J Cancer Res Clin Oncol (2011) 137:795–809 DOI 10.1007/s00432-010-0937-1 123 ORIGINAL PAPER IdentiWcation of metastasis-associated breast cancer genes using a high-resolution whole genome proWling approach Mohamed M. Desouki · Shaoxi Liao · Huayi Huang · JeVrey Conroy · Norma J. Nowak · Lori Shepherd · Daniel P. Gaile · Joseph Geradts Received: 3 July 2010 / Accepted: 5 July 2010 / Published online: 3 August 2010  Springer-Verlag 2010 Abstract Purpose We employed a whole genome tumor proWling approach in an attempt to identify DNA copy number alter- ations (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-posi- tive, formalin-Wxed invasive ductal carcinomas were suit- able for whole genome proWling 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 diVerential 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 diVer- entially ampliWed or deleted. Most of them were localized to chromosomes 7p, 16q and 18q. In the MP-ML compari- son, 131 BACs showed diVerential CNAs. Most of them were localized to chromosomes 1q and 20. By Q-PCR, seven candidate genes could be conWrmed to show diVeren- tial distributions of CNAs. TSPAN1 was ampliWed in UP and deleted in MP tumors. The gene was markedly down- regulated 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 suppres- sor gene belonging to the tetraspanin superfamily. Keywords Array CGH · Breast cancer · Metastasis · Suppressor genes · Tetraspanins · TSPAN1 Introduction One of the hallmarks of human breast cancer is its marked heterogeneity at many diVerent levels including histopa- thology, biomarker expression, clinical aggressiveness, and response to therapy. In the great majority of cases, patient survival is determined by the presence or absence of distant metastases. It is likely that the complex metastatic cascade M. M. Desouki Department of Pathology, Medical University of South Carolina, Charleston, SC 29425, USA S. Liao · J. Geradts (&) Department of Pathology, DUMC 3712, Duke University Medical Center, Durham, NC 27710, USA e-mail: joseph.geradts@duke.edu H. Huang Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, BuValo, NY 14263, USA J. Conroy · N. J. Nowak Department of Cancer Genetics, Roswell Park Cancer Institute, BuValo, NY 14263, USA L. Shepherd · D. P. Gaile Department of Biostatistics, State University of New York, BuValo, NY 14203, USA