Accession PRJCA000102
Title Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer
Umbrella project

eGPS: evolutionary Genotype-Phenotype Systems biology

Key theories & Model

The driving effect of DNA methylation on complex traits

Data type Epigenomics
Organism Homo sapiens
Description Both 5-methylcytosine (5mC) and its oxidized form, 5-hydroxymethylcytosine (5hmC), have been proposed to be involved in tumorigenesis. Because the readout of the broadly used 5mC mapping method, bisulfite sequencing (BS-seq), is the sum of 5mC and 5hmC levels, the aberrant patterns and interdependence of these two modifications separately remain poorly understood. By profiling real 5mC (BS-seq corrected by Tet-assisted bisulfite sequencing, TAB-seq) and 5hmC (TAB-seq) levels simultaneously at single nucleotide resolution, we here demonstrated that there is no global loss of 5mC in kidney tumors compared with matched normal tissues. Conversely, 5hmC was globally lost in virtually all kidney tumor tissues. The 5hmC level in tumor tissues was an independent prognostic marker for kidney cancer, with lower levels of 5hmC associated with shorter overall survival. Furthermore, we demonstrated that loss of 5hmC is linked to hypermethylation in tumors compared with matched normal tissues, particularly in gene body regions. Strikingly, gene body hypermethylation was significantly associated with silencing of tumor-related genes that for a few examples. Down-regulation of IDH1 was identified as a mechanism underlying 5hmC loss in kidney cancer. Rescuing 5hmC levels attenuated the invasion capacity of tumor cells and suppressed tumor growth in a xenograft model. Collectively, our results demonstrate that loss of 5hmC is both a prognostic marker and an oncogenic event in kidney cancer by remodeling the DNA methylation pattern
Sample scope carcinoma
Release date 2016-03-18
Publication
PubMed ID Article title Journal name DOI Year
26680004 Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Research 10.1038/cr.2015.150 2016
Data provider
Data provider Data provider URL
General information
Agency program Grant ID Grant title
Accessions in other database
Accession Database name
GSE63183 NCBI
External link
External link Link description
Submitter ZhengZheng    Xu  (xdzperfect@163.com)
Organization Beijing Institute of Genomics, Chinese Academy of Sciences
Submission date 2015-11-17

Project Data

Resource name Description
BioSample (1) -
SAMC000292 kidney cancer
GSA (1) -
CRA000010 CRA_10
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