Identification of metastasis-associated breast cancer genes using a high-resolution whole genome profiling approach

• Published in: Journal of cancer research and clinical oncology Vol. 137; no. 5; pp. 795 - 809
• Main Authors: Desouki, Mohamed M., Liao, Shaoxi, Huang, Huayi, Conroy, Jeffrey, Nowak, Norma J., Shepherd, Lori, Gaile, Daniel P., Geradts, Joseph
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.05.2011; Springer; Springer Nature B.V
• Subjects: Antineoplastic agents; Biological and medical sciences; Breast cancer; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Cancer Research; Cell Line, Tumor; Chromosomes, Artificial, Bacterial; Comparative Genomic Hybridization; Female; Gene Dosage; Genes; Genes, Tumor Suppressor; Genomics; Gynecology. Andrology. Obstetrics; Hematology; Humans; Internal Medicine; Lymphatic Metastasis; Mammary gland diseases; Medical sciences; Medicine; Medicine & Public Health; Membrane Proteins - genetics; Metastasis; Oncology; Original Paper; Pharmacology. Drug treatments; Polymerase Chain Reaction; RNA, Messenger - analysis; Tetraspanins; Tumors; Suppressor genes; Breast cancer; Metastasis; TSPAN1; Array CGH; Tetraspanins; High resolution; Breast disease; DNA chip; Identification; Malignant tumor; Gene expression; Suppressor gene; Array; Mammary gland diseases; Comparative genomic hybridization; Breast metastasis; Genetics; Genome; Cancer; Tetraspanin
• ISSN: 0171-5216; 1432-1335
• DOI: 10.1007/s00432-010-0937-1

Purpose We employed a whole genome tumor profiling approach in an attempt to identify DNA copy number alterations (CNAs) and new candidate genes that are correlated with the metastatic potential of a primary breast carcinoma and with progression at the metastatic site. Methods Fifty-four small (≤2 cm), high grade, ER-positive, formalin-fixed invasive ductal carcinomas were suitable for whole genome profiling analysis. Twenty-four of them did not form metastases within 5–10 years (unmatched primaries, UP). Thirty tumors had at least one synchronous axillary lymph node metastasis (matched primaries, MP; matched lymph node metastases, ML). Genomic DNA was hybridized to high density (19k) BAC arrays. Statistical analysis revealed differential distributions of CNAs between UP and MP and between MP and ML, respectively. We selected 27 candidate genes for validation experiments using quantitative (Q-)PCR of genomic DNA. For tetraspanin TSPAN1, we studied mRNA expression levels in a separate cohort of primary breast carcinomas and in breast cell lines. Results Matched primary (MP) tumors had a threefold higher rate of DNA copy number losses compared to UP tumors. In the UP-MP comparison, 186 BACs were differentially amplified or deleted. Most of them were localized to chromosomes 7p, 16q and 18q. In the MP-ML comparison, 131 BACs showed differential CNAs. Most of them were localized to chromosomes 1q and 20. By Q-PCR, seven candidate genes could be confirmed to show differential distributions of CNAs. TSPAN1 was amplified in UP and deleted in MP tumors. The gene was markedly downregulated in ER-negative and high-grade breast cancers. Conclusions Metastasizing tumors had a higher rate of deletions, suggesting possible inactivation of metastasis suppressor genes. We provide preliminary evidence that TSPAN1 may be another important breast cancer suppressor gene belonging to the tetraspanin superfamily.