Tet methylcytosine dioxygenase 2 (TET2) is a human
gene.[5] It resides at
chromosome 4q24, in a region showing recurrent microdeletions and copy-neutral loss of
heterozygosity (CN-LOH) in patients with diverse
myeloid malignancies.
Function
TET2 encodes a protein that
catalyzes the conversion of the modified
DNA base methylcytosine to 5-hydroxymethylcytosine.
The first mechanistic reports showed tissue-specific accumulation of
5-hydroxymethylcytosine (
5hmC) and the conversion of
5mC to
5hmC by
TET1 in humans in 2009.[6][7] In these two papers, Kriaucionis and Heintz [6] provided evidence that a high abundance of 5hmC can be found in specific tissues and Tahiliani et al.[7] demonstrated the
TET1-dependent conversion of
5mC to
5hmC. A role for TET1 in cancer was reported in 2003 showing that it acted as a complex with MLL (myeloid/lymphoid or mixed-lineage leukaemia 1) (KMT2A),[8][9] a positive global regulator of gene transcription that is named after its role cancer regulation.
An explanation for protein function was provided in 2009 [10] via computational search for
enzymes that could modify
5mC. At this time, methylation was known to be crucial for gene silencing, mammalian development, and retrotransposon silencing. The mammalian TET proteins were found to be orthologues of Trypanosoma brucei base J-binding protein 1 (JBP1) and JBP2.
Base J was the first hypermodified base that was known in eukaryotic DNA and had been found in T. brucei DNA in the early 1990s,[11] although the evidence of an unusual form of DNA modification goes back to at least the mid 1980s.[12]
In two articles published back-to-back in Science journal in 2011, firstly[13] it was demonstrated that (1) TET converts 5mC to 5fC and 5caC, and (2) 5fC and 5caC are both present in mouse
embryonic stem cells and organs, and secondly[14] that (1) TET converts 5mC and 5hmC to 5caC, (2) the 5caC can then be excised by thymine DNA glycosylase (
TDG), and (3) depleting
TDG causes 5caC accumulation in mouse
embryonic stem cells.
In general terms, DNA methylation causes specific sequences to become inaccessible for gene expression. The process of demethylation is initiated through modification of the 5mC to 5hmC, 5fC, etc. To return to the unmodified form of cytosine (C), the site is targeted for
TDG-dependent base excision repair (TET–TDG–BER).[13][15][16] The “
thymine” in TDG (
thymine DNA glycosylase) might be considered a misnomer; TDG was previously known for removing thymine moieties from G/T mismatches.
The process involves hydrolysing the carbon-nitrogen bond between the sugar-phosphate DNA backbone and the mismatched
thymine. Only in 2011, two publications [13][14] demonstrated the activity for TDG as also excising the oxidation products of
5-methylcytosine. Furthermore, in the same year [15] it was shown that TDG excises both 5fC and 5caC. The site left behind remains abasic until it is repaired by the base excision repair system. The biochemical process was further described in 2016 [16] by evidence of base excision repair coupled with TET and TDG.
The most striking outcome of aberrant TET activity is its association with the development of cancer.
Mutations in this
gene were first identified in myeloid
neoplasms with deletion or uniparental disomy at 4q24.[17] TET2 may also be a candidate for active
DNA demethylation, the catalytic removal of the methyl group added to the fifth carbon on the cytosine base.
Damaging variants in TET2 were attributed as the cause of several myeloid malignancies around the same time as the protein’s function was reported for TET-dependent oxidation.[18][19][20][21][22][23][24] Not only were damaging TET2 mutations found in disease, but the levels of 5hmC were also affected, linking the molecular mechanism of impaired demethylation with disease [75].[25] In mice the depletion of TET2 skewed the differentiation of
haematopoietic precursors,[25] as well as amplifying the rate of haematopoietic or progenitor cell renewal.[26][27][28][29]
TET2 mutations have prognostic value in cytogenetically normal acute myeloid leukemia (CN-AML). "Nonsense" and "frameshift" mutations in this gene are associated with poor outcome on standard therapies in this otherwise favorable-risk patient subset.[31]
Loss-of-function TET2 mutations may also have a possible causal role in atherogenesis as reported by Jaiswal S. et al, as a consequence of clonal hematopoiesis.[32] Loss-of-function due to somatic variants are frequently reported in cancer, however
homozygousgermline loss-of-function has been shown in humans, causing childhood
immunodeficiency and
lymphoma.[33] The phenotype of
immunodeficiency, autoimmunity and
lymphoproliferation highlights requisite roles of TET2 in the
human immune system.
WIT pathway
TET2 is mutated in 7%–23% of acute myeloid leukemia (AML) patients.[34] Importantly, TET2 is mutated in a
mutually exclusive manner with WT1, IDH1, and IDH2.[35][36] TET2 can be recruited by WT1, a sequence-specific zinc finger
transcription factor, to WT1-target genes, which it then activates by converting methylcytosine into 5-hydroxymethylcytosine at the genes’
promoters.[36] Additionally, isocitrate dehydrogenases 1 and 2, encoded by IDH1 and IDH2, respectively, can inhibit the activity of TET proteins when present in mutant forms that produce the TET inhibitor D-2-hydroxyglutarate.[37] Together, WT1, IDH1/2 and TET2 define the WIT pathway in AML.[34][36] The WIT pathway might also be more broadly involved in suppressing tumor formation, as a number of non-hematopoietic malignancies appear to harbor mutations of WIT genes in a non-exclusive manner.[34]
^Lorsbach RB, Moore J, Mathew S, Raimondi SC, Mukatira ST, Downing JR (March 2003). "TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23)". Leukemia. 17 (3): 637–41.
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10.1038/sj.leu.2402834.
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^Ono R, Taki T, Taketani T, Taniwaki M, Kobayashi H, Hayashi Y (July 2002). "LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23)". Cancer Research. 62 (14): 4075–80.
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^Gommers-Ampt JH, Van Leeuwen F, de Beer AL, Vliegenthart JF, Dizdaroglu M, Kowalak JA, et al. (December 1993). "beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei". Cell. 75 (6): 1129–36.
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10.1016/0092-8674(93)90322-h.
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^Langemeijer SM, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop M, et al. (July 2009). "Acquired mutations in TET2 are common in myelodysplastic syndromes". Nature Genetics. 41 (7): 838–42.
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Langemeijer SM, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop M, et al. (July 2009). "Acquired mutations in TET2 are common in myelodysplastic syndromes". Nature Genetics. 41 (7): 838–42.
doi:
10.1038/ng.391.
PMID19483684.
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