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  • Review Article
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Early detection

The power and the promise of DNA methylation markers

Key Points

  • Cytosine-5 DNA methylation occurs in mammals at CpG dinucleotides. About 70% of the CpG dinucleotides in the mammalian genome are methylated.

  • The complexity of varying distributions of methylated cytosines across the approximately 50 million CpG dinucleotides of each mammalian genome in a DNA sample that is derived from a heterogenous tissue sample is a diagnostic dream and an analytical nightmare.

  • A nomenclature for the three principal approaches to methylation analysis — methylation content, methylation levels and methylation patterns — is proposed. The latter two types of analysis can be performed at multiple sites in the genome to yield methylation profiles.

  • In the past decade, DNA methylation analysis has been revolutionized by two technological advances — bisulphite modification of DNA and methylation-specific polymerase chain reaction (MSP).

  • CpG islands are approximately 1-kb stretches of DNA-containing clusters of CpG dinucleotides that are usually unmethylated in normal cells and are often located near the 5′ ends of genes. Methylation of promoter CpG islands is associated with a closed chromatin structure and transcriptional silencing of the associated gene.

  • Hypermethylation of CpG islands is a common event in carcinogenesis. The transcriptional silencing of tumour-suppressor genes by promoter CpG island hypermethylation can contribute to oncogenesis.

  • DNA methylation profiles represent a more chemically and biologically stable source of molecular diagnostic information than RNA or most proteins. The diagnostic potential of DNA methylation profiles is still largely untapped.

  • Cancer-specific DNA methylation patterns can be detected in tumour-derived free DNA in the bloodstream and in epithelial tumour cells shed into the lumen, offering a promising approach to the early detection of cancer. Clinical application will first require further validation and will ultimately be based on standardized MSP-based technologies, such as MethyLight, rather than on gel-based techniques.

  • A distinction between the clinical and analytical sensitivities of DNA methylation biomarkers is proposed.

Abstract

The past few years have seen an explosion of interest in the epigenetics of cancer. This has been a consequence of both the exciting coalescence of the chromatin and DNA methylation fields, and the realization that DNA methylation changes are involved in human malignancies. The ubiquity of DNA methylation changes has opened the way to a host of innovative diagnostic and therapeutic strategies. Recent advances attest to the great promise of DNA methylation markers as powerful future tools in the clinic.

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Figure 1: Principles of DNA methylation analysis.
Figure 2: Principle of sodium bisulphite conversion.

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Acknowledgements

I apologize to colleagues whose contributions could not be cited due to space constraints. Supported by National Institutes of Health grants. Disclosure: Peter W. Laird is shareholder and Scientific Advisory Board Member of Epigenomics, AG, which has a commercial interest in the development of DNA methylation markers for disease detection and diagnosis. None of the work performed in the laboratory of Peter W. Laird is or has been supported by Epigenomics.

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DATABASES

Cancer.gov

colorectal cancer

lung cancer

ovarian cancer

pancreatic cancer

prostate cancer

LocusLink

DNMT1

DNMT3A

DNMT3B

GSTP1

MGMT

MLH1

FURTHER INFORMATION

CpG Island Searcher

DNA Methylation Society

Early Detection Network

MethDB – Public DNA Methylation Database

Glossary

GENOMIC IMPRINTING

Process by which genes are selectively expressed by the maternal or paternal homologue of a chromosome.

X-INACTIVATION

Mammalian females have two X chromosomes per genome, whereas males have only one. In female mammals, one X chromosome is functionally silenced during embryogenesis to ensure that the stoichiometry of X-chromosomal and autosomal gene products is the same in males and females.

CpG ISLAND

First described by Adrian Bird as an unmethylated HpaII tiny fragment (HTF) and formerly commonly defined as a contiguous window of DNA of at least 200 base pairs in which the G:C content is at least 50% and the ratio of observed CpG frequency over the expected frequency exceeds 0.6. Recently, a more stringent definition of a 500-base-pair window with a G:C content of at least 55% and an observed over expected CpG frequency of at least 0.65 has been proposed to exclude most Alu repeat sequences.

DNA HYPERMETHYLATION

An increased level of DNA methylation in a DNA sample at either an individual CpG dinucleotide or at a group of CpG dinucleotides relative to a reference DNA sample, usually derived from a normal tissue.

DNA HYPOMETHYLATION

A decreased level of DNA methylation in a DNA sample at either an individual CpG dinucleotide or at a group of CpG dinucleotides (or even the entire genome) relative to a reference DNA sample, usually derived from a normal tissue.

POLYMORPHISM

A sequence variant that is present among human populations.

BIOMARKER

In cancer research and detection, a biomarker refers to a substance or process that is indicative of the presence of cancer in the body. It might be either a molecule secreted by a malignancy itself, or it can be a specific response of the body to the presence of cancer.

APC

(Adenomatous polyposis coli). A tumour-suppressor gene that encodes a component of the WNT–β-catenin signalling pathway that is inactivated in most colorectal adenocarcinomas.

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Laird, P. The power and the promise of DNA methylation markers. Nat Rev Cancer 3, 253–266 (2003). https://doi.org/10.1038/nrc1045

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