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Unformatted text preview: ement in regulation of these processes in melanoma by instigating melanoma‐exclusive mechanisms. 85 Chapter IV – Medic, Rizos and Ziman, 2011 In addition, genomic sites for SOX9, MCAM and CSPG4, even though common for both cell types, show significantly higher fold enrichment in melanoma cells compared to melanocytes. This suggests that PAX3 utilises the same mechanisms (via MCAM and CSPG4) to regulate migration of melanocytes and melanoma cells. In summary, the fourteen potential PAX3 target genes analysed here can be categorised as follows: i) PAX3 targets specific for melanoma (NES, TPD52, PTEN and BCL2L1); ii) PAX3 targets common to both melanocytes and melanoma (MITF, DCT, HES1, SOX9, CCNA2, TGFβ1, MCAM, CSPG4, and CXCR4); and iii) not a PAX3 target, such is NFKβ2). Expression of PAX3 targets in HEM1455 and A2058 We next analysed the expression of the thirteen identified target genes in the two cell lines to confirm that the mRNA profile corresponds to PAX3 binding (Fig. 4.3). Results here show downregulation of MITF, BCL2L1, and PTEN in A2058 compared to HEM1455, by 4.96*, 2.47, and 1.81*‐fold, respectively (asterisk indicates statistical significance, p<0.05). HES1 shows no change in expression levels between the two cell lines (0.86‐fold). By contrast, the remaining nine genes show upregulation in A2058 cells compared to HEM1455: DCT (2.74), SOX9 (6.13*), NES (10.66*), CCNA2 (2.17*), TPD52 (6.09*), TGFβ1 (3.24*), MCAM (38.04*), CSPG4 (2.37*), and CXCR4 (11.35*) (asterisk indicates statistical significance, p<0.05). Figure 4.3. PAX3 “target” gene expression levels in melanocyte and melanoma cells. Relative expression of PAX3 targets was analysed by RT‐qPCR. Asterisk (*) indicates statistically significant fold difference, p<0.05 86 Chapter IV – Medic, Rizos and Ziman, 2011 We observe here a correlation between PAX3 binding to the target gene and its expression level; ie genes showing statistically significant enrichment in PAX3 bin...
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