Formalin-fixed paraffin-embedded (FFPE) tumour samples may provide crucial data regarding biomarkers for neoplasm progression. Analysis of gene expression is frequently used for this purpose. Therefore, mRNA expression needs to be normalized through comparison to reference genes. In this study, we establish which of the usually reported reference genes is the most reliable one in cutaneous malignant melanoma (MM) and cutaneous squamous cell carcinoma (CSCC). ACTB, TFRC, HPRT1 and TBP expression was quantified in 123 FFPE samples (74 MM and 49 CSCC biopsies) using qPCR. Expression stability was analysed by NormFinder and Bestkeeper softwares, and the direct comparison method between means and SD. The in-silico analysis with BestKeeper indicated that HPRT1 was more stable than ACTB and TFRC in MM (1.85 vs. 2.15) and CSCC tissues (2.09 vs. 2.33). The best option to NormFinder was ACTB gene (0.56) in MM and TFRC (0.26) in CSCC. The direct comparison method showed lower SD means of ACTB expression in MM (1.17) and TFRC expression in CSCC samples (1.00). When analysing the combination of two reference genes for improving stability, NormFinder indicated HPRT1 and ACTB to be the best for MM samples, and HPRT1 and TFRC genes for CSCC. In conclusion, HPRT1 and ACTB genes in combination are the most appropriate choice for normalization in gene expression studies in MM FFPE tissue, while the combination of HPRT1 and TFRC genes are the best option in analysing CSCC FFPE samples. These may be used consistently in forthcoming studies on gene expression in both tumours.

Melanoma is one of the most common cancers in the world. The main routes of tumor progression are related to angiogenesis and lymphangiogenesis. These routes can occur by local invasion, which is called angiolymphatic invasion (ALI). In this study, we assess gene expression of relevant biomarkers of angiogenesis and lymphangiogenesis in 80 FFPE melanoma samples to determine a molecular profile that correlates with ALI, tumor progression, and disease-free survival. The results were enhanced by a posttranscriptional analysis by an immunofluorescence assay. Three SNPs in the VEGFR-2 gene were genotyped in 237 malignant melanoma (MM) blood DNA samples by qPCR. A significant correlation was found for LYVE-1 and ALI, qualitative (P = 0.017) and quantitative (P = 0.005). An increased expression of protein LIVE-1 in ALI samples supported these results (P = 0.032). VEGFR2 was lower in patients who showed disease progression (P = 0.005) and protein VEGFR2 posttranscriptional expression decreased (P = 0.016). DFS curves showed differences (P = 0.023) for VEGFR2 expression detected versus the absence of VEGFR2 expression. No significant influence on DFS was detected for the remaining analyzed genes. Cox regression analysis suggested that VEGFR2 expression has a protective role (HR = 0.728; 95% CI = 0.552-0.962; P = 0.025) on disease progression. No significant association was found between any of the studied SNPs of VEGFR2 and DFS or progression rate. Our main results suggest that LYVE-1 gene expression is closely related to ALI; the relationship with the development of metastases in MM deserves further studies. Low expression of VEGFR2 was associated with disease progression and the expression of VEGFR2 correlates with an increased DFS. Melanoma