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Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping.

Publication ,  Journal Article
Ou, K; Yu, K; Kesuma, D; Hooi, M; Huang, N; Chen, W; Lee, SY; Goh, XP; Tan, LK; Liu, J; Soon, SY; Bin Abdul Rashid, S; Putti, TC; Jikuya, H ...
Published in: J Proteome Res
April 2008

Proteomic and transcriptomic platforms both play important roles in cancer research, with differing strengths and limitations. Here, we describe a proteo-transcriptomic integrative strategy for discovering novel cancer biomarkers, combining the direct visualization of differentially expressed proteins with the high-throughput scale of gene expression profiling. Using breast cancer as a case example, we generated comprehensive two-dimensional electrophoresis (2DE)/mass spectrometry (MS) proteomic maps of cancer (MCF-7 and HCC-38) and control (CCD-1059Sk) cell lines, identifying 1724 expressed protein spots representing 484 different protein species. The differentially expressed cell-line proteins were then mapped to mRNA transcript databases of cancer cell lines and primary breast tumors to identify candidate biomarkers that were concordantly expressed at the gene expression level. Of the top nine selected biomarker candidates, we reidentified ANX1, a protein previously reported to be differentially expressed in breast cancers and normal tissues, and validated three other novel candidates, CRAB, 6PGL, and CAZ2, as differentially expressed proteins by immunohistochemistry on breast tissue microarrays. In total, close to half (4/9) of our protein biomarker candidates were successfully validated. Our study thus illustrates how the systematic integration of proteomic and transcriptomic data from both cell line and primary tissue samples can prove advantageous for accelerating cancer biomarker discovery.

Duke Scholars

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Published In

J Proteome Res

DOI

ISSN

1535-3893

Publication Date

April 2008

Volume

7

Issue

4

Start / End Page

1518 / 1528

Location

United States

Related Subject Headings

  • alpha-Crystallin B Chain
  • Tissue Array Analysis
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Reproducibility of Results
  • Proteomics
  • Proteome
  • Humans
  • Gene Expression Profiling
  • Female
  • Electrophoresis, Gel, Two-Dimensional
 

Citation

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Ou, K., Yu, K., Kesuma, D., Hooi, M., Huang, N., Chen, W., … Tan, P. (2008). Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. J Proteome Res, 7(4), 1518–1528. https://doi.org/10.1021/pr700820g
Ou, Keli, Kun Yu, Djohan Kesuma, Michelle Hooi, Ning Huang, Wei Chen, Suet Ying Lee, et al. “Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping.J Proteome Res 7, no. 4 (April 2008): 1518–28. https://doi.org/10.1021/pr700820g.
Ou K, Yu K, Kesuma D, Hooi M, Huang N, Chen W, et al. Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. J Proteome Res. 2008 Apr;7(4):1518–28.
Ou, Keli, et al. “Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping.J Proteome Res, vol. 7, no. 4, Apr. 2008, pp. 1518–28. Pubmed, doi:10.1021/pr700820g.
Ou K, Yu K, Kesuma D, Hooi M, Huang N, Chen W, Lee SY, Goh XP, Tan LK, Liu J, Soon SY, Bin Abdul Rashid S, Putti TC, Jikuya H, Ichikawa T, Nishimura O, Salto-Tellez M, Tan P. Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. J Proteome Res. 2008 Apr;7(4):1518–1528.
Journal cover image

Published In

J Proteome Res

DOI

ISSN

1535-3893

Publication Date

April 2008

Volume

7

Issue

4

Start / End Page

1518 / 1528

Location

United States

Related Subject Headings

  • alpha-Crystallin B Chain
  • Tissue Array Analysis
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Reproducibility of Results
  • Proteomics
  • Proteome
  • Humans
  • Gene Expression Profiling
  • Female
  • Electrophoresis, Gel, Two-Dimensional