Applied Biochemistry and Biotechnology

, Volume 182, Issue 4, pp 1276–1289 | Cite as

Identification of Caveolin-1 as an Invasion-Associated Gene in Liver Cancer Cells Using Dendron-Coated DNA Microarrays



The conventional gene expression profiling approaches have been replaced with DNA microarrays with exhibiting a powerful high-throughput capacity. Most solid surfaces of DNA microarrays contain such a high area density of functional groups to immobilize capture DNAs to the surface that the hybridization of capture DNAs with cDNA can be hindered, resulting in low intensity and reproducibility. Since our previous works showed that the 9-acid dendron was able to increase the hybridization efficiency, we aimed to demonstrate the feasibility of 9-acid dendron-coated glass slides as an advanced microarray platform for gene expression profiling. The 9-acid dendron-coated DNA microarray could reproducibly obtain the expression levels of 2800 human cancer-associated genes in the two liver cancer lines: Hep3B and SK-Hep1. Among the differentially expressed genes, Caveolin-1 (Cav-1) was identified as the most highly up-regulated gene in invasive SK-Hep1 in comparison to non-motile Hep3B. The overexpression of Cav-1 in Hep3B promoted the cell invasion, whereas its knockdown in SK-Hep1 suppressed the invasive feature, which confirms that the overexpression of Cav-1 is closely associated with cell invasion of liver carcinoma. Collectively, the 9-acid dendron-coated surface could successfully detect the transcript levels of cells, demonstrating its feasible potential to identify the candidate genes for further functional studies or diagnosis of diseases.


9-Acid dendron DNA microarray Caveolin-1 Cell invasion Gene expression profiling Liver cancer 



Complementary DNA




Differentially expressed gene


Dimethyl sulfoxide


Ethylenediaminetetraacetic acid


Epithelial-mesenchymal transition


Fetal bovine serum




Polyacrylamide gel electrophoresis


Phosphate-buffered saline


Photomultiplier tube


Quantitative real-time PCR


Significance analysis of microarrays


Standard deviation


Sodium dodecyl sulfonate


Small interfering RNA


Saline sodium citrate


Transmission electron microscopy





This research was supported by Basic Science Research Program through the National Research Foundation (NRF) of Korea funded by the Ministry of Science, ICT and Future Planning (grant number NRF-2015R1C1A1A01052498 to ESK). This study was also financially supported by Chonnam National University (grant number 2015-1847 to ESK); an NRF grant (grant number 2014R1A2A2A01002931 to KYC) funded by the MEST; and the Next-Generation BioGreen 21 Program (grant number PJ01121601 to KYC) of Rural Development Administration, Republic of Korea. Authors thank Ms. Su-Jung Kim at POSTECH Biotech Center for the help with the sample preparation for TEM imaging. We are also grateful to Dr. Mi Nam Lee for her comments on the immunoblotting results.

Author’s Contributions

ESK and KYC conceived and designed the experiments; ESK, JHK, JHS, and SMH performed the experiments; and SY and ESK analyzed the data.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

12010_2017_2398_MOESM1_ESM.docx (188 kb)
ESM 1 (DOCX 187 kb)


