A neutralizing rna aptamer against egfr causes selective apoptotic cell death

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Abstract

Nucleic acid aptamers have been developed as high-affinity ligands that may act as antagonists of disease-associated proteins. Aptamers are non immunogenic and characterised by high specificity and low toxicity thus representing a valid alternative to antibodies or soluble ligand receptor traps/decoys to target specific cancer cell surface proteins in clinical diagnosis and therapy. The epidermal growth factor receptor (EGFR) has been implicated in the development of a wide range of human cancers including breast, glioma and lung. The observation that its inhibition can interfere with the growth of such tumors has led to the design of new drugs including monoclonal antibodies and tyrosine kinase inhibitors currently used in clinic. However, some of these molecules can result in toxicity and acquired resistance, hence the need to develop novel kinds of EGFR-targeting drugs with high specificity and low toxicity. Here we generated, by a cell-Systematic Evolution of Ligands by EXponential enrichment (SELEX) approach, a nuclease resistant RNA-aptamer that specifically binds to EGFR with a binding constant of 10 nM. When applied to EGFR-expressing cancer cells the aptamer inhibits EGFR-mediated signal pathways causing selective cell death. Furthermore, at low doses it induces apoptosis even of cells that are resistant to the most frequently used EGFR-inhibitors, such as gefitinib and cetuximab, and inhibits tumor growth in a mouse xenograft model of human non-small-cell lung cancer (NSCLC). Interestingly, combined treatment with cetuximab and the aptamer shows clear synergy in inducing apoptosis in vitro and in vivo. In conclusion, we demonstrate that this neutralizing RNA-aptamer is a promising bio-molecule that can be developed as a more effective alternative to the repertoire of already existing EGFR-inhibitors. © 2011 Esposito et al.

