Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy

Abstract

Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.

Keywords: DNA methylation; biomarkers; cell-free circulating tumor DNA; circulating melanoma cells; liquid biopsy; melanoma; tumor extracellular vesicles.

Figure 1

Schematic mechanism of DNA methylation and demethylation. In the DNA sequence, unmethylated cytosines are converted to 5’-methylcytosines (addition of the -CH3 group) by DNMTs. This event encompasses the CpG islands enriched in gene promoters and is generally associated with gene silencing. This reaction is potentially reversible due to the activity of TET enzymes, resulting in the loss of DNA methylation (hypomethylation). The white circles indicate unmethylated CpG sites, and the red circles denote methylated CpG sites. The crossed arrow on the left indicates the absence of transcription after DNA promoter methylation. The thick arrow on the right indicates the start of gene transcription as a consequence of promoter demethylation. Abbreviations: DNMTs, DNA methyltransferases; TETs, ten-eleven translocation methylcytosine dioxygenases. The above diagram was created using BioRender (https://biorender.com/ (accession date 8 October 2021)).

Figure 2

Pathways and genes involved in melanoma development. Aberrantly methylated genes and signal transduction pathways frequently altered during melanoma development and/or progression. (a) Shows the MAPK and PI3K-Akt pathways; while (b) depicts the p53, Rb, retinoic acid signaling, and DNA repair pathways. Hypermethylated TSGs are marked with a red dot; the alteration induced in the downstream pathway by TSG hypermethylation is represented by a red cross. The diagrams were created by means of https://biorender.com/ (accession date 8 October 2021).

Figure 3

Liquid biopsy in cancer patients. Circulating tumor cells (CTCs), circulating cell-free tumor DNA (ctDNA), circulating cell-free RNA (cfRNA), and extracellular vesicles (EVs) can be isolated simultaneously from the same blood sample. Their analysis provides real-time information on tumor progression, minimal residual disease, treatment response, and resistance. Abbreviations: CTCs, circulating tumor cells; ctDNA, circulating cell-free tumor DNA; cfRNA, cell-free circulating RNA; EVs, extracellular vesicles. Diagram created by means of Biorender (https://biorender.com/ (accession date 8 October 2021)).