b) Luciferase reporters for the conserved target sequences Gag-5, Pol-1, Pol-47, and R/T-5 were co-transfected with the control shNef expressing vector (black bars) or the specific shRNA vector (gray bars). Averages and SDs represent three independent transfections, the average activitiy of the shNef control for each promoter was set at 1.0. RLU, relative light units.

Figure 4

Single or multiple short hairpin RNA (shRNA) expression results in similar inhibition per shRNA. (a) Multiple shRNA expression construct. From a single construct, four different shRNAs (Pol-47, Gag-5, Pol-1, and R/T-5) were expressed from a human polymerase III promoter: H1, U6, and 7SK, and the U1 human polymerase II promoter, respectively. (b) Detection of small interfering RNAs expressed from shRNA4 (4) and the single shRNAs expressed from the corresponding promoters (1). As controls, a pBS (B) or a control shRNA construct (C) was used. Total RNA was isolated from transfected 293T cells and used for Northern blotting. 5S ribosomal RNA (rRNA) was used as loading control. M, size markers. (c) The indicated Luciferase reporters were co-transfected with the control shNef expressing vector (ctrl), the indicated single shRNA expression vector and the shRNA4 vector. Averages and SDs represent three independent transfections, the average activity of the shNef control was set at 1.0.

Figure 5

The shRNA4 cassette is intact in transduced cells. (a) 293T cells were transduced with the shRNA4 lentiviral vector at low multiplicity of infection (0.15) and cell clones were selected. A polymerase chain reaction was performed on genomic DNA of 10 selected cell clones. Bands corresponding to the quadruple cassette were observed for all cell clones. As controls, the shRNA4 plasmid and genomic DNA obtained from untransduced 293T (–) and shRNA1-transduced cell clones were included. (b) 293T cells transduced with the shRNA4 vector and green fluorescent protein positive cells were selected with live fluorescence-activated cell sorting. Cells were transfected with the indicated reporters. Controls were included, untransduced cells (293T) and the previously made shRNA1-transduced stable cell lines. Averages and SDs represent four independent transfections, the average activity of the 293T control was set at 1.0 for each reporter. shRNA, short hairpin RNA.

Figure 6

Prevention of escape with four short hairpin RNAs (shRNAs). (a) Six Pol-47 transduced SupT1 cell lines (circle) were infected with human immunodeficiency virus type 1 (HIV-1) and virus replication was monitored by measuring CA-p24 for up to 75 days. A control vector–transduced cell line was included (closed circles). In five of six cultures, HIV-1 started to replicate. (b) This replicating virus showed a resistant phenotype to the shRNA against Pol-47. For example, the replicating virus (marked with a star in a) was cell-free passaged on a control cell line (JS1), shRNA1 cell lines (Gag-5, Pol-1, Pol-47, and R/T-5) and the shRNA4 cell line. The virus replicated only on the control cell line and the Pol-47 cell line. (c) Six shRNA4-transduced SupT1 cell lines were infected with HIV-1 and virus replication was monitored for up to 75 days. A control vector–transduced cell line was included (closed circles). Initial virus replication was potently inhibited. After 40 days slow virus spread was scored in two cultures. (d) Cell-free virus (marked with a star in c) was used to infect a control cell line (JS1), shRNA1 cell lines (Gag-5, Pol-1, Pol-47, and R/T-5) and the shRNA4 cell line. The virus could replicate exclusively in the control cell line, indicating that the virus emerging in c is not resistant. The same result was obtained for the other positive culture.

Figure 7

Potent inhibition of wild-type and Pol-47 resistant human immunodeficiency virus type 1 (HIV-1) in shRNA4-transduced primary CD4⁺ cells. Primary CD4⁺ cells were transduced with JS1 (closed circle), Pol-47 (open circle) and shRNA4 (cross) lentiviral vectors at low multiplicity of infection and green fluorescent protein positive cells selected with live fluorescence-activated cell sorting. Transduced cells were infected with (a) the wild-type virus or (b) a Pol-47 resistant virus. Virus replication was monitored by measuring CA-p24.