New candidate breast cancer genes

5 August 2005

The genetic mutations underlying the development of the common, non-familial forms of breast cancer (the most common form of cancer among women in the UK) are an area of ongoing research. A region of human chromosome 8 (8p11-12) is frequently amplified in breast cancer cells, but the oncogene responsible for this has yet to be identified, although various candidate genes have been proposed. New research by Cambridge based scientists, published in Oncogene, presents evidence implicating four new candidate genes in breast cancer [Garcia MJ et al. (2005) Oncogene 24, 5235−5245].

The researchers analysed gene expression of the the 8p11−12 region in samples from 33 breast tumors, 20 ovarian tumors and 27 breast cancer cell lines at high resolution, using a technique called array comparative genomic hybridization, or array-CGH. Low resolution analysis of genome-wide copy-number changes was also performed, and identified certain regions commonly gained, lost or amplified in the tumour samples; 8p11−12 was one of the regions found to be amplified. In all, 13 samples showed amplification of 8p11−12: eight out of 33 breast tumours (24%), four out of 27 (15%) breast cancer cell lines and one out of 20 (5%) ovarian tumours. The size of the amplified region varied from 1-11 Mb. Some breast tumour samples also showed small regions of loss within 8p11−12. Fluorescence in situ hybridization (FISH) was performed on a selection of tumour samples, and showed reasonable agreement with the copy-number changes estimated by array-CGH.

Within a defined 1 Mb minimal common region of amplification, a total of six genes were identified: FLJ14299, C8orf2, PROSC, GPR124, BRF2 and RAB11FIP1; these do not include those previously proposed as putative oncogenes for the 8p11−12 amplicon. Real-time quantitative PCR (rtq-PCR) and/or oligo-microarray profiling was used to analyse expression of 10 genes in the 8p11−12 region (including FLJ14299 , GPR124 and RAB11FIP1) from 51 breast cell tumours and cell lines, to determine whether amplification of the region was associated with gene overexpression. 49 of these samples showed overexpression of most genes within the region. GPR124 and FLJ14299 showed moderate levels of increased expression compared with normal cells (13-fold and 4-fold) whilst RAB11FIP1 displayed a minimal increase of 1.6-fold. Comparison with gene expression in samples where the 8p11−12 region was not amplified suggested that expression levels of several genes including FLJ14299, RAB11FIP1, C8orf2 and BRF2 differed significantly between the two groups, although overexpression of GPR124 was not found to be specifically related to the presence of amplification and PROSC did not show consistent overexpression.

The authors propose that the genes FLJ14299, C8orf2, BRF2 and RAB11FIP are the most likely candidates for the oncogene driving amplification of 8p11−12 in the development of breast cancer. FLJ14299 is a novel gene containing zinc-finger domains, functional regions that bind to nucleic acids and which are present in some known tumour-related genes. BRF2 is the gene for a RNA polymerase III transcription factor complex subunit; RAB11FIP1 encodes the Rab coupling protein, which interacts with a group of enzymes involved in the regulation of intracellular transport vesicles. Little is known about the function of C8orf2. The authors also note that although the presence of 8p11−12 amplification in the 33 breast tumour samples showed no significant association with clinical features such as metastasis, recurrence or survival, larger numbers of samples would be required for a proper evaluation of any associations.

Comment: This research implicates a further four genes as potential oncogenes driving the development of breast cancer, although further research is required to validate any of these genes as a genuine oncogene. Moreover, as only around a quarter of the samples analysed showed amplification of the 8p11−12 region, even the definitive linking of one of these candidate genes with 8p11−12 amplification would only confirm one small contribution to the highly complex genetic processes that lead to the formation of breast cancer. However, it may be a a valuable piece of the puzzle. Lead author Professor Carlos Caldas has said that, although they have not identified any of the candidate genes as a key oncogene: "we know that women who have increased copies of this fragment of chromosome eight have a poor prognosis

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