  1. 1.
    Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995). Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science, 270(5235), 467–470.CrossRefGoogle Scholar
  2. 2.
    International Human Genome Sequencing, C. (2004). Finishing the euchromatic sequence of the human genome. Nature, 431(7011), 931–945.CrossRefGoogle Scholar
  3. 3.
    Duffy, M. J., McGowan, P. M., & Gallagher, W. M. (2008). Cancer invasion and metastasis: changing views. The Journal of Pathology, 214(3), 283–293.CrossRefGoogle Scholar
  4. 4.
    Hanahan, D., & Weinberg, R. A. (2011). Hallmarks of cancer: the next generation. Cell, 144(5), 646–674.CrossRefGoogle Scholar
  5. 5.
    van't Veer, L. J., Dai, H., van de Vijver, M. J., He, Y. D., Hart, A. A., Mao, M., Peterse, H. L., van der Kooy, K., Marton, M. J., Witteveen, A. T., Schreiber, G. J., Kerkhoven, R. M., Roberts, C., Linsley, P. S., Bernards, R., & Friend, S. H. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415(6871), 530–536.Google Scholar
  6. 6.
    Yamaguchi, H., Wyckoff, J., & Condeelis, J. (2005). Cell migration in tumors. Current Opinion in Cell Biology, 17(5), 559–564.CrossRefGoogle Scholar
  7. 7.
    Lin, A. Y., Chua, M. S., Choi, Y. L., Yeh, W., Kim, Y. H., Azzi, R., Adams, G. A., Sainani, K., van de Rijn, M., So, S. K., & Pollack, J. R. (2011). Comparative profiling of primary colorectal carcinomas and liver metastases identifies lef1 as a prognostic biomarker. PloS One, 6(2), e16636.CrossRefGoogle Scholar
  8. 8.
    Nimse, S. B., Song, K., Sonawane, M. D., Sayyed, D. R., & Kim, T. (2014). Immobilization techniques for microarray: challenges and applications. Sensors, 14(12), 22208–22229.CrossRefGoogle Scholar
  9. 9.
    Kim, E. S., Hong, B. J., Park, C. W., Kim, Y., Park, J. W., & Choi, K. Y. (2011). Effects of lateral spacing on enzymatic on-chip DNA polymerization. Biosensors and Bioelectronics, 26(5), 2566–2573.CrossRefGoogle Scholar
  10. 10.
    Kim, E. S., Kim, J. S., Lee, Y., Choi, K. Y., & Park, J. W. (2012). Following the DNA ligation of a single duplex using atomic force microscopy. ACS Nano, 6(7), 6108–6114.CrossRefGoogle Scholar
  11. 11.
    Kim, E. S., Lee, N., Park, J. W., & Choi, K. Y. (2013). Kinetic characterization of on-chip DNA ligation on dendron-coated surfaces with nanoscaled lateral spacings. Nanotechnology, 24(40), 405703.CrossRefGoogle Scholar
  12. 12.
    Oh, S. J., Ju, J. M., Kim, B. C., Ko, E., Hong, B. J., Park, J. G., Park, J. W. and Choi, K. Y. (2005). DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene. Nucleic Acids Research, 33 (10).Google Scholar
  13. 13.
    Kim, Y., Kim, E. S., Lee, Y., Kim, J. H., Shim, B. C., Cho, S. M., Lee, J. S., & Park, J. W. (2014). Reading single DNA with DNA polymerase followed by atomic force microscopy. Journal of the American Chemical Society, 136(39), 13754–13760.CrossRefGoogle Scholar
  14. 14.
    Eun, J. R., Jung, Y. J., Zhang, Y., Zhang, Y., Tschudy-Seney, B., Ramsamooj, R., Wan, Y. J., Theise, N. D., Zern, M. A., & Duan, Y. (2014). Hepatoma SK Hep-1 cells exhibit characteristics of oncogenic mesenchymal stem cells with highly metastatic capacity. PloS One, 9(10), e110744.CrossRefGoogle Scholar
  15. 15.
    Kim, J. R., & Kim, C. H. (2004). Association of a high activity of matrix metalloproteinase-9 to low levels of tissue inhibitors of metalloproteinase-1 and -3 in human hepatitis B-viral hepatoma cells. The International Journal of Biochemistry & Cell Biology, 36(11), 2293–2306.CrossRefGoogle Scholar
  16. 16.
    Hong, B. J., Oh, S. J., Youn, T. O., Kwon, S. H., & Park, J. W. (2005). Nanoscale-controlled spacing provides DNA microarrays with the SNP discrimination efficiency in solution phase. Langmuir, 21(10), 4257–4261.CrossRefGoogle Scholar
