National Cancer Research Institute South of England
Prostate Cancer Collaborative
Research

Identifying genes involved in prostate cancers using Comparative Expressed Sequence Hybridisation analysis

Author
Janet Shipley
Institute of Cancer Research

Tumors are associated with altered or deregulated gene products which affect critical functions such as cell division and differentiation. This may determine the morphological features and biological behaviour of malignancies.

Our aim is to identify involvement of specific chromosomal regions associated with prostate cancers and identify the key genes involved. Work is also directed at assessing any correlations between these changes and clinicopathological data which may ultimately impact on clinical management or highlight novel targets for therapy.

Ribonucleic acid, RNA, is encoded by genes and translates in cells to make proteins. The approach we are taking involves comparing RNA from prostate cancer samples with those from a control sample. The RNAs are treated to differentially tag them with different coloured fluorochromes. These can then be co-hybridised to chromosomes or arrayed clones which represent specific genes.

Aberrant ratios in the intensity of the fluorochromes at either a particular chromosome location or for a particular clone represent a difference in RNA expression levels between a tumour and a control sample (figure 1).

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We have recently developed and validated the methodology to hybridise probes derived from RNA to chromosomes. This completely novel technique (termed Comparative Expressed Sequence Hybridisation, CESH) identifies chromosomal regions corresponding to differential gene expression (Lu et al 2001). CESH produces patterns characteristic for tumour types and subtypes. We have also shown that the changes can be used to predict clinical behaviour in Wilms tumours and some sarcoma (Lu et al 2002; unpublished data). We hypothesize that changes in expression patterns identified by CESH may also be predictive in prostate cancer.
 


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This may address one of the main issues in prostate cancer diagnosis as to which cases identified through prostate-specific antigen (PSA) testing will progress into a life threatening disease and which will not. CESH analysis as illustrated in figure 2

is a rapid approach which has been successfully applied to small biopsy or microdissected samples. This is particularly appropriate to study early stages of prostate cancer and prostate cancer cells microdissected from surrounding normal tissue.

The key chromosomal regions will be identified from statistical analysis of the data and corresponding clinical information. Differences in the same regions may also be identified in cell lines or samples where material is not limiting allowing investigation of these regions in more detail by interogating many clones representing genes from the regions of interest (microarray analysis - figure 3). This may indicated which genes are likely to be involved.

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Key candidate genes will then be investigated in a large number of samples by approaches indicated in figure 4 on order to confirm and identify further correlations with the pathology or clinical behaviour of the tumours.


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Acknowledgements We are grateful to Cancer Research UK and the Freemasons' Grand Charity for their support.

Collaborators
Yong-Jie Lu, Sandrine Rodriguez, Brenda Summersgill and Janet Shipley
Molecular Cytogenetics Team, Institute Cancer Research (ICR), Sutton, Surrey
in collaboration with Sandra Edwards and Colin Cooper (Cell Transformation Team, ICR); Alison Falconer (Cancer Genetics, ICR); Anne Fletcher (Tissue Resources, ICR);
Chris Parker, (Department of Radiotherapy, ICR); Chris Foster (Department Pathology, Liverpool University); Yaxin Zheng and Brian Liu(Brigham and Women's Hospital, Boston, USA)

References
Lu Y-J, Williamson D., Clark J., Wang R., Tiffin N., Skelton L., Gordon T., Williams R., Allan B., Jackman A., Cooper C., Pritchard-Jones K., and Shipley J. (2001) Comparative Expressed Sequence Hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression. Proc Natl Acad Sci (USA). 98: 9197-9202. Highlighted as Editors' Choice in Science 293; 1015.

Lu Y-J, Hing S, Williams R, Pinkerton R, Shipley J. and Pritchard-Jones K. On behalf of the UK Children's Cancer Study Group (UKCCSG) Wilms tumour group. (2001) Chromosome 1q expression profiling predicts relapse in favourable histology Wilms tumour. Lancet - In press.

 
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