TET family proteins and their role in stem cell differentiation and transformation

Abstract

One of the main regulators of gene expression during embryogenesis and stem cell differentiation is DNA methylation. The recent identification of hydroxymethylcytosine (5hmC) as a novel epigenetic mark sparked an intense effort to characterize its specialized enzymatic machinery and to understand the biological significance of 5hmC. The recent discovery of recurrent deletions and somatic mutations in the TET gene family, which includes proteins that can hydroxylate methylcytosine (5mC), in a large fraction of myeloid malignancies further suggested a key role for dynamic DNA methylation changes in the regulation of stem cell differentiation and transformation.

Figure 1. The role of TET proteins in Passive or Active DNA demethylation

A) The inability of the maintenance methyltransferase, DNMT1, to recognize 5hmC-containing DNA may lead to passive demethylation following replication. B) Active DNA methylation can be catalyzed by TET-mediated (i) hydroxylation of 5mC to 5hmC followed by AID and APOBEC-mediated (ii) deamination of 5hmC to 5hmU or (iii) further carboxylation of 5hmC to 5caC by the TET proteins and the subsequent cleavage of 5hmU or 5caC by DNA glycosylases (e.g. SMUG1, UNG and TDG) and replacement with cytosine by (iv) a base excision repair (BER) enzymatic pathway.

Figure 2. A dual role for TET1 and 5hmC in transcriptional regulation

A) Schematic of TET1 binding profile in the genome of mouse ESCs. TET1 is most highly enriched at the transcriptional start site (TSS) of genes with high CpG promoters (HCPs) compared to those with intermediate and low CpG promoters (ICPs and LCPs, respectively). B) TET1 directly binds to the co-repressors Sin3a and HDACs. TET1 target genes co-bound by polycomb repressor complex (PRC) proteins and Sin3a are repressed and display bivalent H3K4me3 and H3K27me3 marks. C) TET1-only target genes are actively transcribed and enriched for H3K4me3 and H3K36me3.

Figure 3. Schema of somatic TET2 mutations in hematopoietic malignancies

Displayed are the known somatic missense, nonsense, and frameshift mutations throughout the open-reading frame of TET2 in myelodisplastic syndromes (MDS), myeloproliferative neoplasms (MPN), chronic myelomonocytic leukemia (CMML) and acute myeloid leukemia (AML). In addition mutations that were seen in more than one sample amongst studies are highlighted in yellow. Data are compiled from several studies (Abdel-Wahab et al., 2009; Bejar et al., 2011; Delhommeau et al., 2009; Figueroa et al., 2010; Jankowska et al., 2009; Koh et al., 2011).

Figure 4. Mutation of TET2 or IDH proteins is associated with myeloid malignancies and aberrant DNA methylation

IDH proteins normally catalyze the conversion of NADP+ into NADPH and isocitrate into α-ketoglutarate (α-KG), a substrate required for normal TET2 enzymatic activity. Mutant IDH proteins cause loss of function of TET2 by exhibiting neomorphic enzymatic activity that results in the consumption of NADPH and production of the oncometabolite 2-hydroxyglutarate (2-HG) instead of α-KG. IDH mutations are mutually exclusive with TET2 mutations found in patients that exhibit reduced hydroxylase activity, due in part to mutations in the 2-OG and Fe(II)-dependant dioxygenase domain that cause decreased 5hmC production and aberrant DNA methylation patterns.