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S. L. Lake, B. E. Damato, A. F. G. Taktak, S. E. Coupland; High Resolution Analysis of Chromosomes 3 and 8 in Metastasizing Uveal Melanoma Reveals Genes of Interest in Metastatic Progression. Invest. Ophthalmol. Vis. Sci. 2010;51(13):3806.
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© ARVO (1962-2015); The Authors (2016-present)
Monosomy 3 and polysomy 8q are strongly associated with metastatic death from uveal melanoma (UM). Using multiplex ligation-dependent probe amplification (MLPA) and SNP microarrays (aSNP), we investigated changes in copy number and loss of heterozygosity (LOH) of genes on these chromosomes in fatal metastasizing primary UM. The aim of this study was to identify genes consistently perturbed only in metastasizing UM that are therefore potentially key to metastatic death.
A rare subset of 19 disomy-3 fatal (Di3F), formalin-fixed, paraffin-embedded UM were analysed using the P027 MLPA assay. Disomy of chromosome 3 had previously been detected by fluorescence in situ hybridisation (FISH).A further four Di3F-UM, two monosomy-3 fatal UM (M3F) and three disomy-3 non-metastic UM (Di3S) were analysed by aSNP. The Affymetrix SNP 6.0 chip was applied to DNA from snap-frozen tissues and data analysed using the Partek Genomic Suite. Aberrant genes not exclusive to metastatic UM (i.e., also perturbed in the Di3S-UM) were not considered essential for metastasis.
Despite showing apparent disomy 3 with FISH, two UM were found to have monosomy 3 by MLPA and a third showed loss of 11 of the 13 loci tested, indicating large areas of chromosome 3 deletion. None of the 13 genes detected on chromosome 3 was consistently deleted in all fatal Di3F-UM. Amplification of the MYC and DDEF1 loci on 8q occurred in most, but not all Di3F-UM.aSNP analysis revealed 95 deleted genes on chromosome 3 that were exclusive to Di3F-UM and three of these also showed LOH. Genes whose known function suggests they are of particular relevance to metastatic progression include PPARG, ROBO1 and RBM5 on chromosome 3. In the M3M-UM, eight genes on the remaining copy of chromosome 3 showed LOH. On chromosome 3, no consistent homozygous deletions and only one gene with LOH (SLC6A6) were observed exclusively in fatal metastatic UM. On chromosome 8q, 287 genes were amplified exclusively in metastatic UM; 17 of these genes also showed LOH.
Aberration of specific genes in metastasizing fatal UM is more readily detected using aSNP than with MLPA. Deletion and/or LOH of specific genes on chromosome 3 and amplification of genes on 8q are exclusive in metastasizing fatal UM. Validation and functional investigation of these candidate metastasis-suppressor genes is essential to help identify novel cell signalling targets for therapeutic intervention.
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