D11S146 and BCL1 are physically linked but can be discriminated by their amplification status in human breast cancer

Disruption of oncogene/tumor suppressor networks during human carcinogenesis

Oncogenes were initially discovered as retrovirally transmitted tumor causing agents. The realization that such retroviral oncogenes constitute specifically altered versions of cellular genes-proto-oncogenes, was a landmark discovery that set the stage for the molecular and mechanistic era of cancer research. Moreover, the studies on oncogene functions have been instrumental in delineating many of the paradigms of cellular signal transduction. In contrast to the original studies in animals, oncogenic activation through retroviral transmission does not appear to be a major factor in human tumorigenesis. However, oncogenes are frequently activated by gain of function mutations or fusions with other genes, or they are aberrantly expressed due to amplification, increased promoter activity, or protein stabilization, and hence they play integral roles in the genesis of human tumors.

Framework YAC contig anchored into a 3.2-Mb high-resolution physical map in proximal 11q13

Despite the presence on band q13 of chromosome 11 of a number of genes predisposing individuals to various human diseases, most of this genomic region remains loosely mapped. Moreover, there is a relative dearth of yeast artificial chromosome (YAC) contigs from genome-wide studies: YACs are irregularly distributed over this chromosomal region and have not been arranged into contigs. We have thus undertaken fine-scale mapping of a 3.2-Mb region flanked by ACTN3 and FGF3. Since this region has demonstrated a high degree of YAC instability, we have established a framework contig by anchoring YACs and cosmids into a high-resolution physical map based on fluorescence in situ hybridization and long-range restriction mapping. The 3.2-Mb area studied includes the boundaries of regions thought to contain genes predisposing individuals to osteoporosis-pseudoglioma syndrome and insulin-dependent diabetes mellitus, as well as genes driving amplification events in human carcinomas. Another feature of this genomic area is that it cross-hybridizes to nonsyntenic regions of the genome. In addition, it spans the region where syntenic conservation with mouse chromosome 19 ends, making clones that we have anchored there valuable tools in understanding genome evolution.

The involvement of the chromosome 11q13 region in human malignancies: cyclin D1 and EMS1 are two new candidate oncogenes--a review

Amplification of oncogenes has been observed frequently in various human malignancies and might be of clinical relevance. In the last decade, the exploration of oncogene activation due to DNA amplification in cancer research has mainly focussed on three aspects: (i) the assessment of oncogene amplification as a prognostic marker for survival of cancer patients, (ii) the development of reliable methods for detection of tumors which harbor DNA amplification of oncogenes and (iii) the identification of the gene or genes responsible for the biological (prognostic) significance in tumors with DNA amplification and the characterization of these candidate proto-oncogenes that might help to elucidate their normal function and the role in tumor development. In this review, these three aspects will be highlighted with regard to DNA amplification of the chromosome 11q13 region. Chromosome 11q13 amplification has been found frequently in certain human malignancies; in cancer of the breast and of the head and neck region, amplification of this region is observed in 13 and 29% of tumors, respectively. The 11q13 amplification has been reported to be of clinical relevance in these cancers, since patients with this amplification show a poor clinical course of disease. The amplified 11q13 region is estimated to be 3-5 Mb in size and to harbor many (putative) genes. Recently, two candidate genes, CCND1 and EMS1, were identified which were both over-expressed in all carcinomas with an 11q13 amplification. Therefore, the activation of these genes might confer the selective advantage to these tumors. In addition, the characterization of these two novel genes sustained their potential role in carcinomas with 11q13 amplification.

