TET2 Mutations Affect Non-CpG Island DNA Methylation at Enhancers and Transcription Factor–Binding Sites in Chronic Myelomonocytic Leukemia

Abstract

TET2 enzymatically converts 5-methylcytosine to 5-hydroxymethylcytosine as well as other covalently-modified cytosines and its mutations are common in myeloid leukemia. However, the exact mechanism and the extent to which TET2 mutations affect DNA methylation remain in question. Here we report on DNA methylomes in TET2 wild type (TET2-WT) and mutant (TET2-MT) cases of chronic myelomonocytic leukemia (CMML). We analyzed 85,134 CpG sites (28,114 sites in CpG islands (CGIs) and 57,020 in non-CpG islands (NCGIs)). TET2 mutations do not explain genome-wide differences in DNA methylation in CMML, and we found few and inconsistent differences at CGIs between TET2-WT and TET2-MT cases. By contrast, we identified 409 (0.71%) TET2-specific differentially methylated CpGs (tet2-DMCs) in NCGIs, 86% of which were hypermethylated in TET2-MT cases, suggesting a strikingly different biology of the effects of TET2 mutations at CGIs and NCGIs. DNA methylation of tet2-DMCs at promoters and non-promoters repressed gene expression. Tet2-DMCs showed significant enrichment at hematopoietic-specific enhancers marked by H3K4me1, and at binding sites for the transcription factor p300. Tet2-DMCs showed significantly lower 5-hydroxymethylcytosine in TET2-MT cases. We conclude that leukemia-associated TET2 mutations affect DNA methylation at NCGI regions containing hematopoietic-specific enhancers and transcription factor binding sites.

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

“…We detected two synonymous (T > C, A > G) SNPs in exons 6 and 10 of the LPL gene from low-milk production group, leading to change in secondary structure (see Supplementary Information, Figure S1 online). Due to change in secondary structure, there was increase in G for mutant compared to wild type (-95.80 to -94.10 kcal/mol), which in turn might affect the properties of transcription factor binding pockets, leading to change in the gene expression [44][45][46][47] . In our study, LPL gene expression was decreased, whereas under usual conditions, it is found to be highly expressed in mammary cells during lactation and also associated with traits like carcass trait and visceral fat deposition in cattle which is important for supplying fatty acids to mammary gland by hydrolysis of triglycerides from very-low density lipoproteins 42,43,48,49 .…”

The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia

“…TET2 is one of the most commonly altered genes in MDS, with inactivating mutations found in approximately 30% of cases 25,59,66 . These mutations are associated with hypermethylation of cytosines at enhancer sequences and subsequent repression of a number of genes important for myeloid differentiation 67–69 .…”

DNA Hypomethylating Drugs in Cancer Therapy

“…IDH usually converts isocitrate to a-ketoglutarate, but mutant IDH will convert a-ketoglutarate to 2-hydroxyglutarate (2-HG) (Cohen et al 2013), and 2-HG is an inhibitor of the TET proteins that mediates DNA demethylation (Xu et al 2011). Patients with mutations in TET2 or IDH have specific hypermethylation signatures in both acute myelogenous leukemia (AML) (Figueroa et al 2010;TCGA 2013;Yamazaki et al 2015Yamazaki et al , 2016 and glioblastoma (Noushmehr et al 2010;Turcan et al 2012;Brennan et al 2013).…”