Transgenic expression of the SV40 large T-antigen under control of the insulin gene regulatory region in the RIP-Tag mouse model results in development of islet-cell carcinomas. Tumorigenesis involves a distinct progression as the islets move from normal quiescence to a hyperproliferative state, followed by angiogenic induction and finally to reduced apoptosis, resulting in solid tumour formation. LOH and CGH analyses have identified putative tumour-suppressor genes, as recurrent loss of DNA on chromosomes 16 (LOH16) and 9 (LOH9) have been observed corresponding to the angiogenic and reduced apoptosis switches in tumour development, respectively. Although partial loss of chromosomal DNA in some tumours and tumour-derived cell lines (TCL) has narrowed the regions of interest, the regions remain large (∼15 Mb on chromosome 9 and ∼12 Mb on chromosome 16) and no known tumour-suppressor genes are known to map to these loci. To further delineate each region and to facilitate gene discovery, we are using an array-CGH (CGHa) approach using BAC clones as array elements that map to LOH9 or LOH16. Thus far, 12 BACs have been isolated from the LOH9 region based on known marker and gene sequence information available in public databases and FISH mapped to confirm chromosomal location. The clones are then arrayed onto silynated glass slides using using a high-throughput, custom-made arraying device developed at UCSF. Additional BAC and P1 clones known to map elsewhere in the mouse genome serve as controls in the CGHa analyses. Tumour and TCL genomic DNA derived from RIP-Tag mice are being used for CGHa to analyse DNA copy-number loss and to identify BAC clones consistently deleted in the LOH regions of interest.
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