Generating Aptamers by Cell-SELEX for Applications in Molecular Medicine
Abstract
:1. Introduction
2. Cell-SELEX
3. Cell-Specific Aptamers for Biomarker Discovery
4. Cell-Specific Aptamers for Targeted Cancer Therapy
5. Cancer Cell Enrichment and Detection Using Aptamers
6. Conclusion
Acknowledgements
References
- Mandal, M.; Breaker, R.R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol 2004, 5, 451–463. [Google Scholar]
- Ellington, A.D.; Szostak, J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818–822. [Google Scholar]
- Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505–510. [Google Scholar]
- Gold, L. The SELEX process: A surprising source of therapeutic and diagnostic compounds. Harvey Lect 1995, 91, 47–57. [Google Scholar]
- Famulok, M.; Mayer, G.; Blind, M. Nucleic acid aptamers-from selection in vitro to applications in vivo. Acc. Chem. Res 2000, 33, 591–599. [Google Scholar]
- Kurreck, J. Antisense technologies. Improvement through novel chemical modifications. Eur. J. Biochem 2003, 270, 1628–1644. [Google Scholar]
- Conrad, R.; Keranen, L.M.; Ellington, A.D.; Newton, A.C. Isozyme-specific inhibition of protein kinase C by RNA aptamers. J. Biol. Chem 1994, 269, 32051–32054. [Google Scholar]
- Shoji, A.; Kuwahara, M.; Ozaki, H.; Sawai, H. Modified DNA aptamer that binds the (R)-isomer of a thalidomide derivative with high enantioselectivity. J. Am. Chem. Soc 2007, 129, 1456–1464. [Google Scholar]
- Ruta, J.; Ravelet, C.; Baussanne, I.; Decout, J.L.; Peyrin, E. Aptamer-based enantioselective competitive binding assay for the trace enantiomer detection. Anal. Chem 2007, 79, 4716–4719. [Google Scholar]
- Farokhzad, O.C.; Cheng, J.; Teply, B.A.; Sherifi, I.; Jon, S.; Kantoff, P.W.; Richie, J.P.; Langer, R. Targeted nanoparticle-aptamer bioconjugates for cancer chemotherapy in vivo. Proc. Natl. Acad. Sci. USA 2006, 103, 6315–6320. [Google Scholar]
- Bagalkot, V.; Farokhzad, O.C.; Langer, R.; Jon, S. An aptamer-doxorubicin physical conjugate as a novel targeted drug-delivery platform. Angew. Chem. Int. Ed. Engl 2006, 45, 8149–8152. [Google Scholar]
- Chen, C.H.; Dellamaggiore, K.R.; Ouellette, C.P.; Sedano, C.D.; Lizadjohry, M.; Chernis, G.A.; Gonzales, M.; Baltasar, F.E.; Fan, A.L.; Myerowitz, R.; et al. Aptamer-based endocytosis of a lysosomal enzyme. Proc. Natl. Acad. Sci. USA 2008, 105, 15908–15913. [Google Scholar]
- Tong, G.J.; Hsiao, S.C.; Carrico, Z.M.; Francis, M.B. Viral capsid DNA aptamer conjugates as multivalent cell-targeting vehicles. J. Am. Chem. Soc 2009, 131, 11174–11178. [Google Scholar]
- McNamara, J.O., II; Andrechek, E.R.; Wang, Y.; Viles, K.D.; Rempel, R.E.; Gilboa, E.; Sullenger, B.A.; Giangrande, P.H. Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat. Biotechnol 2006, 24, 1005–1015. [Google Scholar]
- Brody, E.N.; Gold, L. Aptamers as therapeutic and diagnostic agents. J. Biotechnol 2000, 74, 5–13. [Google Scholar]
- Ferreira, C.S.; Matthews, C.S.; Missailidis, S. DNA aptamers that bind to MUC1 tumour marker: Design and characterization of MUC1-binding single-stranded DNA aptamers. Tumour Biol 2006, 27, 289–301. [Google Scholar]
- Lupold, S.E.; Hicke, B.J.; Lin, Y.; Coffey, D.S. Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res 2002, 62, 4029–4033. [Google Scholar]
- Gutsaeva, D.R.; Parkerson, J.B.; Yerigenahally, S.D.; Kurz, J.C.; Schaub, R.G.; Ikuta, T.; Head, C.A. Inhibition of cell adhesion by anti-P-selectin aptamer: A new potential therapeutic agent for sickle cell disease. Blood 2011, 117, 727–735. [Google Scholar]
