5-Hydroxymethylcytosine Is Strongly Depleted in Human Cancers but Its Levels Do Not Correlate with IDH1 Mutations

Abstract

The base 5-hydroxymethylcytosine (5hmC) was recently identified as an oxidation product of 5-methylcytosine (5mC) in mammalian DNA. Here, using sensitive and quantitative methods to assess levels of 5-hydroxymethyl-2′-deoxycytidine (5hmdC) and 5-methyl-2′-deoxycytidine (5mdC) in genomic DNA, we investigated whether levels of 5hmC can distinguish normal tissue from tumor tissue. In squamous cell lung cancers, levels of 5hmdC were depleted substantially with up to 5-fold reduction compared to normal lung tissue. In brain tumors, 5hmdC showed an even more drastic reduction with levels up to >30-fold lower than in normal brain, but 5hmdC levels were independent of mutations in isocitrate dehydrogenase-1 (IDH1). Furthermore, immunohistochemical analysis indicated that 5hmC is remarkably depleted in many types of human cancer. Importantly, an inverse relationship between 5hmC levels and cell proliferation was observed with lack of 5hmC in proliferating cells. The data therefore suggest that 5hmdC is strongly depleted in human malignant tumors, a finding that adds another layer of complexity to the aberrant epigenome found in cancer tissue. In addition, a lack of 5hmC may become a useful biomarker for cancer diagnosis.

Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation

“…1C). This finding is consistent with previous reports that 5hmC is depleted in proliferating cancer cells compared with post-mitotic cells (Jin et al 2011;Lian et al 2012).…”

Cancer Metabolism and Elevated O-GlcNAc in Oncogenic Signaling

“…O-GlcNAc may also contribute to epigenetic control through regulation of chromatin-modifying enzymes and complexes. The TET (teneleven translocation) family proteins are 5-methylcytosine oxidases required during DNA demethylation at a step in 5-hydroxymethylcytosine formation, a modification that is strongly reduced in cancer tissues (88,89). TET1 binds OGT and is O-GlcNAcylated, leading to nuclear export of TET1 and inhibition of 5-hydroxymethylcytosine formation (90).…”

Robust quantitative assessments of cytosine modifications and changes in the expressions of related enzymes in gastric cancer

“…and 2-oxoglutarate (2-OG), and 2-OG is dependent on the activity of isocitrate dehydrogenase IDH1 and IDH2 [5,6] ( Figure S1). The loss of 5-hydroxymethylcytosine and the down-regulation of the TET family and IDH2 have been found in human cancers [7][8][9][10][11], but comprehensive evaluations of the modified cytosines and the enzymes that are involved have remained largely unperformed and most previous studies have used dot blot analyses as a means of measuring 5-hydroxymethyldeoxycytidine (5-hmC), which is at best a semi-quantitative method. Because dot blot analysis is based on the antigen-antibody reaction direct assessments of the absolute amount of 5-mC, 5-hmC, 5-fC, and 5-caC are not possible.…”