Abstract
The base 5-hydroxymethylcytosine (5hmC) was recently identified as an oxidation product of 5-methylcytosine 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 with normal lung tissue. In brain tumors, 5hmdC showed an even more drastic reduction with levels up to more than 30-fold lower than in normal brain, but 5hmdC levels were independent of mutations in isocitrate dehydrogenase-1. 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.
Publication types
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Research Support, N.I.H., Extramural
MeSH terms
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5-Methylcytosine / chemistry
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5-Methylcytosine / metabolism
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Animals
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Base Sequence
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Brain / metabolism
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Brain / pathology
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Brain Neoplasms / genetics
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Brain Neoplasms / metabolism
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Brain Neoplasms / pathology
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Carcinoma, Squamous Cell / genetics
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Carcinoma, Squamous Cell / metabolism
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Carcinoma, Squamous Cell / pathology
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Cell Line, Tumor
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Chromatography, Liquid
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Cytosine / analogs & derivatives*
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Cytosine / chemistry
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Cytosine / metabolism
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DNA, Neoplasm / genetics
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DNA, Neoplasm / metabolism
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DNA-Binding Proteins / genetics
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DNA-Binding Proteins / metabolism
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Female
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Gene Expression Regulation, Neoplastic
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HEK293 Cells
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Humans
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Immunohistochemistry
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Isocitrate Dehydrogenase / genetics*
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Lung Neoplasms / genetics
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Lung Neoplasms / metabolism
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Lung Neoplasms / pathology
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Male
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Mice
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Mixed Function Oxygenases
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Molecular Structure
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Mutation*
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Neoplasms / genetics*
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Neoplasms / metabolism*
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Neoplasms / pathology
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Proto-Oncogene Proteins / genetics
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Proto-Oncogene Proteins / metabolism
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Reverse Transcriptase Polymerase Chain Reaction
Substances
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DNA, Neoplasm
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DNA-Binding Proteins
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Proto-Oncogene Proteins
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5-hydroxymethylcytosine
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5-Methylcytosine
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Cytosine
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Mixed Function Oxygenases
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TET1 protein, human
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Isocitrate Dehydrogenase
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IDH1 protein, human