Review
TET proteins in cancer: Current ‘state of the art’

https://doi.org/10.1016/j.critrevonc.2015.07.008Get rights and content

Highlights

  • Enzymes involved in DNA demethylation-TET play role in cell differentiation and carcinogenesis.

  • Level of TETs and their products (oxidized 5-methylcytosines) is altered in many malignances.

  • Increasing information is available regarding regulation of TET expression/activity in cancer.

  • Readers of 5-mC derivatives need to be identified to estimate its role in cells.

Abstract

Aberrations in DNA methylation patterns are observed from the early stages of carcinogenesis. However, the mechanisms that drive these changes remain elusive. The recent characterization of ten-eleven translocation (TET) enzymes as a source of newly modified cytosines (5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine) has shed new light on the DNA demethylation process. These cytosines are intermediates of an active DNA demethylation process and are epigenetic markers per se. In this review, we discuss the mechanism and function of TET proteins in biological processes as well as current knowledge regarding their expression and regulation in cancer.

Introduction

Epigenetic changes are observed from the early stages of tumor cell growth (Baylin and Jones, 2011). Epigenetics, the study of the heritable and reversible changes that alter gene expression without affecting DNA sequences, encompasses many mechanisms, including but not limited to DNA methylation, histone covalent modifications, chromatin remodeling and microRNAs (Dawson and Kouzarides, 2012). Among the first described modifications was DNA methylation, which is observed in most plant, animal and fungal models (Law and Jacobsen, 2010). Covalent modification (the addition of a methyl group) at the fifth position of the cytosine pyrimidine ring maintains the information content at the base level and is an important epigenetic marker that is simultaneously recognized by specific proteins. In mammals, 5-methylcytosine (5-mC) occurs most commonly in CpG dinucleotides (Li, 2002). CpG methylation in gene promoters represses transcription by preventing the binding of transcription factors and by influencing interactions between enhancers and promoters (Wiench et al., 2011). Overall, 60–80% of approximately 28 million CpGs are methylated (Smith and Meissner, 2013). Regions with high CpG density are termed CpG islands and are prevalent at promoter regions of housekeeping genes and developmental regulators where they are mostly unmethylated (Deaton and Bird, 2011). CpG sites are also embedded in regions of repetitive sequences and gene bodies where they are primarily methylated in contrast to the previous example (Portela and Esteller, 2010). DNA methylation prevents the translocation of retroelements, which cause chromosome instability, whereas DNA methylation in gene bodies may contribute to the alternative initiation of transcription and affect the efficiency of elongation (Portela and Esteller, 2010, Chodavarapu et al., 2010, Shukla et al., 2011). Moreover, DNA methylation occurs at regions with low CpG density called CpG shores, which are in close proximity to CpG islands (Portela and Esteller, 2010). Non-CpG methylation at sites such as CpA, CpT, or CpC has also been observed (Patil et al., 2014). Non-CpG methylation is thought to repress promoter activity by blocking binding sites for transcription factors (Patil et al., 2014).

DNA methylation is established by DNA methyltransferases (DNMTs). The classical model of methylation, which was presented more than 30 years ago, involves two types of DNMTs: maintenance and de novo DNMTs (Holliday and Pugh, 1975, Riggs, 1975). In this model, the global CpG methylation pattern is maintained faithfully in daughter cells during mitosis through the action of DNA methyltransferase type 1 (DNMT1), which preferentially recognizes hemimethylated CpGs after each replication cycle (Bostick et al., 2007). DNMT3A and DNMT3B are primarily responsible for de novo methylation in embryos (Holliday and Pugh, 1975). Another member of this family, DNMT3L, lacks methyltransferase catalytic activity but regulates the establishment of genomic imprints in oocytes and the inactivation of dispersed repeated sequences in male germ cells (Bourc’his and Bestor, 2004, Webster et al., 2005). However, the presented model does not explain many recent experimental results. Inconsistency in CpG site-specific methylation and alterations in methylation on proviral reporter constructs suggest that no single enzyme is able to maintain genome-wide DNA methylation patterns (Zhang et al., 2009, Lorincz et al., 2002). Moreover, DNMT knockout experiments have demonstrated that the preservation of DNA methylation patterns relies on cooperation between DNMT1 and DNMT3 enzymes. Specifically, DNMT3 enzymes are required for maintaining methylation at repeats (Liang et al., 2002, Chen et al., 2003, Arand et al., 2012). Another contradiction to the classical view involves the observation of permanent de novo activity at non-CpG sites (Arand et al., 2012, Shirane et al., 2013). The landscape of genome methylation patterns is also influenced by chromatin structure and factors that control the activities and targeting of DNMTs. A recent excellent review clearly describes these phenomena and proposes a unified stochastic model of DNA methylation (Jeltsch and Jurkowska, 2014).

