Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer

Abstract

DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine–guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine–guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.

Keywords:

• cancer diagnosis
• DNA methylation
• epigenomics
• microarray
• sequencing

Acknowledgements

We want to thank Jamie Huynh, Michelle Liu and Nellie Nelson for their critical revisions of this manuscript.

Financial & competing interests disclosure

D Hoon was supported by the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, the Ruth and Martin H. Weil Foundation, Gonda Research Foundation and the National Institute of Health, National Cancer Institute, USA (1R01CA167967-01A1, P01CA029605 Project II/Core C). Both authors were supported by the Associates for Breast and Prostate Cancer Studies (ABCs) Grant Award. Both authors were supported by the Margie and Robert E. Petersen Foundation. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Key issues

• Cancer DNA methylation mapping has rapidly increased with the emergence of high-throughput technologies.

• The traditional view that DNA methylation occurs predominantly at cytosine–guanine (CpG) dinucleotides has been challenged with new findings based on next-generation sequencing approaches.

• The preconception that gene expression is mainly regulated by DNA methylation at promoter CpG islands has been expanded to other functional intra- and intergenic regions.

• Non-CpG methylation in gene bodies is positively correlated with gene expression levels.

• DNA methylation of CpGs outside a CpG island context, such as CpG shores, shelves and the so-called ‘open sea’, demonstrate functionality for gene expression in normal and tumor cells.

• DNA methylation maps are starting to gain importance as current theranostic markers for cancer management.

• Genome-wide and whole-genome DNA methylation mapping approaches are replacing the traditional locus-specific approaches for the discovery of novel cancer biomarkers.

• DNA methylomes generated from formalin-fixed paraffin embedded tissues maintain a high correlation with those generated from frozen tissues. However, DNA methylomes generated from cultured cells present significant differences with formalin-fixed paraffin embedded and frozen tissues.

• In contrast to genetic profiling, DNA methylation mapping can identify the cancer type.

• The human reference methylome of normal tissues is needed to accelerate the discovery of cancer-related DNA methylation variations.

Notes