Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis

  • Authors:
    • Harri Lähdesmäki
    • Xishan Hao
    • Baocun Sun
    • Limei Hu
    • Olli Yli-Harja
    • Ilya Shmulevich
    • Wei Zhang
  • View Affiliations

  • Published online on: June 1, 2004     https://doi.org/10.3892/ijo.24.6.1589
  • Pages: 1589-1596
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )


Abstract

In order to identify key biological pathways that can distinguish between primary breast cancers and their lymph node metastases, we employed gene expression profiling together with gene function-based clustering analysis. We first acquired gene expression profiles of 9 matched primary tumors and the corresponding metastases that contained at least 75% of tumor cells. Then, we applied a clustering algorithm to the preprocessed data. In order to focus on the most informative genes, we ranked all the genes individually based on their abilities to separate the primary breast tumor and metastases samples. Further, we separated these genes into six functional groups according to the Stanford SOURCE database: ‘cell cycle,’ ‘apoptosis,’ ‘metabolism,’ ‘cell adhesion and migration,’ ‘signal transduction,’ and ‘transcriptional factor and DNA binding molecules.’ Unsupervised clustering analysis using all of the 2,303 genes on the microarrays was not able to separate the primary and metastases samples. Clustering analysis using the most informative genes revealed that primary tumors were more tightly clustered, whereas the metastases samples were relatively heterogeneous. The clustering analysis with the genes belonging to different functional groups showed that different functional gene sets varied in their abilities to separate primary tumors and their metastases. Marked separations were found with genes involved in metabolism, signal transduction, cell cycle, and transcriptional factor and DNA binding molecules. In contrast, apoptosis and cell adhesion and migration genes did not provide a clear separation of the two groups of samples. These results suggest that metastatic cells have different metabolism and signal transduction activities, regulated by transcriptional events, from the primary tumor cells. The results also suggest that the altered cell adhesion and migration potentials that are required for tumors to metastasize already exist in the primary tumors as a whole.

Related Articles

Journal Cover

June 2004
Volume 24 Issue 6

Print ISSN: 1019-6439
Online ISSN:1791-2423

Sign up for eToc alerts

Recommend to Library

Copy and paste a formatted citation
x
Spandidos Publications style
Lähdesmäki H, Hao X, Sun B, Hu L, Yli-Harja O, Shmulevich I and Zhang W: Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis. Int J Oncol 24: 1589-1596, 2004
APA
Lähdesmäki, H., Hao, X., Sun, B., Hu, L., Yli-Harja, O., Shmulevich, I., & Zhang, W. (2004). Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis. International Journal of Oncology, 24, 1589-1596. https://doi.org/10.3892/ijo.24.6.1589
MLA
Lähdesmäki, H., Hao, X., Sun, B., Hu, L., Yli-Harja, O., Shmulevich, I., Zhang, W."Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis". International Journal of Oncology 24.6 (2004): 1589-1596.
Chicago
Lähdesmäki, H., Hao, X., Sun, B., Hu, L., Yli-Harja, O., Shmulevich, I., Zhang, W."Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis". International Journal of Oncology 24, no. 6 (2004): 1589-1596. https://doi.org/10.3892/ijo.24.6.1589