Figures

  • Figure 1. The anti-EGFR CL4 aptamer. (A) Secondary structure of CL4 Full Length predicted by using MFOLD software version 3.1. The structure of CL4 (nucleotides from 42 to 81) is shown in red. (B) Binding isotherm for CL4:EC-EGFR complexes. Kd value was derived by fitting bound CL4 versus the protein concentration to the equation Y = BmaxX/(Kd+X), where Bmax is the extrapolated maximal amount of RNA:protein complex bound. The specific binding was determined by subtracting the background values obtained with CL4sc from the values obtained with CL4. (C) EC-EGFR or ECErbB3 (20 and 40 nM, with and without DTT treatment) were incubated with 1 nM CL4 and radiolabeled protein-bound RNA was collected by nitrocellulose filters and quantified. doi:10.1371/journal.pone.0024071.g001
  • Figure 2. CL4 specifically interacts with EGFR. (A) Lysates from NIH3T3 or NIH/EGFR cells were immunoblotted with anti-EGFR antibodies. atubulin was used as an internal control. (B) Binding of radiolabeled CL4 on NIH3T3 or NIH/EGFR. (C) Lysates from A549 cells following 72 htransfection with a specific EGFR shRNA (shRNAEGFR) or a non-related shRNA (shRNActrl) were immunoblotted with anti-EGFR antibodies. atubulin was used as an internal control. Values below the blot indicate signal levels relative to control non transfected, arbitrarily set to 1 (labeled with asterisk). Intensity of bands has been calculated using the NIH Image Program on at least two different expositions to assure the linearity of each acquisition. (D) Binding of 100 nM radiolabeled CL4 on A549 cells in the absence or in the presence of 1 mM EGF or on A549 cells following 72 htransfection with shRNAEGFR or shRNActrl. (E) Binding of 100 nM radiolabeled CL4, prior incubated with 300 nM EC-EGFR or EC-ErbB3 for 15 min at
  • Figure 3. CL4 inhibits EGF-dependent EGFR activation. (A) Serum starved A549 cells (150,000 cells per 3.5-cm plate) were either left untreated or treated for 3 h with 200 nM CL4 or CL4sc and then stimulated for the indicated times with EGF (50 ng/ml) alone or in the presence of each aptamer. Cell lysates were immunoblotted with anti-(phospho)-EGFR (pEGFR), anti-EGFR, anti-(phospho)-ERK1/2 (pERK), anti-(phospho)-STAT3 (pSTAT3), anti-(phospho)-AKT (pAKT) antibodies, as indicated. (B,C) Calu 1 and A431 cells were treated as in (A) and cell lysates were immunoblotted with anti-pEGFR, anti-EGFR and anti-pSTAT3 antibodies, as indicated. In (A–C), atubulin was used as an internal control. Values below the blots indicate signal levels relative to 5 min-EGF stimulated control, arbitrarily set to 1 (labeled with asterisk). (D Lysates from SKBr3 cells treated as in (A), were immunoprecipitated with anti-(phospho)-tyrosine (pTyr) antibodies and immunoblotted with anti-ErbB2 and anti-EGFR antibodies, as indicated. Values below the blots indicate signal levels relative to 5 min-EGF stimulated CL4sc control, arbitrarily set to 1 (labeled with asterisk). In (A–D), molecular weights of indicated proteins are reported, ‘‘C’’ indicates mock-treated cells. Quantitation was done as in Figure 2. Blots shown are representative of at least four independent experiments. doi:10.1371/journal.pone.0024071.g003
  • Figure 4. CL4 inhibits Hrg-dependent EGFR activation. (A,B) Serum starved A549 and Calu1 cells (150,000 cells per 3.5-cm plate) were either left untreated or treated for 3 h with 200 nM CL4 or CL4sc and then stimulated for 5 min with Hrg (100 ng/ml) alone or in the presence of each aptamer. Cell lysates were immunoblotted with anti-(phospho)-ErbB3 (pErbB3), anti-ErbB3, anti-pEGFR, anti-EGFR, anti-pERK, anti-ERK, anti-pAKT and anti-AKT antibodies, as indicated. Values below the blots indicate signal levels relative to Hrg stimulated control, arbitrarily set to 1 (labeled with asterisk). Molecular weights of indicated proteins are reported, ‘‘C’’ indicates mock-treated cells. Quantitation was done as in Figure 2. Blots shown are representative of at least four independent experiments. doi:10.1371/journal.pone.0024071.g004
  • Figure 5. CL4 induces apoptosis. (A) A549 and H460 cells (5,000 cells/well in 96-well plates) were either left untreated or treated for 24 h and 48 h with 3 mM CL4 or CL4sc, renewing treatment each 24 h and the percentage of apoptotic cells (sub-G1 peak) was determined by FACS following PI incorporation. (B,C) A549 were left untreated or treated with 200 nM-final concentration of CL4 or CL4sc for the indicated incubation times (B) or for 6 h with increasing amounts of each aptamer (C) and cell lysates were analyzed by caspase-3 activation fluorimetric assay. (D) Lysates from A549 cells left untreated or treated for 6 h with 200 nM of indicated aptamers or 200 ng/ml TRAIL were immunoblotted with anti-caspase-3, anti-PARP and antiatubulin antibodies, as indicated. (E,F) Cell lysates as in (D) were analyzed by caspase-8 and caspase-9 activation fluorimetric assays (E) or by immunoblotting with anti-caspase-8 and anti-atubulin antibodies, as indicated (F). In (D,F), ‘‘C’’ indicates mock-treated cells. Blots shown are representative of at least three independent experiments. Molecular weights of full-length and cleaved caspase-3, 8 and PARP are reported. In (A– C,E), error bars depict means 6 s.d. (n = 3). doi:10.1371/journal.pone.0024071.g005

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Esposito, C. L., Passaro, D., Longobardo, I., Condorelli, G., Marotta, P., Affuso, A., … Cerchia, L. (2011). A neutralizing rna aptamer against egfr causes selective apoptotic cell death. PLoS ONE, 6(9). https://doi.org/10.1371/journal.pone.0024071

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