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

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Abstract

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.

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Abbreviations

cDNA:

Complementary DNA

Cav-1:

Caveolin-1

DEG:

Differentially expressed gene

DMSO:

Dimethyl sulfoxide

EDTA:

Ethylenediaminetetraacetic acid

EMT:

Epithelial-mesenchymal transition

FBS:

Fetal bovine serum

NHS:

N-hydrosuccinylimide

PAGE:

Polyacrylamide gel electrophoresis

PBS:

Phosphate-buffered saline

PMT:

Photomultiplier tube

qPCR:

Quantitative real-time PCR

SAM:

Significance analysis of microarrays

SD:

Standard deviation

SDS:

Sodium dodecyl sulfonate

siRNA:

Small interfering RNA

SSC:

Saline sodium citrate

TEM:

Transmission electron microscopy

Vim:

Vimentin

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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Biological Sciences, Chonnam National University, Gwangju, South Korea

    Eung-Sam Kim

  2. School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea

    Eung-Sam Kim & Sungyong You

  3. Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea

    Jung Hee Kwon, Ji Hye Shin & Sun Mi Hong

  4. Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea

    Sun Mi Hong & Kwan Yong Choi

Authors
  1. Eung-Sam Kim
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  2. Jung Hee Kwon
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  3. Ji Hye Shin
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  4. Sungyong You
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  5. Sun Mi Hong
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Correspondence to Eung-Sam Kim or Kwan Yong Choi.

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Kim, ES., Kwon, J.H., Shin, J.H. et al. Identification of Caveolin-1 as an Invasion-Associated Gene in Liver Cancer Cells Using Dendron-Coated DNA Microarrays. Appl Biochem Biotechnol 182, 1276–1289 (2017). https://doi.org/10.1007/s12010-017-2398-3

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  • DOI: https://doi.org/10.1007/s12010-017-2398-3

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