TET-Mediated Epigenetic Regulation in Immune Cell Development and Disease

Abstract

TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. The oxidized methylcytosines (oxi-mCs) facilitate DNA demethylation and are also novel epigenetic marks. TET loss-of-function is strongly associated with cancer; TET2 loss-of-function mutations are frequently observed in hematological malignancies that are resistant to conventional therapies. Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we seek to provide a conceptual framework of the mechanisms that fine tune TET activity. Then, we specifically focus on the multifaceted roles of TET proteins in regulating gene expression in immune cell development, function, and disease.

Keywords: 5hmC; TET proteins; cancer; epigenetics; immune cell development.

Figure 1

Regulation of DNA methylation in mammalian cells. Cytosine (C) is methylated by DNA methyltransferases (DNMTs) to 5-methylcytosine (5mC). Cytosine demethylation can occur in the absence of enzymatic activity during cell division. In addition, Ten Eleven Translocation (TET) proteins can oxidize 5mC to 5-hydroxymethylcytosine (5hmC). A significant portion of 5hmC will be diluted during cell division. TET proteins can further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The TDG through the Base Excision Repair (BER) can convert 5fC and 5caC to unmodified C.

Figure 2

The TET family of proteins. TET1, TET2, and TET3 share a C-terminal catalytic domain consisting of cysteine-rich (orange) and double stranded β-helix (gray) domains, and binding sites for cofactors Fe(II) (black) and 2-oxoglutarate (red). TET1 and TET3 have an N-terminal CXXC DNA binding domain, but this was lost in TET2 from a chromosomal inversion and became a separate protein IDAX.

Figure 3

TET proteins orchestrate the differentiation of immune cells. (A) Hematopoietic stem cells give rise to the various lineages of our immune system. Mice that are deficient for TET proteins have been used to explore their impact in immune cell development. TET1, TET2, and TET3 have been shown to regulate the methylation status of FOXP3, and they impact the stability of the regulatory T cells (Treg). TET2 and TET3 regulate the iNKT cell lineage specification and are critical for NKT1 and NKT2 cell differentiation. TET2 regulates the formation of memory and effector CD8 cells upon viral infection. During B cell differentiation, TET2 and TET3 orchestrate B cell maturation and function. TET2 also regulates mast cell differentiation and function in both a catalytic-dependent and -independent manner. Moreover, TET2 regulates the function of monocytic populations such as dendritic cells, macrophages, and osteoclasts. (B) Mechanistically, TET proteins are recruited by pioneer transcription factors (PTF) at cell-specific enhancers to oxidize 5mC and induce the expression of lineage specifying transcription factors (LSTF). Then, the LSTF execute their cell-specific gene expression program and shape cell identity.

Figure 4

TET2 mutations in hematological malignancies. In hematopoietic stem cells, TET2 mutations are an early event that results in increased self-renewal and subsequently clonal hematopoiesis. As the cells acquire additional mutations, malignant transformation and tumorigenesis occur. TET2 mutations have been reported in various hematological malignancies, affecting myeloid cells as well as T-cell and B-cell lymphomas.

Figure 5

Regulatory mechanisms of TET enzymatic activity. TET2 catalytic activity is Fe (II), alpha-ketoglutarate (α-KG), and oxygen dependent. Mutations in isocitrate dehydrogenase 1 and 2 (IDH), an enzyme in the TCA cycle that converts isocitrate to α-KG, often are gain-of-function (GOF), allowing the enzyme to produce the oncometabolite 2-hydroxyglutarate (2-HG). 2-HG competitively inhibits binding of α-KG to TET2, compromising its function. Vitamin C can enhance the catalytic activity of TET proteins.