- Townshend, B.; Aubry, I.; Marcellus, R.C.; Gehring, K.; Tremblay, M.L. An RNA aptamer that selectively inhibits the enzymatic activity of protein tyrosine phosphatase 1B in vitro. ChemBioChem 2010, 11, 1583–1593. [Google Scholar]
- Liu, Y.; Kuan, C.T.; Mi, J.; Zhang, X.; Clary, B.M.; Bigner, D.D.; Sullenger, B.A. Aptamers selected against the unglycosylated EGFRvIII ectodomain and delivered intracellularly reduce membrane-bound EGFRvIII and induce apoptosis. Biol. Chem 2009, 390, 137–144. [Google Scholar]
- Sefah, K.; Shangguan, D.; Xiong, X.; O’Donoghue, M.B.; Tan, W. Development of DNA aptamers using Cell-SELEX. Nat. Protoc 2010, 5, 1169–1185. [Google Scholar]
- Morris, K.N.; Jensen, K.B.; Julin, C.M.; Weil, M.; Gold, L. High affinity ligands from in vitro selection: Complex targets. Proc. Natl. Acad. Sci. USA 1998, 95, 2902–2907. [Google Scholar]
- Shangguan, D.; Li, Y.; Tang, Z.; Cao, Z.C.; Chen, H.W.; Mallikaratchy, P.; Sefah, K.; Yang, C.J.; Tan, W. Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. USA 2006, 103, 11838–11843. [Google Scholar]
- Sefah, K.; Tang, Z.W.; Shangguan, D.H.; Chen, H.; Lopez-Colon, D.; Li, Y.; Parekh, P.; Martin, J.; Meng, L.; Phillips, J.A.; et al. Molecular recognition of acute myeloid leukemia using aptamers. Leukemia 2009, 23, 235–244. [Google Scholar]
- Shangguan, D.; Meng, L.; Cao, Z.C.; Xiao, Z.; Fang, X.; Li, Y.; Cardona, D.; Witek, R.P.; Liu, C.; Tan, W. Identification of liver cancer-specific aptamers using whole live cells. Anal. Chem 2008, 80, 721–728. [Google Scholar]
- Kunii, T.; Ogura, S.; Mie, M.; Kobatake, E. Selection of DNA aptamers recognizing small cell lung cancer using living cell-SELEX. Analyst 2011, 136, 1310–1312. [Google Scholar]
- Chen, H.W.; Medley, C.D.; Sefah, K.; Shangguan, D.; Tang, Z.; Meng, L.; Smith, J.E.; Tan, W. Molecular recognition of small-cell lung cancer cells using aptamers. ChemMedChem 2008, 3, 991–1001. [Google Scholar]
- Zhao, Z.; Xu, L.; Shi, X.; Tan, W.; Fang, X.; Shangguan, D. Recognition of subtype non-small cell lung cancer by DNA aptamers selected from living cells. Analyst 2009, 134, 1808–1814. [Google Scholar]
- Van Simaeys, D.; Lopez-Colon, D.; Sefah, K.; Sutphen, R.; Jimenez, E.; Tan, W. Study of the molecular recognition of aptamers selected through ovarian cancer cell-SELEX. PLoS One 2010, 5. [Google Scholar] [CrossRef]
- Santoni, V.; Molloy, M.; Rabilloud, T. Membrane proteins and proteomics: Un amour impossible? Electrophoresis 2000, 21, 1054–1070. [Google Scholar]
- Mirza, S.P.; Halligan, B.D.; Greene, A.S.; Olivier, M. Improved method for the analysis of membrane proteins by mass spectrometry. Physiol. Genomics 2007, 30, 89–94. [Google Scholar]
- Daniels, D.A.; Chen, H.; Hicke, B.J.; Swiderek, K.M.; Gold, L. A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment. Proc. Natl. Acad. Sci. USA 2003, 100, 15416–15421. [Google Scholar]
- Orend, G.; Chiquet-Ehrismann, R. Tenascin-C induced signaling in cancer. Cancer Lett 2006, 244, 143–163. [Google Scholar]
- Shangguan, D.; Li, Y.; Tang, Z.; Cao, Z.C.; Chen, H.W.; Mallikaratchy, P.; Sefah, K.; Yang, C.J.; Tan, W. From the cover: Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. USA 2006, 103, 11838–11843. [Google Scholar]
- Shangguan, D.; Cao, Z.; Meng, L.; Mallikaratchy, P.; Sefah, K.; Wang, H.; Li, Y.; Tan, W. Cell-specific aptamer probes for membrane protein elucidation in cancer cells. J. Proteome Res 2008, 7, 2133–2139. [Google Scholar]