Chromosome 11q13 markers and D-type cyclins in breast cancer

One in six primary human breast cancers has DNA amplification centered on the cyclin D1 gene (CCND1) on chromosome 11q13. This genetic abnormality is preferentially associated with estrogen-receptor positive tumors and may define a sub-class of patients with an adverse prognosis. Although CCND1 has the credentials of a cellular oncogene, being a target for chromosomal translocation and retroviral integration, the 11q13 amplicon encompasses several other markers and CCND1 is not the only candidate for the key gene on the amplified DNA. To assess their relative importance, we have constructed a physical map of the amplified DNA and compared the extent and frequency of amplification across the region. Since it is likely that the gene providing the selective force for amplification will be expressed at elevated levels, we have also examined expression of both RNA and protein. By these criteria, cyclin D1 remains the strongest candidate for the key oncogene on the amplicon and we are currently investigating the functional consequences of its over-expression.

Oesophageal cancer and amplification of the human cyclin D gene CCND1/PRAD1

The human CCND1/PRAD1 gene, located in the 11q13 chromosomal region, encodes a cyclin D protein with potential oncogenic capacity and is involved in several human malignancies. The amplification and expression status of CCND1 was investigated in a series of oesophageal tumours. CCND1 is amplified in 54% and overexpressed in 63% of the tumours of the squamous cell type.

Patterns of DNA amplification at band q13 of chromosome 11 in human breast cancer

In an attempt to verify the nature of amplification events at band q13 on chromosome 11 we surveyed the amplification status of ten molecular markers specific for this region (GSTP, SEA, D11S97, D11S146, BCLI, PRADI/CCNDI, HST/FGF4, INT2/FGF3, EMSI, and DIIS833E) in a panel of 389 primary breast carcinoma DNA samples. Eighty-eight tumors (23%) showed at least one of these markers amplified, but in a majority of the cases amplification encompassed more than one of the tested loci. Our data confirm that amplicons at 11q13 can cover large portions of DNA and are consistent with the existence of several cores of amplification. One important core seems to be, as previously described, centered around PRADI/CCNDI; 57 tumors (14.7%) showed amplification at PRADI/CCNDI either alone (one tumor) or along with amplification of BCLI or INT2/FGF3. The level of amplification of PRADI/CCNDI sometimes exceeded that of surrounding markers. Three additional amplification events occurring independently of amplification of PRADI/CCNDI were also detected. Centromeric to BCLI, probes to DIIS97, and DIIS146 detected amplification in 60 tumors (15.4%) and were often the only amplified markers. Telomeric to INT2/FGF3, DIIS833E was found amplified alone in ten tumors, and it was the most amplified marker in another six cases. At a shorter distance of INT2/FGF3, EMSI was the only amplified marker in two tumors, with a level of amplification that could exceed that of PRADI/CCNDI and DIIS833E. Our data thus suggest the existence of four independent amplified regions within band 11q13 in breast cancer.

Genomic organization and localization of the gene encoding human preprogalanin

An approximately 35-kb region of genomic DNA encoding the human preprogalanin gene including 5' and 3' flanking sequences has been cloned and characterized. Exons and flanking introns were sequenced to determine the structural organization of the gene. The gene spans 6.5 kb, with the first exon encoding only the 5' untranslated sequence. The coding region of preprogalanin and the 3' untranslated sequence is divided into five exons. Using high-resolution fluorescence in situ hybridization, the position of the single human preprogalanin gene was localized to chromosome 11q13.3-q13.5. Several oncogenes have been mapped to this region, which is also the breakpoint for the translocation t(11;14)(q13;q32) in chronic lymphocytic leukemia and diffuse B-cell lymphoma.

Amplified region of chromosome band 11q13 in breast and squamous cell carcinomas encompasses three CpG islands telomeric of FGF3, including the expressed gene EMS1

DNA markers that map within the karyotypically defined band q13 on human chromosome 11 are amplified in a subset of mammary and squamous cell carcinomas. It is assumed that the amplified DNA includes a critical gene (or genes) whose overexpression provides a selective force in the development of the tumor. To help identify such genes, we have begun to construct a physical map of CpG islands in the region, making use of a squamous cell carcinoma cell line (UMSCC2) in which the 11q13 region is amplified 11-fold. We previously described the proximal end of this amplicon and the order of markers extending approximately 800 kb centromeric of the FGF3 locus (formerly INT2). We now report the use of chromosome jumping techniques to define additional CpG islands that lie distal to FGF3. These map within the amplified region in UMSCC2 cells and the most telomeric corresponds to the EMS1 gene. The data imply that the amplified DNA in UMSCC2 cells extends for over 1,500 kb and includes at least 7 potential genes. EMS1 and CCND1 (formerly PRAD1), the best candidates for the key gene on the 11q13 amplicon, are > or = 800 kb apart.

