High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells

Abstract

Amplification of chromosomal band 11q13 is a common event in human cancer. It has been reported in about 45% of head and neck carcinomas and in other cancers including esophageal, breast, liver, lung, and bladder cancer. To understand the mechanism of 11q13 amplification and to identify the potential oncogene(s) driving it, we have fine-mapped the structure of the amplicon in oral squamous cell carcinoma cell lines and localized the proximal and distal breakpoints. A 5-Mb physical map of the region has been prepared from which sequence is available. We quantified copy number of sequence-tagged site markers at 42-550 kb intervals along the length of the amplicon and defined the amplicon core and breakpoints by using TaqMan-based quantitative microsatellite analysis. The core of the amplicon maps to a 1.5-Mb region. The proximal breakpoint localizes to two intervals between sequence-tagged site markers, 550 kb and 160 kb in size, and the distal breakpoint maps to a 250 kb interval. The cyclin D1 gene maps to the amplicon core, as do two new expressed sequence tag clusters. We have analyzed one of these expressed sequence tag clusters and now report that it contains a previously uncharacterized gene, TAOS1 (tumor amplified and overexpressed sequence 1), which is both amplified and overexpressed in oral cancer cells. The data suggest that TAOS1 may be an amplification-dependent candidate oncogene with a role in the development and/or progression of human tumors, including oral squamous cell carcinomas. The approach described here should be useful for characterizing amplified genomic regions in a wide variety of tumors.

Fig 1.

Physical map of the 11q13 amplicon in oral cancer cell lines. (A) Region of amplification found in each of the 14 amplified cell lines. The red bars indicate the extent of amplification measured by QuMA for each cell line. Dashes at the end of a bar indicate that the amplified region extends outside of the area shown. The BAC contig is shown; a key to the names of the BACs can be found in Table 4, which is published as supporting information on the PNAS web site. (B) Map of the amplicon core showing the location of selected key genes in the amplicon and the QuMA data for five representative cell lines with amplification that define the amplicon core. Also shown are the locations of one new EST () and the gene, TAOS1, both of which are highly amplified. The dashed lines represent the validation results of the primers used in QuMA. MTC, major translocation cluster identified in lymphomas.

Fig 2.

Expression study of the new ESTs in the core of 11q13 amplicon. (A and B) Multiple tissue Northern blots for the two ESTs in the core of the 11q13 amplicon. EST is included in TAOS1. Both show wide tissue expression. (C) EST /TAOS1 is expressed in oral cancer cell lines with 11q13 amplification (UPCI:SCC131, UPCI:SCC056, UPCI:SCC040, UPCI:SCC036, and UPCI:SCC016) and at much lower levels in cell lines without amplification and in normal human oral keratinocytes (UP3–277).

Fig 3.

Identification of the TAOS1 gene. (A) Gene structure of TAOS1. The five exons are labeled 1–5. The coding region is 411 bp and covers all five exons. (B) Amino acid sequence of TAOS1. (C) Sequence alignment of TAOS1 from human (Hs) and mouse (Mm). Black boxes with white letters highlight identical residues, and the “+” signs indicate the conserved residues.

Fig 4.

Expression of the CCND1, OCIM, and TAOS1 genes measured by TaqMan quantitative RT-PCR in the UPCI:SCC OSCC cell lines and the correlation between their gene copy number and gene expression. (A, C, and E) Expression levels of CCND1, OCIM, and TAOS1 in 17 OSCC cell lines; the first 6 cell lines in the graph do not have 11q13 amplification. Data are reported relative to 18S rRNA expression and normalized to normal human oral keratinocytes (ker). (B, D, and F) Correlation of gene copy numbers and expression levels.