Mechanisms that drive DNA methylation alterations in cancer remain elusive. The hypermethylation of CpG islands in the promoter regions of tumor suppressor genes has been demonstrated in various malignancies (Baylin and Jones, 2011, Rawluszko et al., 2013, Esteller, 2002). In addition, the genomes of cancer cells are characterized by global hypomethylation, which primarily affects repetitive and gene body sequences (Hansen et al., 2011). Aberrant methylation patterns in cancer can result from initial random methylation that results in proliferative advantages, the recruitment of DNMTs to their target sites by estrogen receptor α or histone methyltransferases, or the loss of transcription factors, which subsequently enable DNMT binding (Turker, 2002, Jones and Baylin, 2007, Metivier et al., 2008, Tachibana et al., 2008). Demethylation processes that build up the DNA methylation landscape may also be disrupted in cancer cells. DNA demethylation processes are classified as passive and active. Passive mechanisms involve a failure of the repair system to maintain DNA methylation patterns during replication or DNA synthesis and are associated with the dilution of hemimethylated CpG in subsequent replication cycles (Ehrlich and Lacey, 2013). Active DNA demethylation involves the replacement of 5-methylcytosine (5-mC) by C (Ehrlich and Lacey, 2013). Evidence supporting active mechanisms continue to be controversial (Ooi and Bestor, 2008). Publications by Tahiliani et al. and Kriaucionis et al. in 2009 that described an enzyme that can modify 5-mC by oxidation and the presence of a new nucleotide, 5-hydroxymethylcytosine (5-hmC), respectively, served as milestones in understanding the mechanisms of DNA demethylation (Tahiliani et al., 2009, Kriaucionis and Heintz, 2009). The enzyme that converts 5-mC to 5-hmC is ten-eleven translocation 1 (TET1), which was identified initially in 2003 (Lorsbach et al., 2003). Soon after this first report, two other TET family members, TET2 and TET3, were characterized (Ito et al., 2010). The described so-called “sixth base”, i.e., 5-hmC, was considered an intermediate of active DNA demethylation and was initially observed in Purkinje cells, granule cells and mouse embryonic stem cells (ESCs) (Tahiliani et al., 2009, Kriaucionis and Heintz, 2009). Subsequent studies revealed the ability of TET to further oxidize 5-hmC to 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) (He et al., 2011, Ito et al., 2011, Pfaffeneder et al., 2011). Concomitantly, 5-hmC expression was detected in many tissues, and the locations of the oxidative derivatives of 5-mC and TET proteins were mapped by various techniques (Globisch et al., 2010, Munzel et al., 2010, Szwagierczak et al., 2010, Pastor et al., 2011, Yu et al., 2012, Hahn et al., 2013, Lister et al., 2013, Song et al., 2013a). These and many other reports have brought new insights to the field of epigenetics and raised many questions regarding the mechanism of TET action and the role of newly identified bases in DNA demethylation during development and cancer. In this review, we present the TET proteins and their enzymatic activity and discuss their roles with an emphasis on cancer.