- Mallikaratchy, P.; Tang, Z.; Kwame, S.; Meng, L.; Shangguan, D.; Tan, W. Aptamer directly evolved from live cells recognizes membrane bound immunoglobin heavy mu chain in Burkitt’s lymphoma cells. Mol. Cell. Proteomics 2007, 6, 2230–2238. [Google Scholar]
- Blank, M.; Weinschenk, T.; Priemer, M.; Schluesener, H. Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. selective targeting of endothelial regulatory protein pigpen. J. Biol. Chem 2001, 276, 16464–16468. [Google Scholar]
- Ohuchi, S.P.; Ohtsu, T.; Nakamura, Y. Selection of RNA aptamers against recombinant transforming growth factor-beta type III receptor displayed on cell surface. Biochimie 2006, 88, 897–904. [Google Scholar]
- Cerchia, L.; Duconge, F.; Pestourie, C.; Boulay, J.; Aissouni, Y.; Gombert, K.; Tavitian, B.; de Franciscis, V.; Libri, D. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol 2005, 3. [Google Scholar] [CrossRef] [Green Version]
- Zueva, E.; Rubio, L.I.; Ducongé, F.; Tavitian, B. Metastasis-focused cell-based SELEX generates aptamers inhibiting cell migration and invasion. Int. J. Cancer 2011, 128, 797–804. [Google Scholar]
- Cerchia, L.; Esposito, C.L.; Jacobs, A.H.; Tavitian, B.; de Franciscis, V. Differential SELEX in human glioma cell lines. PLoS One 2009, 4. [Google Scholar] [CrossRef]
- Boltz, A.; Piater, B.; Toleikis, L.; Guenther, R.; Kolmar, H.; Hock, B. Bi-specific aptamers mediating tumor cell lysis. J. Biol. Chem 2011, 286, 21896–21905. [Google Scholar]
- Ye, M.; Hu, D.; Tu, L.; Zhou, X.; Lu, F.; Wen, B.; Wu, W.; Lin, Y.; Zhou, Z.; Qu, J. Involvement of PI3K/Akt signaling pathway in hepatocyte growth factor-induced migration of uveal melanoma cells. Invest. Ophthalmol. Vis. Sci 2008, 49, 497–504. [Google Scholar]
- Davis, M.I.; Bennett, M.J.; Thomas, L.M.; Bjorkman, P.J. Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase. Proc. Natl. Acad. Sci. USA 2005, 102, 5981–5986. [Google Scholar]
- Liu, H.; Rajasekaran, A.K.; Moy, P.; Xia, Y.; Kim, S.; Navarro, V.; Rahmati, R.; Bander, N.H. Constitutive and antibody-induced internalization of prostate-specific membrane antigen. Cancer Res 1998, 58, 4055–4060. [Google Scholar]
- Dhar, S.; Gu, F.X.; Langer, R.; Farokhzad, O.C.; Lippard, S.J. Targeted delivery of cisplatin to prostate cancer cells by aptamer functionalized Pt(IV) prodrug-PLGA-PEG nanoparticles. Proc. Natl. Acad. Sci. USA 2008, 105, 17356–17361. [Google Scholar]
- Wang, A.Z.; Bagalkot, V.; Vasilliou, C.C.; Gu, F.; Alexis, F.; Zhang, L.; Shaikh, M.; Yuet, K.; Cima, M.J.; Langer, R.; et al. Superparamagnetic iron oxide nanoparticle-aptamer bioconjugates for combined prostate cancer imaging and therapy. ChemMedChem 2008, 3, 1311–1315. [Google Scholar]
- Bagalkot, V.; Zhang, L.; Levy-Nissenbaum, E.; Jon, S.; Kantoff, P.W.; Langer, R.; Farokhzad, O.C. Quantum dot-aptamer conjugates for synchronous cancer imaging, therapy, and sensing of drug delivery based on bi-fluorescence resonance energy transfer. Nano Lett 2007, 7, 3065–3070. [Google Scholar]
- Chu, T.C.; Marks, J.W., III; Lavery, L.A.; Faulkner, S.; Rosenblum, M.G.; Ellington, A.D.; Levy, M. Aptamer: Toxin conjugates that specifically target prostate tumor cells. Cancer Res 2006, 66, 5989–5992. [Google Scholar]
- Wullner, U.; Neef, I.; Eller, A.; Kleines, M.; Tur, M.K.; Barth, S. Cell-specific induction of apoptosis by rationally designed bivalent aptamer-siRNA transcripts silencing eukaryotic elongation factor 2. Curr. Cancer Drug Targets 2008, 8, 554–565. [Google Scholar]
- Dassie, J.P.; Liu, X.Y.; Thomas, G.S.; Whitaker, R.M.; Thiel, K.W.; Stockdale, K.R.; Meyerholz, D.K.; McCaffrey, A.P.; McNamara, J.O., II; Giangrande, P.H. Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat. Biotechnol 2009, 27, 839–849. [Google Scholar]
