Mining Gene Expression Signature for the Detection of Pre-Malignant Melanocytes and Early Melanomas with Risk for Metastasis

Abstract

BackgroundMetastatic melanoma is a highly aggressive skin cancer and currently resistant to systemic therapy. Melanomas may involve genetic, epigenetic and metabolic abnormalities. Evidence is emerging that epigenetic changes might play a significant role in tumor cell plasticity and metastatic phenotype of melanoma cells.Principal findingsIn this study, we developed a systematic approach to identify genes implicated in melanoma progression. To do this, we used the Affymetrix GeneChip Arrays to screen 34,000 mouse transcripts in melan-a melanocytes, 4C pre-malignant melanocytes, 4C11− non-metastatic and 4C11+ metastatic melanoma cell lines. The genome-wide association studies revealed pathways commonly over-represented in the transition from immortalized to pre-malignant stage, and under-represented in the transition from non-metastatic to metastatic stage. Additionally, the treatment of cells with 10 µM 5-aza-2′-deoxycytidine (5AzaCdR) for 48 hours allowed us to identify genes differentially re-expressed at specific stages of melan-a malignant transformation. Treatment of human primary melanocytes with the demethylating agent 5AzaCdR in combination to the histone deacetylase inhibitor Trichostatin A (TSA) revealed changes on melanocyte morphology and gene expression which could be an indicator of epigenetic flexibility in normal melanocytes. Moreover, changes on gene expression recognized by affecting the melanocyte biology (NDRG2 and VDR), phenotype of metastatic melanoma cells (HSPB1 and SERPINE1) and response to cancer therapy (CTCF, NSD1 and SRC) were found when Mel-2 and/or Mel-3-derived patient metastases were exposed to 5AzaCdR plus TSA treatment. Hierarchical clustering and network analyses in a panel of five patient-derived metastatic melanoma cells showed gene interactions that have never been described in melanomas.SignificanceDespite the heterogeneity observed in melanomas, this study demonstrates the utility of our murine melanoma progression model to identify molecular markers commonly perturbed in metastasis. Additionally, the novel gene expression signature identified here may be useful in the future into a model more closely related to translational research.

Melanocytes in the Skin – Comparative Whole Transcriptome Analysis of Main Skin Cell Types

“…In agreement with previous studies [11] , [13] the expression of ABCC2, DNAJA1, GPR143, MLANA, OCA2, QPCT, RRAGD, TBC1D7 and GPR137B was detected at a higher level in MC compared to KC and FB ( S2 Table ). Majority of these genes are also related to the melanogenesis pathway, controlling the growth and maturation of melanosomes, being involved in melanosome biogenesis, transporting melanin precursor molecules or being candidate genes in melanocytic tumor progression [26] – [30] .…”

The Role of Nuclear Receptor–Binding SET Domain Family Histone Lysine Methyltransferases in Cancer

“…Also, NSD1 expression was upregulated in patient-derived metastatic melanoma cell lines compared to primary epidermal melanocytes. However, during the progression from non-metastatic to metastatic melanoma expression of NSD1 was downregulated (de Souza et al 2012). Furthermore, a transposon screen for frequently occurring mutations in skin tumors of mice revealed that NSD1 is among those genes with significantly decreased expression during tumor development (Quintana et al 2013).…”

Melanoma risk is associated with vitamin D receptor gene polymorphisms

“…Cutaneous melanoma, in its advanced stage, is one of the most aggressive and, despite recent advances in treatment, still incurable diseases, with a median survival of less than 1 year [1][2][3]. The incidence of melanoma is increasing worldwide [4] and the main risk factors for its development are ultraviolet radiation, number of nevi, and skin phototype [5].…”