Novel MITF targets identified using a two‐step DNA microarray strategy

Abstract

Malignant melanoma is a chemotherapy-resistant cancer with high mortality. Recent advances in our understanding of the disease at the molecular level have indicated that it shares many characteristics with developmental precursors to melanocytes, the mature pigment-producing cells of the skin and hair follicles. The development of melanocytes absolutely depends on the action of the microphthalmia-associated transcription factor (MITF). MITF has been shown to regulate a broad variety of genes, whose functions range from pigment production to cell-cycle regulation, migration and survival. However, the existing list of targets is not sufficient to explain the role of MITF in melanocyte development and melanoma progression. DNA microarray analysis of gene expression offers a straightforward approach to identify new target genes, but standard analytical procedures are susceptible to the generation of false positives and require additional experimental steps for validation. Here, we introduce a new strategy where two DNA microarray-based approaches for identifying transcription factor targets are combined in a cross-validation protocol designed to help control false-positive generation. We use this two-step approach to successfully re-identify thirteen previously recorded targets of MITF-mediated upregulation, as well as 71 novel targets. Many of these new targets have known relevance to pigmentation and melanoma biology, and further emphasize the critical role of MITF in these processes.

Signatures of MicroRNAs and Selected MicroRNA Target Genes in Human Melanoma

“…S1), TYR (tyrosinase), TRPM1 (transient receptor potential cation channel 1), MLANA (Melan-A), and others]. All of these genes have previously been implicated in melanoma development (25)(26)(27). We further validated and confirmed the array-based expression levels for four additional genes [CDKN1B (p27), CDK6, E-cadherin, and N-cadherin] for NHEM, IGR39, and IGR37 ( Supplementary Fig.…”

The MITF family of transcription factors: Role in endolysosomal biogenesis, Wnt signaling, and oncogenesis

“…In these datasets MITF was found bound to promoters of many lysosomal genes [15]. Furthermore, DNA microarray analysis of MITF targets had also identified lysosomal genes such as acid Ceramidase (ASAH1), GM2 ganglioside activator (GM2A), and various ATPases [50]. Finally, MITF was known to activate transcription of the lysosomal genes acid phosphatase 5 (ACP5), chloride channel voltage-sensitive 7 (CLCN7), osteopetrosis-associated transmembrane protein 1 (OSTM1) and cathepsin K [51][52][53].…”

Control of melanocyte differentiation by a MITF–PDE4D3 homeostatic circuit

“…The transcriptional regulation of PDE4D3 by MITF is particularly notable because MITF is a central regulator of the pigmentation cascade via targeting of numerous enzymes and other factors important for melanocyte-specific synthesis, maturation, and transport of melanin. Interestingly, examination of a gene expression data set from MITF-overexpressing melanoma cells showed PDE4D up-regulation by MITF (Hoek et al 2008). Also, PDE4D was found to be regulated by the MC1R pathway in mouse melanocytes (Le Pape et al 2008).…”