Review
5-Hydroxymethylcytosine: An epigenetic mark frequently deregulated in cancer

https://doi.org/10.1016/j.bbcan.2015.01.001Get rights and content

Highlights

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    5hmC levels are frequently deregulated in cancer.

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    Mutations in TET2, IDH1, IDH2, FH or SDH lead to decreased levels of 5hmC.

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    Changes in DNA (hydroxy)methylation are an important target for cancer therapy.

Abstract

The epigenetic mark 5-hydroxymethylcytosine (5hmC) has gained interest since 2009, when it was discovered that Ten-Eleven-Translocation (TET) proteins catalyze the conversion of 5-methylcytosine (5mC) into 5hmC. This conversion appears to be an intermediate step in the active DNA demethylation pathway. Factors that regulate DNA hydroxymethylation are frequently affected in cancer, leading to deregulated 5hmC levels. In this review, we will discuss the regulation of DNA hydroxymethylation, defects in this pathway in cancer, and novel therapies that may correct deregulated (hydroxy)methylation of DNA.

Introduction

DNA methylation is essential for normal development and plays an important role in many processes, including X-chromosome inactivation, imprinting and transcriptional regulation. Methylation of promoter regions is associated with transcriptional repression, while actively transcribed genes may contain high levels of gene body methylation (from the transcription start site to the end of the transcript) [1]. DNA methylation is mediated by DNA methyltransferases (DNMTs) and predominantly occurs on cytosine residues present in CpG context. DNMT3A and DNMT3B are responsible for de novo methylation, while DNMT1 is mainly involved in maintaining methylcytosine marks during DNA replication (Fig. 1) [2].

DNA demethylation may take place as a passive process due to lack of maintenance methylation during DNA replication. In addition, recent studies presented evidence for an active DNA demethylation pathway initiated by the Ten-Eleven Translocation (TET) protein family. The TET proteins are responsible for the conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) through three consecutive oxidation reactions [3], [4]. 5fC and 5caC marks are recognized by thymine DNA glycosylase (TDG). TDG activates the base excision repair pathway (BER), which replaces the modified cytosine with an unmodified cytosine (Fig. 1) [5].

Many proteins and cofactors control the balance between methylation and demethylation. In cancer, this balance is frequently deregulated, leading to altered methylation patterns. These changes in methylation can lead to repression of tumor suppressor genes or activation of oncogenes. Recently, it has been shown that hydroxymethylation levels are also altered in various types of cancer [6], [7], [8], [9]. Key events that contributed to the elucidation of the link between deregulated 5hmC levels and cancer are summarized in Fig. 2. Several mechanisms have been described that may be involved in these changes in 5hmC, which will be the focus of this review. Insights into these mechanisms may open new possibilities for treatment.

Section snippets

DNA hydroxymethylation and its regulation

5hmC was initially found in the DNA of bacteriophages [10], and was first reported to be present in mammalian DNA in 1972 [11]. After 1972, the interest for this cytosine modification was lost until 2009, when it was shown that TET proteins catalyze the conversion of 5mC to 5hmC [3]. Currently, 5hmC is well-accepted as an intermediate in demethylation. In addition, several studies suggest that it has additional functions as well. First of all, various tissues accumulate substantial levels of

Deregulation of DNA hydroxymethylation in cancer

Several genes that influence hydroxymethylation are mutated in cancer. First of all one of the TET genes, TET2, is affected by mutations in different hematological malignancies. Furthermore, four genes that play a role in the Krebs cycle, namely IDH1, IDH2, SDH and FH, are mutated in hematological malignancies and various types of solid cancers. These 4 genes are able to affect the activity of the TET proteins by changing the levels of metabolites that compete with the TET co-factor αKG. In

Possibilities for treatment

Although the causes and consequences of deregulated 5hmC levels are still under investigation, several opportunities for targeting the underlying mechanisms have already been explored.

A number of specific inhibitors for IDH1 and IDH2 mutations have been developed and tested in in vitro and in vivo settings. Inhibitors for IDH1 R132 (AGI-5198 [90], HMS-101 [91], AG1-14100 [92], ML309 [93]) were shown to specifically inhibit the ability of the mutant enzyme to produce 2HG in leukemia and glioma

Concluding remarks and perspectives

Deregulated 5hmC levels have been observed in many types of cancer, both in solid cancers as well as in hematological malignancies. Several mechanisms can be responsible for the altered 5hmC levels, ranging from mutations to deregulated miRNA expression (Table 3, Fig. 4). The fact that altered 5hmC levels are frequently observed in cancer suggests that the (de)methylation pathway might be an important target for cancer therapy, however several unanswered questions still need to be addressed.

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Acknowledgments

This work was supported by a grant from the Netherlands Institute for Regenerative Medicine (NIRM, DFES1029161) and ERA-NET/TRANSCAN/FP7 (KUN2013-6395).

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