Identification of metastasis-associated breast cancer genes using a high-resolution whole genome profiling approach.
OBJECTIVE
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.
Desouki
Mohamed M
MM
Department of Pathology, Medical University of South Carolina, Charleston, SC 29425, USA.
Liao
Shaoxi
S
Huang
Huayi
H
Conroy
Jeffrey
J
Nowak
Norma J
NJ
Shepherd
Lori
L
Gaile
Daniel P
DP
Geradts
Joseph
J
D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D045744:Cell Line, Tumor; D022202:Chromosomes, Artificial, Bacterial; D055028:Comparative Genomic Hybridization; D005260:Female; D018628:Gene Dosage; D016147:Genes, Tumor Suppressor; D006801:Humans; D008207:Lymphatic Metastasis; D008565:Membrane Proteins / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000032:analysis; D059470:Tetraspanins
D008565:Membrane Proteins; D012333:RNA, Messenger; C508125:TSPAN1 protein, human; D059470:Tetraspanins