Research article

Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes

Lorenzo Melchor^1,6 , Laura Paula Saucedo-Cuevas¹ , Iván Muñoz-Repeto¹ , Socorro María Rodríguez-Pinilla² , Emiliano Honrado¹ , Alfredo Campoverde³ , Jose Palacios² , Katherine L Nathanson⁴ , María José García^1,5 and Javier Benítez^1,5

¹  Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Center (CNIO), Madrid, E-28029, Spain

²  Breast and Gynecological Group, Molecular Pathology Program, Spanish National Cancer Research Center (CNIO), Madrid, E-28029, Spain

³  The Institute of Cancer SOLCA, Cuenca, Ecuador

⁴  Department of Medicine, Medical Genetics, Abramson Cancer Center, University of Pennsylvania (UPENN), Philadelphia, PA-19104, USA

⁵  Center for Biomedical Research on Rare Diseases (CIBERER), Calle de Alvaro de Bazan, 10 Bajo, 46010 Valencia, Spain

⁶  Current address: The Breakthrough Breast Cancer Research Center, The Institute of Cancer Research (ICR), SW3 6JB, UK

author email corresponding author email

Breast Cancer Research 2009, 11:R86doi:10.1186/bcr2456

Published:	8 December 2009

Abstract

Introduction

Breast cancer subtypes exhibit different genomic aberration patterns with a tendency for high-level amplifications in distinct chromosomal regions. These genomic aberrations may drive carcinogenesis through the upregulation of proto-oncogenes. We have characterized DNA amplification at the human chromosomal region 13q34 in breast cancer.

Methods

A set of 414 familial and sporadic breast cancer cases was studied for amplification at region 13q34 by fluorescence in situ hybridization (FISH) analysis on tissue microarrays. Defining the minimal common region of amplification in those cases with amplification at 13q34 was carried out using an array-based comparative genomic hybridization platform. We performed a quantitative real-time - polymerase chain reaction (qRT-PCR) gene expression analysis of 11 candidate genes located within the minimal common region of amplification. Protein expression levels of two of these genes (TFDP1 and CUL4A) were assessed by immunohistochemical assays on the same tissue microarrays used for FISH studies, and correlated with the expression of a panel of 33 antibodies previously analyzed.

Results

We have found 13q34 amplification in 4.5% of breast cancer samples, but the frequency increased to 8.1% in BRCA1-associated tumors and to 20% in basal-like tumors. Tumors with 13q34 amplification were associated with high grade, estrogen receptor negativity, and expression of EGFR, CCNE, CK5, and P-Cadherin, among other basal cell markers. We have defined a 1.83 megabases minimal common region of genomic amplification and carried out mRNA expression analyses of candidate genes located therein, identifying CUL4A and TFDP1 as the most likely target genes. Moreover, we have confirmed that tumors with 13q34 amplification significantly overexpress CUL4A and TFDP1 proteins. Tumors overexpressing either CUL4A or TFDP1 were associated with tumor proliferation and cell cycle progression markers.

Conclusions

We conclude that 13q34 amplification may be of relevance in tumor progression of basal-like breast cancers by inducing overexpression of CUL4A and TFDP1, which are both important in cell cycle regulation. Alternatively, as these genes were also overexpressed in non-basal-like tumor samples, they could play a wider role in cancer development by inducing tumor proliferation.