Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis

Abstract

Among the major mechanisms involved in tumorigenesis, DNA methylation is an important epigenetic modification impacting both genomic stability and gene expression. Methylation of promoter-proximal CpG islands (CGIs) and transcriptional silencing of tumor suppressors represent the best characterized epigenetic changes in neoplastic cells. The global cancer-associated effects of DNA hypomethylation influence chromatin architecture and reactivation of repetitive elements. Moreover, recent analyses of cancer cell methylomes highlight the role of the DNA hypomethylation of super-enhancer regions critically controlling the expression of key oncogenic players. We will first summarize some basic aspects of DNA methylation in tumorigenesis, along with the role of dysregulated DNA methyltransferases and TET (Ten-Eleven Translocation)-family methylcytosine dioxygenases. We will then examine the potential contribution of epimutations to causality and heritability of cancer. By reviewing some representative genes subjected to hypermethylation-mediated silencing, we will survey their oncosuppressor functions and roles as biomarkers in various types of cancer. Epithelial-to-mesenchymal transition (EMT) and the gain of stem-like properties are critically involved in cancer cell dissemination, metastasis, and therapeutic resistance. However, the driver vs passenger roles of epigenetic changes, such as DNA methylation in EMT, are still poorly understood. Therefore, we will focus our attention on several aspects of DNA methylation in control of EMT and metastasis suppressors, including both protein-coding and noncoding genes.

Keywords: DNA methylation; biomarkers; cancer stem cells; epithelial-to-mesenchymal transition; metastasis; neoplastic transformation; tumor suppressors.

Figure 1

Scheme of aberrant DNA methylation in cancer cells. Left (orange): Locus-specific hypermethylation of CpG island in promoter sequences leads to transcriptional inactivation of tumor suppressor genes in cancer cells. Right (green): Global cancer-associated hypomethylation affects both unique and repeated sequences. Hypomethylation of unique sequences participates to the activation of oncogenes, mediated by transcriptional enhancers and LOI of imprinted genes involved in cell growth control and tumorigenesis. Hypomethylation of tandem repeats (centromeric and juxta-centromeric satellite DNA), interspersed repeats (Alu and LINE-1), and transposable elements is mainly responsible for chromosomal instability and genomic rearrangements. Loss of DNA methylation within heterochromatic regions corresponding to the LOCKs and LADs (exhibiting high DNA methylation levels and association with nuclear membrane in nonneoplastic cells), results in structural reorganization of large heterochromatin blocks and disorganization of the nuclear membrane.

Figure 2

Scheme of the sequential steps of cancer cell dissemination from primary tumor to distant metastases. EMT indicates the Epithelial-to-Mesenchymal Transition required for the gain of invasive properties and anoikis resistance. MET (Mesenchymal-to-Epithelial Transition) refers to the reversion to the epithelial phenotype at sites of metastatic tumor growth. The numbers indicate various strategies for studying the changes of DNA methylation in the multistep metastatic process. (1) DNA methylome and RNA expression profiling in metastatic tissues vs primary tumor specimens; (2) liquid biopsy: DNA methylome analysis in circulating tumor DNA (in cfDNA extracted from blood samples); (3) liquid biopsy: enrichment by microfluidics devices of (single vs clustered) CTCs from blood samples; (4) detection of EMT and cancer-stem-cell markers, by FACS analyses and cell sorting; (5) DNA methylome and RNA expression profiling in various CTC subpopulations (cancer-stem-cell assays: in vitro colonies and spheroids formation).