Genome-wide expression microarray data of MCSP- and ABCB5-enriched CTCs

Circulating Tumour Cells (CTCs) act as tumour seeds for haematogeneous melanoma spread of melanoma. Since CTCs have been reported to be heterogeneous in melanoma, the characterisation of the different melanoma CTC subpopulations harbours biological and clinical significance. For detection of melanoma CTCs, melanoma-associated markers (i.e. MCSP, melanoma-associated chondroitin sulphate proteoglycan) have been used; however, recent studies have found that melanoma CTCs commonly express ABCB5 (ATP-binding cassette sub-family B member 5) a melanoma-initiating marker. Here, we used a genome-wide expression microarray to interrogate the transcriptome of MCSP-enriched and ABCB5-enriched CTC fraction in order to provide a better understanding of their biology and role in melanoma metastasis. Findings from this study highlited the distinct transcriptional programming of both CTC subpopulations. Blood samples from healthy donors (n=6) and metastatic melanoma patients (n=6) were incubated with magnetic beads coated with antibodies against MCSP or ABCB5 for immunomagnetic enrichment of either MCSP or ABCB5 CTCs. Total RNA was extracted from the total of 24 samples and microarray gene expression profiling was performed uisng the Affymetrix® GeneChip® genome 2.0 ST array protocol (Affymetrix, US). Gene expression data from MCSP or ABCB5 enriched CTCs of healthy donors and melanoma patient blood samples were compared.