Chromosomal structure of the amplified region 11q13

Proc Amer Assoc Cancer Res, Volume 46, 2005 889 DNA amplification is a common mechanism to increase expression of genes in human malignancies. The 11q13 region is frequently amplified in carcinomas of the breast (20%), bladder (18%) and head and neck region (36%). The structure and size of these 11q13 amplicons can provide useful information on the mechanism of this specific region and the concomitant selection of the affected genes. For this purpose, we have compared the 11q13 amplifications in 28 head/neck squamous cell carcinomas (HNSCC) as well as 10 cell lines derived from HNSCC that carried 11q13 aberrations that were previously identified by conventional CGH or whole genome array CGH. We generated an 11q13 specific high-density array CGH containing 400 clones from the 11q13 region (20 Mbp; NCBI build 35). With an average of 1 clone per 70 kbp this array can provide us with detailed information on copy number, size and structure of amplified region. The commonly amplified region is restricted to 13 genes including EMS1, FADD and cyclin D1. This amplicon was identified in 28/28 HNSCC and 9/10 HNSCC cell lines. Interestingly, both the centromeric and telomeric amplification boundaries were clustered in regions of a few hundred kb surrounding positions at 67.4 Mbp and 71 Mbp. Both these regions appear to be syntenic transition regions and are implicated as regions with changes in replication timing. This suggests that, both genetic and epigenetic environment determine the site of DNA breakage necessary to initiate DNA amplification. In order to identify the gene that might trigger the biological behavior of carcinomas with 11q13 amplification, we performed quantitative RT-PCR of all 13 genes within the commonly amplified 11q13 region. Not a single, but several genes become upregulated when amplified. This is in good agreement with the fact, that thus far the expression of no single gene in the 11q13 amplicon has been correlated with clinico-pathological features associated with poor prognosis as observed with 11q13 DNA amplification. To find the key gene(s), all amplified and overexpressed genes have to be validated in biological assays.