Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
권호 표지
DOI QR코드

DOI QR Code

Identification of DNA Aptamers toward Epithelial Cell Adhesion Molecule via Cell-SELEX

  • Kim, Ji Won (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Eun Young (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Sun Young (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Byun, Sang Kyung (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Dasom (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Oh, Kyoung-Jin (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Won Kon (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Han, Baek Soo (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Chi, Seung-Wook (Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Sang Chul (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology) ;
  • Bae, Kwang-Hee (Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2014.07.28
  • Accepted : 2014.08.18
  • Published : 2014.10.31
Download PDF
⟨ Previous Next ⟩

Abstract

The epithelial cell adhesion molecule (EpCAM, also known as CD326) is a transmembrane glycoprotein that is specifically detected in most adenocarcinomas and cancer stem cells. In this study, we performed a Cell systematic evolution of ligands by exponential enrichment (SELEX) experiment to isolate the aptamers against EpCAM. After seven round of Cell SELEX, we identified several aptamer candidates. Among the selected aptamers, EP166 specifically binds to cells expressing EpCAM with an equilibrium dissociation constant (Kd) in a micromolar range. On the other hand, it did not bind to negative control cells. Moreover, EP166 binds to J1ES cells, a mouse embryonic stem cell line. Therefore, the isolated aptamers against EpCAM could be used as a stem cell marker or in other applications in both stem cell and cancer studies.

