Malignant melanoma is one of the most aggressive and deadliest forms of cancer, characterised by early metastasis, bad prognosis and poor survival. Unfortunately, the incidence of melanoma is increasing each year, with little improvement in respect to treatment for metastatic disease, which generally fails to respond to conventional chemotherapy. So far, only high-dose interferon alpha 2b (IFNa2b) has shown to have a beneficial effect on relapse-free and overall survival, by 20-30%, in stage III disease; however, no treatments have yet displayed significant increases in overall survival for distant metastasis or stage IV disease.

Gene expression profiling experiments have begun to identify differences in transcriptomic patterns in melanoma progression. A key study by Winnepenninckx et al. (2006) represents one of the most extensive transcriptomic investigation of melanoma to date, where a 254-gene classifier for 4-year distant metastasis–free survival was determined. In further experimental work, several down regulated genes were shown to be DNA methylated- which causes a loss of expression of tumour suppressor genes, which may in turn contribute to the progression of cancer .

apply the latest developments in tissue microarray (TMA), DNA methylation and in vitro techniques to fast-track validation of putative melanoma targets identified from transcriptomic screens.

The main goals of this Target-Melanoma is as follows

• Identification of methylated genes involved in melanoma progression (benign nevi to metastasis) and methylation profiling in clinical samples.
• Validation and functional interrogation of melanoma progression-associated genes via tissue microarray (TMA) technologies and in vitro analysis.

Our first goal is to identify novel methylated genes via high-throughput screening methods and in silico analysis of existing transcriptomic datasets for the presence of CpG islands. These targets will then be validated on the extensive melanoma cohorts available to the consortium.

The following specific objectives are envisaged:

• To identify novel methylated genes using high-throughput approaches.
• To analyse gene expression data generated by Winnepenninckx et al. to predict methylation targets.
• To validate these methylation targets by qualitative and quantitative methylation-specific PCR (MSP) and determine if these methylation events correlate with melanoma progression.

Our second goal is to validate genes that associate with melanoma progression and prognosis. For this aspect of the project, we will concentrate on the application of TMA technology and associated image analysis approaches to validate molecular determinants of melanoma progression. These targets will then be functionally validated by in vitro studies.

The following specific objectives are envisaged:

• To examine the physiological relevance of findings from gene expression profiling data via the use of TMAs.
• To develop and apply automated image analysis approaches to immunohistochemically stained melanoma TMAs. 
• To determine the functional relevance of prioritised genes of interest in vitrovia gene knockdown and overexpression approaches.