Functions of TET Proteins in Hematopoietic Transformation

Abstract

DNA methylation is a well-characterized epigenetic modification that plays central roles in mammalian development, genomic imprinting, X-chromosome inactivation and silencing of retrotransposon elements. Aberrant DNA methylation pattern is a characteristic feature of cancers and associated with abnormal expression of oncogenes, tumor suppressor genes or repair genes. Ten-eleven-translocation (TET) proteins are recently characterized dioxygenases that catalyze progressive oxidation of 5-methylcytosine to produce 5-hydroxymethylcytosine and further oxidized derivatives. These oxidized methylcytosines not only potentiate DNA demethylation but also behave as independent epigenetic modifications per se. The expression or activity of TET proteins and DNA hydroxymethylation are highly dysregulated in a wide range of cancers including hematologic and non-hematologic malignancies, and accumulating evidence points TET proteins as a novel tumor suppressor in cancers. Here we review DNA demethylation-dependent and -independent functions of TET proteins. We also describe diverse TET loss-of-function mutations that are recurrently found in myeloid and lymphoid malignancies and their potential roles in hematopoietic transformation. We discuss consequences of the deficiency of individual Tet genes and potential compensation between different Tet members in mice. Possible mechanisms underlying facilitated oncogenic transformation of TET-deficient hematopoietic cells are also described. Lastly, we address non-mutational mechanisms that lead to suppression or inactivation of TET proteins in cancers. Strategies to restore normal 5mC oxidation status in cancers by targeting TET proteins may provide new avenues to expedite the development of promising anti-cancer agents.

Keywords: 5-methylcytosine oxidation; TET protein; hematologic malignancies; hematopoiesis; tumor suppression.

Fig. 1.

DNA methylation and demethylation processes mediated by DNMTs and TET proteins. (A) DNA methylation refers to the transfer of the methyl group from S-adenosyl methoinine (SAM) to the 5-carbon of cytosine to yield 5mC. De novo DNA methyltransferases DNMT3A and DNMT3B originally generate 5mC marks on unmethylated CpG dinucleotides. Replication leads to hemimethylated CpG sites that are remethylated by maintenance methyltransferase DNMT1. (B) Domain structure of the TET family proteins. TET proteins contain the catalytic core region that consists of cysteine-rich and double stranded β-helix (DSBH) domain. Within the DSBH domain, key catalytic residues that bind Fe²⁺ and 2-oxoglutarate (2OG) are present. (C) Oxidative reversal of DNA methylation marks in mammals. TET proteins promote both passive and active DNA demethylation. TET proteins oxidize 5mCs to produce oxi-mCs that antagonize DNA binding of DNMTs, promoting passive demethylation. They also facilitate active DNA demethylation because thymine DNA glycosylase (TDG) directly excise 5fC and 5caC, followed by base excision repair (BER) of the abasic site and replacement with an unmodified cytosine.

Fig. 2.

The catalytic reaction mediated by TET proteins. The catalytic residues within the DSBH domain bind 2OG and Fe²⁺. Incorporation of O₂ yields ferric intermediate Fe³⁺, stimulating the substrate oxidation and oxidative decarboxylation of 2OG. The final products of this process are the oxidized product (oxi-mCs), succinate and CO₂.

Fig. 3.

Oxidized methylcytosines(oxi-mCs) can function as independent epigenetic modifications. (A) Oxi-mCs are enriched at DNA sequences associated with gene expression control. (B) 5hmC and 5fC are suggested as stable modifications that are mainly diluted through cell proliferation. (C) 5fC induces conformational change of DNA to ‘F-DNA’. (D) 5fC and 5caC interact with RNA polymerase II and induce a pausing or retardation during transcription elongation. (E–F) Physical association of oxi-mCs (E) and TET proteins (F) with unique cellular proteins.

Fig. 4.

Non-mutational modulation of TET expression and function. The expression and function of TET proteins are regulated on many levels. For details, please refer to the text.