Keywords

References

  1. Breaker, R.R. (2004). Natural and engineered nucleic acids as tools to explore biology. Nature 432, 838-845. https://doi.org/10.1038/nature03195
  2. Dalerba, P., Dylla, S.J., Park, I.K., Liu, R., Wang, X., Cho, R.W., Hoey, T., Gurney, A., Huang, E.H., Simeone, D.M., et al. (2007). Phenotypic characterization of human colorectal cancer stem cells. Proc. Natl. Acad. Sci. USA 104, 10158-10163. https://doi.org/10.1073/pnas.0703478104
  3. Dan, Y.Y., Riehle, K.J., Lazaro, C., Teoh, N., Haque, J., Campbell, J.S., and Fausto, N. (2006). Isolation of multipotent progenitor cells from human fetal liver capable of differentiating into liver and mesenchymal lineages. Proc. Natl. Acad. Sci. USA 103, 9912-9917. https://doi.org/10.1073/pnas.0603824103
  4. Ellington, A.D., and Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822. https://doi.org/10.1038/346818a0
  5. Fang, X., and Tan, W. (2010). Aptamers generated from cell-SELEX for molecular medicine: a chemical biology approach. Acc. Chem. Res. 43, 48-57. https://doi.org/10.1021/ar900101s
  6. Gonzalez, B., Denzel, S., Mack, B., Conrad, M., and Gires, O. (2009). EpCAM is involved in maintenance of the murine embryonic stem cell phenotype. Stem Cells 27, 1782-1791. https://doi.org/10.1002/stem.97
  7. Hao, P.P., Lee, M.J., Yu, G.-R., Kim, I.-H., Cho, Y.-G., and Kim, D.-G. (2013). Isolation of $EpCM^+/CD133^-$ hepatic progenitor cells. Mol. Cells 36, 424-431. https://doi.org/10.1007/s10059-013-0190-y
  8. Jayasena, S.D. (1999). Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45, 1628-1650.
  9. Keefe, A.D., Pai, S., and Ellington, A. (2010). Aptamers as therapeutics. Nat. Rev. Drug Discov. 9, 537-550. https://doi.org/10.1038/nrd3141
  10. Kim, W.K., Jung, H., Kim, D.H., Kim, E.Y., Chung, J.W., Cho, Y.S., Park, S.G., Park, B.C., Bae, K.-H., and Lee, S.C. (2009). Regulation of adipocyte differentiation by LAR tyrosine phosphatase in human mesenchymal stem cells and 3T3-L1 preadipocytes. J. Cell Sci. 122, 4160-4167. https://doi.org/10.1242/jcs.053009
  11. Kim, W.K., Jung, H., Kim, E.Y., Kim, D.H., Cho, Y.S., Park, B.C., Park, S.G., Ko, Y., Bae, K.-H., and Lee, S.C. (2011). RPTP$\mu$ tyrosine phosphatase promotes adipogenic differentiation via modulation of p120 catenin phosphorylation. Mol. Biol. Cell 22, 4883-4891. https://doi.org/10.1091/mbc.E11-03-0175
  12. Kim, E.Y., Kim, W.K., Kang, H.J., Kim, J.-H., Chung, S.J., Seo, Y.S., Park, S.G., Lee, S.C., and Bae, K.-H. (2012). Acetylation of malate dehydrogenase 1 promotes adipogenic differentiation via activating its enzymatic activity. J. Lipid Res. 53, 1864-1876. https://doi.org/10.1194/jlr.M026567
  13. Kim, E.Y., Han, B.S., Kim, W.K., Lee, S.C., and Bae, K.-H. (2013). Acceleration of adipogenic differentiation via acetylation of malate dehydrogenase 2. Biochem. Biophys. Res. Comm. 441, 77-82. https://doi.org/10.1016/j.bbrc.2013.10.016
  14. Kim, E.Y., Kim, J.W., Kim, W.K., Han, B.S., Park, S.G., Chung, B.H., Lee, S.C., and Bae, K.-H. (2014). Selection of aptamers for mature white adipocytes by Cell SELEX using flow cytometry. PLoS One 9, e97747. https://doi.org/10.1371/journal.pone.0097747
  15. Lee, J.F., Stovall, G.M., and Ellington, A.D. (2006). Aptamer therapeutics advance. Curr. Opin. Chem. Biol. 10, 282-289. https://doi.org/10.1016/j.cbpa.2006.03.015
  16. Litvinov, S.V., Balzar, M., Winter, M.J., Bakker, H.A., Briaire-de Bruijn, I.H., Prins, F., Fleuren, G.J., and Warnaar, S.O. (1997). Epithelial cell adhesion molecule (Ep-CAM) modulates cell-cell interactions mediated by classic cadherins. J. Cell Biol. 139, 1337-1348. https://doi.org/10.1083/jcb.139.5.1337
  17. Lu, T.-Y., Lu, R.-M., Liao, M.-Y., Yu, J., Chung, C.-H., Kao, C.-F., and Wu, H.-C. (2010). Epithelial cell adhesion molecule regulation is associated with the maintenance of the undifferentiated phenotype of human embryonic stem cells. J. Biol. Chem. 285, 8719-8732. https://doi.org/10.1074/jbc.M109.077081
  18. Maetzel, D., Denzel, S., Mack, B., Canis, M., Went, P., Benk, M., Kieu, C., Papior, P., Baeuerle, P.A., Munz, M., et al. (2009). Nuclear signalling by tumour-associated antigen EpCAM. Nat. Cell Biol. 11, 162-171. https://doi.org/10.1038/ncb1824
  19. Mi, J., Liu, Y., Rabbani, Z.N., Yang, Z., Urban, J.H., Sullenger, B.A., and Clary, B.M. (2010). In vivo selection of tumor-targeting RNA motifs. Nat. Chem. Biol. 6, 22-24. https://doi.org/10.1038/nchembio.277
  20. Ng, V.Y., Ang, S.N., Chan, J.X., and Choo, A.B.H. (2010). Characterization of epithelial cell adhesion molecule as a surface marker on undifferentiated human embryonic stem cells. Stem Cells 28, 29-35. https://doi.org/10.1002/stem.221
  21. Patriarca, C., Macchi, R.M., Marschner, A.K., and Mellstedt, H. (2012). Epithelial cell adhesion molecule expression (CD326) in cancer: a short review. Cancer Treat. Rev. 38, 68-75. https://doi.org/10.1016/j.ctrv.2011.04.002
  22. Sefah, K., Shangguan, D., Xiong, X., O'Donoghue, M.B., and Tan, W. (2010). Development of DNA aptamers using Cell-SELEX. Nat. Protoc. 5, 1169-1185. https://doi.org/10.1038/nprot.2010.66
  23. Shamah, S.M., Healy, J.M., and Cload, S.T. (2008). Complex target SELEX. Acc. Chem. Res. 41, 130-138. https://doi.org/10.1021/ar700142z
  24. Shangguan, D., Li, Y., Tang, Z., Cao, Z.C., Chen, H.W., Mallikaratchy, P., Sefah, K., Yang, C.J., and Tan, W. (2006). Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. USA 103, 11838-11843. https://doi.org/10.1073/pnas.0602615103
  25. Song, Y., Zhu, Z., An, Y., Zhang, W., Zhang, H., Liu, D., Yu, C., Duan, W., and Yang, C.J. (2013). Selection of DNA aptamers against epithelial cell adhesion molecule for cancer cell imaging and circulating tumor cell capture. Anal. Chem. 85, 4141-4149. https://doi.org/10.1021/ac400366b
  26. Stingl, J., Raouf, A., Emerman, J.T., and Eaves, C.J. (2005). Epithelial progenitors in the normal human mammary gland. J. Mammary Gland Biol. Neoplasia 10, 49-59. https://doi.org/10.1007/s10911-005-2540-7
  27. Sundberg, M., Jansson, L., Ketolainen, J., Pihlajamaki, H., Suuronen, R., Skottman, H., Inzunza, J., Hovatta, O., and Narkilahti, S. (2009). CD marker expression profiles of human embryonic stem cells and their neural derivatives, determined using flowcytometric analysis, reveal a novel CD marker for exclusion of pluripotent stem cells. Stem Cell Res. 2, 113-124. https://doi.org/10.1016/j.scr.2008.08.001
  28. Tan, W., Wang, H., Chen, Y., Zhang, X., Zhu, H., Yang, C., Yang, R., and Liu, C. (2011). Molecular aptamers for drug delivery. Trends Biotechnol. 29, 634-640. https://doi.org/10.1016/j.tibtech.2011.06.009
  29. Tuerk, C., and Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510. https://doi.org/10.1126/science.2200121
  30. Zhao, W., Ji, X., Zhang, F., Li, L., and Ma, L. (2012). Embryonic stem cell markers. Molecules 17, 6196-6136. https://doi.org/10.3390/molecules17066196

