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  • Oncogenomics
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Discovery of differentially expressed genes in human breast cancer using subtracted cDNA libraries and cDNA microarrays

Oncogene volume 21, pages 2270–2282 (2002)Cite this article

Abstract

Identifying novel and known genes that are differentially expressed in breast cancer has important implications in understanding the biology of breast tumorigenesis and developing new diagnostic and therapeutic agents. In this study we have combined two powerful technologies, PCR-based cDNA subtraction and cDNA microarray, as a high throughput methodology designed to identify cDNA clones that are breast tumor- and tissue-specific and are overexpressed in breast tumors. Approximately 2000 cDNA clones generated from the subtracted breast tumor library were arrayed on the microarray chips. The arrayed target cDNAs were then hybridized with 30 pairs of fluorescent-labeled cDNA probes generated from breast tumors and normal tissues to determine the tissue distribution and tumor specificity. cDNA clones showing overexpression in breast tumors by microarray were further analysed by DNA sequencing, GenBank and EST database searches, and quantitative real time PCR. We identified several known genes, including mammaglobin, cytokeratin 19, fibronectin, and hair-specific type II keratin, which have previously been shown to be overexpressed in breast tumors and may play an important role in the malignance of breast. We also discovered B726P which appears to be an isoform of NY-BR-1, a breast tissue-specific gene. Two additional clones discovered, B709P and GABAA receptor π subunit, were not previously described for their overexpression profile in breast tumors. Thus, combining PCR-based cDNA subtraction and cDNA microarray allowed for an efficient way to identify and validate genes with elevated mRNA expression levels in breast cancer that may potentially be involved in breast cancer progression. These differentially expressed genes may be of potential utility as therapeutic and diagnostic targets for breast cancer.

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Abbreviations

EST:

expressed sequence tag

GABAπ:

γ-aminobutyrate type A receptor π subunit

ORF:

open reading frame

PBMC:

peripheral blood mononuclear cells

PCR:

polymerase chain reaction

RT:

reverse transcription

SSH:

suppression subtractive hybridization

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Acknowledgements

We thank Incyte Pharmaceutical Inc. for their help in microarray technology. Some tissue samples were obtained from the Cooperative Human Tissue Network, which is funded by the National Cancer Institute, and from National Disease Research Interchange. This work was supported in part by the NIH grant CA75794 (RL Houghton).

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Authors and Affiliations

  1. Corixa Corporation, 1124 Columbia Street, Suite 200, Seattle, 98104, Washington, WA, USA

    Yuqiu Jiang, Susan L Harlocker, David A Molesh, David C Dillon, John A Stolk, Raymond L Houghton, Steven G Reed & Jiangchun Xu

  2. Department of Immunology, Roswell Park Cancer Institute, Buffalo, 14263, New York, NY, USA

    Elizabeth A Repasky

  3. Hospital Aristides Maltez, Salvador, Bahia, Brazil

    Roberto Badaro

  4. Department of Pathobiology, University of Washington, Seattle, 98195, Washington, WA, USA

    Steven G Reed

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  1. Yuqiu Jiang
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  2. Susan L Harlocker
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  4. David C Dillon
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  9. Steven G Reed
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  10. Jiangchun Xu
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Correspondence to Yuqiu Jiang.

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Jiang, Y., Harlocker, S., Molesh, D. et al. Discovery of differentially expressed genes in human breast cancer using subtracted cDNA libraries and cDNA microarrays. Oncogene 21, 2270–2282 (2002). https://doi.org/10.1038/sj.onc.1205278

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