A 14-Mb physical map of the region at chromosome 11q13 harboring the MEN1 locus and the tumor amplicon region

We have constructed a physical map of chromosome 11q13, using 54 DNA markers that had been localized to 11q13.1----q13.5 by means of somatic hybrid cell panels. Although the map has some gaps, it spans nearly 14 Mb and includes the region containing the gene responsible for multiple endocrine neoplasia type 1 (MEN1) and also the region that is amplified in several types of malignant tumors. As the estimated average distance between each locus is roughly 300 kb, the markers reported here will be valuable resources for construction of contig maps with yeast artificial chromosomes and/or cosmid clones. Furthermore, these clones will be useful in efforts to identify the MEN1 gene and in analyses of the amplification units present at 11q13 in certain tumors.

Linkage map of a region of human chromosome band 11q13 amplified in breast and squamous cell tumors

DNA amplification involving markers on human chromosome band 11q13 is a consistent feature of several major cancers, notably adenocarcinoma of the breast and squamous cell carcinoma of the head, neck, lung, and esophagus. Since the presence of the amplification may be clinically significant, by defining a subset of patients at increased risk, it is important to establish which of the several genes on the amplified DNA provides the selective force. Here we describe a physical map of the centromeric end of the amplified DNA as it exists in a particular squamous carcinoma cell line (UMSCC2) and establish an unambiguous order for several known markers in the region, including pMS51/D11S97, pHB159/D11S146, BCL1, PRAD1/D11S287, HSTF1/FGF4 and INT2/FGF3. Significantly, PRAD1 is within 120-150 kb of the BCL1 translocation breakpoint and the data identify a new CpG island (D11S814) between PRAD1 and HSTF1. The ordering of the HSTF1 and INT2 genes and the clustering of CpG islands in the region have important implications in assessing whether the frequently observed amplifications at 11q13 are centered on one or more genes.

Localization of 11q13 loci with respect to regional chromosomal breakpoints

We have employed two strategies to map 13 markers located at 11q13. First, we used pulsed-field gel electrophoresis of DNA fragments obtained with methylation-sensitive restriction enzymes. The markers used in this study were scattered over 8.4 Mb and, for most of them, could not be linked one to another. A second mapping strategy employed hybridization to either DNA of somatic hybrids containing various parts of the long arm of chromosome 11 or metaphase chromosomes of a B-cell line containing the t(11;14)(q13;q32) translocation. We were able to sort out the centromeric from the telomeric probes with respect to translocation breakpoints taken as reference chromosomal landmarks by this approach. BCL1, which corresponds to the region where the t(11;14)(q13;q32) translocation breakpoints are clustered, appears as a boundary between two areas of human/mouse homology present in conserved syntenic regions on mouse chromosomes 7 and 19.

New gene in the homologous human 11q13-q14 and mouse 7F chromosomal regions

Alterations in the chromosomal region 11q13-11q14 are involved in several pathologies in which most of the key genes remain to be identified. In an effort to isolate as many candidates as possible, we are cloning genes from this region. We report here the mapping of a new sequence from 11q13.5-11q14. This sequence, designated D11S833E, putatively encodes a new gene, provisionally named GARP. We cloned its homologous sequence in the mouse and located it on Chromosome (Chr) 7, region F. The human and mouse genes belong to a conserved group of synteny. This, together with the similar conservation of the FGF and TYR genes, indicates that the human 11q13-q14 and mouse 7E-7F regions share homology.