Cited by

  1. Current approaches in SELEX: An update to aptamer selection technology vol.33, pp.6, 2015, https://doi.org/10.1016/j.biotechadv.2015.02.008
  2. Aptamers as smart ligands for nano-carriers targeting vol.82, 2016, https://doi.org/10.1016/j.trac.2016.06.018
  3. Development of Cell-SELEX Technology and Its Application in Cancer Diagnosis and Therapy vol.17, pp.12, 2016, https://doi.org/10.3390/ijms17122079
  4. Progress and Challenges in Developing Aptamer-Functionalized Targeted Drug Delivery Systems vol.16, pp.10, 2015, https://doi.org/10.3390/ijms161023784
  5. Aptamers: Promising Tools for the Detection of Circulating Tumor Cells vol.26, pp.6, 2016, https://doi.org/10.1089/nat.2016.0632
  6. Development of targeted multimodal imaging agent in ionizing radiation-free approach for visualizing hepatocellular carcinoma cells vol.245, 2017, https://doi.org/10.1016/j.snb.2017.02.012
  7. c-Jun regulates adipocyte differentiation via the KLF15-mediated mode vol.469, pp.3, 2016, https://doi.org/10.1016/j.bbrc.2015.12.035
  8. Selection of Nucleic Acid Aptamers Targeting Tumor Cell-Surface Protein Biomarkers vol.9, pp.6, 2017, https://doi.org/10.3390/cancers9060069
  9. Aptamer Cell-Based Selection: Overview and Advances vol.5, pp.3, 2017, https://doi.org/10.3390/biomedicines5030049
  10. Selection and characterization of DNA aptamer against glucagon receptor by cell-SELEX vol.7, pp.1, 2017, https://doi.org/10.1038/s41598-017-05840-w
  11. Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine vol.18, pp.10, 2017, https://doi.org/10.3390/ijms18102142
  12. Shedding light on the EpCAM: An overview pp.00219541, 2019, https://doi.org/10.1002/jcp.28132
  13. Cell-targeting aptamers act as intracellular delivery vehicles vol.100, pp.16, 2014, https://doi.org/10.1007/s00253-016-7686-2
  14. Aptamer: A potential oligonucleotide nanomedicine in the diagnosis and treatment of hepatocellular carcinoma vol.9, pp.2, 2014, https://doi.org/10.18632/oncotarget.23359
  15. Selection and characterization of single-stranded DNA aptamers against interleukin-5 vol.14, pp.6, 2019, https://doi.org/10.4103/1735-5362.272560
  16. Recent Advances in Aptamer Discovery and Applications vol.24, pp.5, 2014, https://doi.org/10.3390/molecules24050941
  17. Development of α4 integrin DNA aptamer as a potential therapeutic tool for multiple sclerosis vol.120, pp.9, 2019, https://doi.org/10.1002/jcb.28907
  18. Aptamer-based nanostructured interfaces for the detection and release of circulating tumor cells vol.8, pp.16, 2014, https://doi.org/10.1039/c9tb02457c
  19. CRISPR-Mediated Isogenic Cell-SELEX Approach for Generating Highly Specific Aptamers Against Native Membrane Proteins vol.13, pp.5, 2014, https://doi.org/10.1007/s12195-020-00651-y
  20. Aptamer-Mediated Nanotheranostics for Cancer Treatment: A Review vol.3, pp.10, 2014, https://doi.org/10.1021/acsanm.0c01785
  21. Isolation of DNA aptamers targeting N-cadherin and high-efficiency capture of circulating tumor cells by using dual aptamers vol.12, pp.44, 2014, https://doi.org/10.1039/d0nr06180h
  22. Ni-Nitrilotriacetic Acid Affinity SELEX Method for Selection of DNA Aptamers Specific to the N-Cadherin Protein vol.22, pp.12, 2014, https://doi.org/10.1021/acscombsci.0c00165
  23. Generation of HBsAg DNA aptamer using modified cell-based SELEX strategy vol.48, pp.1, 2014, https://doi.org/10.1007/s11033-020-05995-2
  24. The Potential of Aptamer-Mediated Liquid Biopsy for Early Detection of Cancer vol.22, pp.11, 2014, https://doi.org/10.3390/ijms22115601
  25. Polyclonal Aptamers for Specific Fluorescence Labeling and Quantification of the Health Relevant Human Gut Bacterium Parabacteroides distasonis vol.9, pp.11, 2021, https://doi.org/10.3390/microorganisms9112284