Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer

doi:10.1073/pnas.091582298

Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer

^*Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892; ^‡Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, 33520 Tampere, Finland; ^§Institute of Pathology, University of Basel, CH-4003 Basel, Switzerland; ^¶Department of Human Molecular Genetics, National Public Health Institute, 00300 Helsinki, Finland; and ^‖Haartman Institute, Department of Medical Genetics, University of Helsinki and the Folkhälsan Institute of Genetics, 00280 Helsinki, Finland

Edited by Janet D. Rowley, University of Chicago Medical Center, Chicago, IL, and approved March 2, 2001 (received for review December 8, 2000)

Abstract

The biological significance of DNA amplification in cancer is thought to be due to the selection of increased expression of a single or few important genes. However, systematic surveys of the copy number and expression of all genes within an amplified region of the genome have not been performed. Here we have used a combination of molecular, genomic, and microarray technologies to identify target genes for 17q23, a common region of amplification in breast cancers with poor prognosis. Construction of a 4-Mb genomic contig made it possible to define two common regions of amplification in breast cancer cell lines. Analysis of 184 primary breast tumors by fluorescence in situ hybridization on tissue microarrays validated these results with the highest amplification frequency (12.5%) observed for the distal region. Based on GeneMap'99 information, 17 known genes and 26 expressed sequence tags were localized to the contig. Analysis of genomic sequence identified 77 additional transcripts. A comprehensive analysis of expression levels of these transcripts in six breast cancer cell lines was carried out by using complementary DNA microarrays. The expression patterns varied from one cell line to another, and several overexpressed genes were identified. Of these, RPS6KB1, MUL, APPBP2, and TRAP240 as well as one uncharacterized expressed sequence tag were located in the two common amplified regions. In summary, comprehensive analysis of the 17q23 amplicon revealed a limited number of highly expressed genes that may contribute to the more aggressive clinical course observed in breast cancer patients with 17q23-amplified tumors.

Footnotes

↵ † O.M. and M.B. contributed equally to this work.
↵ ** To whom reprint requests should be addressed at: National Human Genome Research Institute, National Institutes of Health, 49 Convent Drive, Room 4B24, Bethesda, MD 20892-4465. E-mail: akallion{at}nhgri.nih.gov.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations:

BAC,

bacterial artificial chromosome;

cDNA,

complementary DNA;

CGH,

comparative genomic hybridization;

EST,

expressed sequence tag;

FISH,

fluorescence in situ hybridization;

STS,

sequence tag site;

YAC,

yeast artificial chromosome