- Xiao, Z.; Shangguan, D.; Cao, Z.; Fang, X.; Tan, W. Cell-specific internalization study of an aptamer from whole cell selection. Chemistry 2008, 14, 1769–1775. [Google Scholar]
- Huang, Y.-F.; Shangguan, D.; Liu, H.; Phillips, J.A.; Zhang, X.; Chen, Y.; Tan, W. Molecular assembly of an aptamer-drug conjugate for targeted drug delivery to tumor cells. ChemBioChem 2009, 10, 862–868. [Google Scholar]
- Shangguan, D.; Tang, Z.; Mallikaratchy, P.; Xiao, Z.; Tan, W. Optimization and modifications of aptamers selected from live cancer cell lines. ChemBioChem 2007, 8, 603–606. [Google Scholar]
- Taghdisi, S.M.; Abnous, K.; Mosaffa, F.; Behravan, J. Targeted delivery of daunorubicin to T-cell acute lymphoblastic leukemia by aptamer. J. Drug Target 2010, 18, 277–281. [Google Scholar]
- Castano, A.P.; Mroz, P.; Hamblin, M.R. Photodynamic therapy and anti-tumour immunity. Nat. Rev. Cancer 2006, 6, 535–545. [Google Scholar]
- Mallikaratchy, P.; Tang, Z.; Tan, W. Cell specific aptamer–photosensitizer conjugates as a molecular tool in photodynamic therapy. ChemMedChem 2008, 3, 425–428. [Google Scholar]
- Medley, C.D.; Smith, J.E.; Tang, Z.; Wu, Y.; Bamrungsap, S.; Tan, W. Gold nanoparticle-based colorimetric assay for the direct detection of cancerous cells. Anal. Chem 2008, 80, 1067–1072. [Google Scholar]
- Zhu, X.; Cao, Y.; Liang, Z.; Li, G. Aptamer-based and DNAzyme-linked colorimetric detection of cancer cells. Protein Cell 2010, 1, 842–846. [Google Scholar]
- Phillips, J.A.; Xu, Y.; Xia, Z.; Fan, Z.H.; Tan, W. Enrichment of cancer cells using aptamers immobilized on a microfluidic channel. Anal. Chem 2009, 81, 1033–1039. [Google Scholar]
- Herr, J.K.; Smith, J.E.; Medley, C.D.; Shangguan, D.; Tan, W. Aptamer-conjugated nanoparticles for selective collection and detection of cancer cells. Anal. Chem 2006, 78, 2918–2924. [Google Scholar]
- Smith, J.E.; Medley, C.D.; Tang, Z.; Shangguan, D.; Lofton, C.; Tan, W. Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells. Anal. Chem 2007, 79, 3075–3082. [Google Scholar]
Aptamer | Cell Type | Target | Ref. |
---|---|---|---|
GBI-10 (ssDNA) | Glioblastoma cell line U251 | tenascin-C | [32] |
aptamer III.1 (ssDNA) | Endothelial cell line YPEN-1 | pigpen | [37] |
TD05 (ssDNA) | Burkitt’s lymphoma cell line Ramos | Ig μ heavy chain | [36] |
Sgc8 (ssDNA) | T-cell acute lymphoblastic leukemia CCRF-CEM | PTK7 | [35] |
A07 (RNA) | Chinese hamster ovary (CHO) cell line expressing recombinant transforming growth factor-βtype III receptor | TGF-βRIII | [38] |
D4 (RNA) | NGF-different pheochromocytoma cell line PC12 expressing recombinant MEN2A mutant | MEN2A mutant RET | [39] |
© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
Share and Cite
Ye, M.; Hu, J.; Peng, M.; Liu, J.; Liu, J.; Liu, H.; Zhao, X.; Tan, W. Generating Aptamers by Cell-SELEX for Applications in Molecular Medicine. Int. J. Mol. Sci. 2012, 13, 3341-3353. https://doi.org/10.3390/ijms13033341
Ye M, Hu J, Peng M, Liu J, Liu J, Liu H, Zhao X, Tan W. Generating Aptamers by Cell-SELEX for Applications in Molecular Medicine. International Journal of Molecular Sciences. 2012; 13(3):3341-3353. https://doi.org/10.3390/ijms13033341
Chicago/Turabian StyleYe, Mao, Jun Hu, Minyuan Peng, Jing Liu, Jun Liu, Huixia Liu, Xielan Zhao, and Weihong Tan. 2012. "Generating Aptamers by Cell-SELEX for Applications in Molecular Medicine" International Journal of Molecular Sciences 13, no. 3: 3341-3353. https://doi.org/10.3390/ijms13033341