Efects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemia

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Epigenetics: official journal of the DNA Methylation Society (Impact Factor: 4.78). 02/2012; 7(2):201-7. DOI: 10.4161/epi.7.2.19015
Source: PubMed


TET2 enzymatically converts 5-methyl-cytosine to 5-hydroxymethyl-cytosine, possibly leading to loss of DNA methylation. TET2 mutations are common in myeloid leukemia and were proposed to contribute to leukemogenesis through DNA methylation. To expand on this concept, we studied chronic myelomonocytic leukemia (CMML) samples. TET2 missense or nonsense mutations were detected in 53% (16/30) of patients. In contrast, only 1/30 patient had a mutation in IDH1 or IDH2, and none of them had a mutation in DNMT3A in the sites most frequently mutated in leukemia. Using bisulfite pyrosequencing, global methylation measured by the LINE-1 assay and DNA methylation levels of 10 promoter CpG islands frequently abnormal in myeloid leukemia were not different between TET2 mutants and wild-type CMML cases. This was also true for 9 out of 11 gene promoters reported by others as differentially methylated by TET2 mutations. We found that two non-CpG island promoters, AIM2 and SP140, were hypermethylated in patients with mutant TET2. These were the only two gene promoters (out of 14,475 genes) previously found to be hypermethylated in TET2 mutant cases. However, total 5-methyl-cytosine levels in TET2 mutant cases were significantly higher than TET2 wild-type cases (median = 14.0% and 9.8%, respectively) (p = 0.016). Thus, TET2 mutations affect global methylation in CMML but most of the changes are likely to be outside gene promoters.

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Available from: Jaroslav Jelinek
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    • "TET family gene members (TET1, TET2, and TET3) have functions mostly in hematopoietic differentiation. The TET oncogene family member 2 (TET2) gene located at chromosome band 4q24 catalyzes the conversion of 5-methylcytosine to 5-hydroxymethylcytosine [1] [6] [7]. TET2 mutations are frequently detected during progression of MPN (myeloproliferative neoplasms) or MDS (myleodysplastic syndromes) to AML [1]. "
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    ABSTRACT: Background: Acute myeloid leukemia (AML) is a heterogeneous clonal disorder in terms of cytogenetic and molecular aberrations. Ten-Eleven-Translocation 2 (TET2), Kirsten rat sarcoma viral oncogene homolog (KRAS), and Casitas B-cell lymphoma (CBL) have an important role pathogenesis of acute myeloid leukemia (AML) and their activated mutations confer proliferative and survival signals. Aim: In this study, we aimed to find possible genetic markers for molecular analysis in childhood AML by screening hot-spot exons of TET2, KRAS, and CBL using Next Generation Sequencing (NGS) analysis. In addition, association between found variants and mutations of Januse Kinase-2 (JAK2) and Fms-Related Tyrosine Kinase (FLT3) were analyzed which are important prognostic risk factors for AML. Methods: Eight patients who were diagnosed with pediatric AML at Losante Pediatric Hematology–Oncology Hospital were included to the study. Hot-spot exons of TET2, KRAS and CBL genes were screened using the NGS method. Furthermore, FLT3-Internal Tandem Duplicate (FLT3-ITD) and JAK2-V617F were analyzed by Real Time Polymerase chain Reaction (Real Time-PCR). Results: In total, we identified 20 variants in studied genes by NGS. In our patient group, 16 variants in the TET2 (seven novel, seven missense and two silent), two variants in the KRAS (one missense and one intronic) and two variants in the CBL (two novel) were found. All of AML patients were found negative for JAK V617 F. Three of the eight patients (37.5%) showed mutations of both FLT3-ITD and TET2, KRAS, CBL. Conclusion: We found novel mutations for TET2, KRAS, and CBL. The detected variants in this article seem to be the first screening results of genes studied by NGS in childhood AML patients. Our results also showed some degree of association between FLT3-ITD and TET2, KRAS, CBL mutations.
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    • "These data also have implications for understanding the function of TET2 and TET3 as well. In particular, TET2 mutations that are common in myeloid leukemias seem to have little effects on CGI DNA methylation (63). Dissecting DNA methylation-dependent and -independent effects of TET2 will be important to understand its role in cancer development. "
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    ABSTRACT: TET1 is a 5-methylcytosine dioxygenase and its DNA demethylating activity has been implicated in pluripotency and reprogramming. However, the precise role of TET1 in DNA methylation regulation outside of developmental reprogramming is still unclear. Here, we show that overexpression of the TET1 catalytic domain but not full length TET1 (TET1-FL) induces massive global DNA demethylation in differentiated cells. Genome-wide mapping reveals that 5-hydroxymethylcytosine production by TET1-FL is inhibited as DNA methylation increases, which can be explained by the preferential binding of TET1-FL to unmethylated CpG islands (CGIs) through its CXXC domain. TET1-FL specifically accumulates 5-hydroxymethylcytosine at the edges of hypomethylated CGIs, while knockdown of endogenous TET1 induces methylation spreading from methylated edges into hypomethylated CGIs. We also found that gene expression changes after TET1-FL overexpression are relatively small and independent of its dioxygenase function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically prevents aberrant methylation spreading into CGIs in differentiated cells.
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    • "Despite an expected increase in 5-mC following TET2 inactivation, several studies have reported a global decrease in methylation (Ko et al., 2010; Yamazaki et al., 2012). However, analysis of specific gene promoters shows mixed results in TET2 mutant samples , frequently exhibiting promoter-specific hypermethylation in spite of global hypomethylation (Perez et al., 2012; Wu et al., 2011; Yamazaki et al., 2012). Still, Ko and colleagues noted that several AML patients with wild-type TET2 had 5-hmC levels very similar to those patients with mutant TET2 (Ko et al., 2010). "
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