title: Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes.
abstract: BACKGROUND
  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.
authors.affiliation: Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Center (CNIO), Madrid, E-28029, Spain. lorenzo.melchor@icr.ac.uk
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Melchor
authors.forename: Laura Paula
authors.initials: LP
authors.lastname: Saucedo-Cuevas
authors.forename: Iván
authors.initials: I
authors.lastname: Muñoz-Repeto
authors.forename: Socorro María
authors.initials: SM
authors.lastname: Rodríguez-Pinilla
authors.forename: Emiliano
authors.initials: E
authors.lastname: Honrado
authors.forename: Alfredo
authors.initials: A
authors.lastname: Campoverde
authors.forename: Jose
authors.initials: J
authors.lastname: Palacios
authors.forename: Katherine L
authors.initials: KL
authors.lastname: Nathanson
authors.forename: María José
authors.initials: MJ
authors.lastname: García
authors.forename: Javier
authors.initials: J
authors.lastname: Benítez
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D002869:Chromosome Aberrations; D002882:Chromosomes, Human, Pair 13; D055028:Comparative Genomic Hybridization; D044842:Cullin Proteins / Q000096:biosynthesis / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics*; D005260:Female; D005784:Gene Amplification; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D050680:Transcription Factor DP1 / Q000096:biosynthesis / Q000235:genetics*
chemical_list: C114234:CUL4A protein, human; D044842:Cullin Proteins; D004273:DNA, Neoplasm; D012333:RNA, Messenger; C493735:TFDP1 protein, human; D050680:Transcription Factor DP1