  17. 17.
    Bolstad, B. M., Irizarry, R. A., Astrand, M., & Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19(2), 185–193.CrossRefGoogle Scholar
  18. 18.
    Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America, 98(9), 5116–5121.CrossRefGoogle Scholar
  19. 19.
    Hwang, D., Rust, A. G., Ramsey, S., Smith, J. J., Leslie, D. M., Weston, A. D., de Atauri, P., Aitchison, J. D., Hood, L., Siegel, A. F., & Bolouri, H. (2005). A data integration methodology for systems biology. Proceedings of the National Academy of Sciences of the United States of America, 102(48), 17296–17301.CrossRefGoogle Scholar
  20. 20.
    Tse, E. Y. T., Ko, F. C. F., Tung, E. K. K., Chan, L. K., Lee, T. K. W., Ngan, E. S. W., Man, K., Wong, A. S. T., Ng, I. O. L., & Yam, J. W. P. (2012). Caveolin-1 overexpression is associated with hepatocellular carcinoma tumourigenesis and metastasis. The Journal of Pathology, 226(4), 645–653.CrossRefGoogle Scholar
  21. 21.
    Kim, K. R., Choi, H. N., Lee, H. J., Baek, H. A., Park, H. S., Jang, K. Y., Chung, M. J., & Moon, W. S. (2007). A peroxisome proliferator-activated receptor gamma antagonist induces vimentin cleavage and inhibits invasion in high-grade hepatocellular carcinoma. Oncology Reports, 18(4), 825–832.Google Scholar
  22. 22.
    Tarca, A. L., Romero, R., & Draghici, S. (2006). Analysis of microarray experiments of gene expression profiling. American Journal of Obstetrics and Gynecology, 195(2), 373–388.CrossRefGoogle Scholar
  23. 23.
    Choi, Y. S., Yoon, C. W., Lee, H. D., Park, M., & Park, J. W. (2004). Efficient protein-ligand interaction by guaranteeing mesospacing between immobilized biotins. Chemical Communications, 11, 1316–1317.CrossRefGoogle Scholar
  24. 24.
    Cokakli, M., Erdal, E., Nart, D., Yilmaz, F., Sagol, O., Kilic, M., Karademir, S., & Atabey, N. (2009). Differential expression of caveolin-1 in hepatocellular carcinoma: correlation with differentiation state, motility and invasion. BMC Cancer, 9, 65.CrossRefGoogle Scholar
  25. 25.
    Gagescu, R. (2001). Life without caveolae. Nature Reviews Molecular Cell Biology, 2(11), 788–788.CrossRefGoogle Scholar
  26. 26.
    Liu, P. S., Rudick, M., & Anderson, R. G. W. (2002). Multiple functions of caveolin-1. Journal of Biological Chemistry, 277(44), 41295–41298.CrossRefGoogle Scholar
  27. 27.
    Sotgia, F., Martinez-Outschoorn, U. E., Howell, A., Pestell, R. G., Pavlides, S., & Lisanti, M. P. (2012). Caveolin-1 and cancer metabolism in the tumor microenvironment: markers, models, and mechanisms. Annual Review of Pathology: Mechanisms of Disease, 7, 423–467.CrossRefGoogle Scholar
  28. 28.
    Senetta, R., Stella, G., Pozzi, E., Sturli, N., Massi, D., & Cassoni, P. (2013). Caveolin-1 as a promoter of tumour spreading: when, how, where and why. Journal of Cellular and Molecular Medicine, 17(3), 325–336.CrossRefGoogle Scholar
  29. 29.
    Goetz, J. G., Joshi, B., Lajoie, P., Strugnell, S. S., Scudamore, T., Kojic, L. D., & Nabi, I. R. (2008). Concerted regulation of focal adhesion dynamics by galectin-3 and tyrosine-phosphorylated caveolin-1. Journal of Cell Biology, 180(6), 1261–1275.CrossRefGoogle Scholar
  30. 30.
    Yao, Z. X., & Mishra, L. (2009). Cancer stem cells and hepatocellular carcinoma. Cancer Biology & Therapy, 8(18), 1691–1698.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Biological SciencesChonnam National UniversityGwangjuSouth Korea
  2. 2.School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangSouth Korea
  3. 3.Department of Life SciencesPohang University of Science and TechnologyPohangSouth Korea
  4. 4.Division of Integrative Biosciences and BiotechnologyPohang University of Science and TechnologyPohangSouth Korea

Personalised recommendations