To develop constructs that are effective at silencing human VEGF165, we targeted three different regions of VEGF165, using design criteria similar to those used previously for shRNA-mediated silencing of rhodopsin.
37 These VEGF shRNAs are henceforth referred to as VEGFi4, VEGFi5, and VEGFi7, targeting human VEGF165 codons 100-107, 181-188, and 44-51, respectively
(Fig. 1) . In addition, we adapted a previously published siRNA sequence
20 targeting VEGF codons 110-116 (referred to as VEGFi8) for inclusion in this study. Each shRNA is regulated by the H1 promoter, terminated by five thymidine residues and juxtaposed by an expression cassette for blue fluorescent protein (BFP) regulated by the cytomegalovirus (CMV) promoter
(Fig. 1) . Inclusion of BFP in
cis allows for accurate normalization of transfection efficiency in vitro and the convenient identification of cells containing the VEGF-targeting shRNA in vivo. The ability of each of the shRNA constructs to silence VEGF165 regulated by the viral CMV promoter was measured relative to silencing of VEGF165 by a nonspecific shRNA—a construct referred to as VEGFiNS
(Fig. 1) —selected based on its lack of complete homology to any sequence in the National Center for Biotechnology Information (NCBI; Bethesda, MD) nucleotide database. An expression cassette for red fluorescent protein (RFP) was included in the VEGF-expressing plasmid (pShVEGFRFP) in
cis to allow for accurate normalization of transfection efficiency in vitro and the indirect identification of cells expressing VEGF in vivo. pShVEGFRFP was cotransfected into human embryonic retinoblasts
34 with each of the shRNA constructs and the level of silencing achieved measured qualitatively by Northern blot analysis and quantitatively by real-time RT-PCR. Northern blot analysis clearly revealed knockdown of VEGF165 at the level of mRNA
(Fig. 2A)and real-time RT-PCR revealed
(Fig. 2B)silencing of VEGF165 mRNA by VEGFi7, VEGFi5, VEGFi4, or VEGFi8 to be 77.42% ± 5.62%, 71.01% ± 5.26%, 48.5% ± 8.56%, and 28.94% ± 5.26%, respectively (
n = 8, each experiment;
Fig. 2B ). Given that these experiments were performed in a plasmid molar ratio of 1:1.2 (VEGF:shRNA), the knockdown observed is considerable, especially since VEGF165 was expressed from a strong viral (CMV) promoter relative to the shRNA, which is expressed from a cellular H1 promoter. Not surprisingly, while we observed significant overlap between RFP- and BFP-positive cells, some cells were RFP positive
only, as determined by fluorescent microscopy (data not shown), which may explain in part the lack of complete silencing of VEGF. Whereas each of VEGFi7, VEGFi4, and VEGFi8 were designed to target human VEGF165, VEGFi5 also targets murine VEGF at codons 180-187 by virtue of sequence homology between mouse and human VEGF cDNAs. Based on these data, VEGFi7 and VEGFi5 were selected for further study.