Section snippets

Gene and protein structures and the mechanisms of action of TET family members

TET was first described in 2003 in acute myeloid leukemia (AML) (Lorsbach et al., 2003). TET1 is located on 10q21 and is composed of 134 kb. This gene contains 12 exons that encode a protein composed of 2136 amino acids (AA) (Abdel-Wahab et al., 2009). TET2 is situated in the 4q24 region (Abdel-Wahab et al., 2009, Hussein et al., 2010, Strausberg et al., 2002). Given the alternative splicing of 11 exons, different isoforms may be transcribed. One translated isoform lacks exon 3b, which results

The distribution and roles of TET and 5-mC oxidative derivatives in the genome

The mapping of oxidized cytosines along with TET in the genome helps to understand the roles of TET and its products (5-hmC, 5-fC and 5-caC) in transcriptional regulation. To date, oxidized cytosine modifications have not been recognized at the transcription start site of genes with CpG islands within the promoter region in wild type and Tdg-depleted mouse ESCs (Song et al., 2013a, Shen et al., 2013, Szulwach et al., 2011). However, a few publications have suggested active TET-dependent DNA

The biological role of TET

Genome-wide loss of 5-mC has been observed at distinct developmental stages, including preimplantation embryos and developing primordial germ cells (PGCs) (Hajkova et al., 2002, Feng et al., 2010a). Additionally, evidence suggests a role for TET enzymes in the generation of pluripotent stem cells (iPSCs) that are phenotypically similar to ESCs (Takahashi and Yamanaka, 2006). Moreover, the formation of distinct populations of neurons and glia in the brain is also orchestrated by changes in DNA

TET proteins in cancer

Aberrant DNA methylation is a hallmark of cancer; growing evidence has suggested that an imbalance in TET-mediated DNA demethylation may participate in carcinogenesis (Baylin and Jones, 2011, Wu and Zhang, 2011a, Cimmino et al., 2011, Esteller, 2007).

The first reports implicating a role for TET proteis in cancer involved the identification of human TET1 as a translocation partner of the mixed lineage leukemia (MLL) gene in patients with AML (Tefferi et al., 2009). Recently, MLL was found to

Summary

The discovery of TET enzymes and the oxidative derivatives of 5-mC serve as true milestones for epigenetic research. Studies conducted in the past few years have emphasized the role of active DNA demethylation in cell reprogramming and differentiation. Therefore, not surprisingly, altered TET expression and 5-hmC levels have been observed for numerous cancers. However, a deficiency in understanding the exact mechanism of decreased 5-hmC levels and its role in transcriptional control during

Conflict of interest statement

All authors declare that no conflict of interest exists.

Funding source

Supported by 502-01-01124182-07474 and grant 2012/05/N/NZ5/00844; National Science Center, Poland.

Agnieszka Anna Rawłuszko-Wieczorek was born in 1984. In 2014, she obtained her PhD from Poznan University of Medical Sciences in Poland. Currently, she continues her research regarding the epigenetic regulation of colorectal cancer at the Department of Biochemistry and Molecular Biology. She has been a member of the Polish Biochemical Society since 2009.

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    Agnieszka Anna Rawłuszko-Wieczorek was born in 1984. In 2014, she obtained her PhD from Poznan University of Medical Sciences in Poland. Currently, she continues her research regarding the epigenetic regulation of colorectal cancer at the Department of Biochemistry and Molecular Biology. She has been a member of the Polish Biochemical Society since 2009.

    Agnieszka Siera was born in 1989. Currently, she is pursuing her Master of Science studies at Poznan Medical University in Poland. Her thesis is directly related to TET gene activity during colorectal carcinogenesis.

    Paweł Piotr Jagodziński, Professor in Medical Sciences, currently serves as the head of the Department of Biochemistry and Molecular Biology of Poznan University of Medical Sciences in Poland. His scientific interests include the genetic and epigenetic background of cancer, non-syndromic cleft palate, diabetes and systemic lupus erythematosus. He is the author of more than 200 original publications and reviews, an honored member of the Polish Biochemical Society, and a member of the editorial board of Journal of Medical Science.

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