Chen Ke, Zhang Jing, Guo Zhongqiang, Ma Qin, Xu Zhengzheng, Zhou Yuanyuan, Xu Ziying, Li Zhongwu, Liu Yiqiang, Ye Xiongjun, Li Xuesong, Yuan Bifeng, Ke Yuwen, He Chuan, Zhou Liqun, Liu Jiang, Ci Weimin
Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Cell Res. 2016 Jan;26(1):103-18. doi: 10.1038/cr.2015.150. Epub 2015 Dec 18.
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 5mC/5hmC patterns and relationship of these two modifications remain poorly understood. By profiling real 5mC (BS-seq corrected by Tet-assisted BS-seq, TAB-seq) and 5hmC (TAB-seq) levels simultaneously at single-nucleotide resolution, we here demonstrate 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 is 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 the tumor-related genes. Downregulation of IDH1 was identified as a mechanism underlying 5hmC loss in kidney cancer. Restoring 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.
5-甲基胞嘧啶（5mC）及其氧化形式5-羟甲基胞嘧啶（5hmC）均被认为与肿瘤发生有关。由于广泛使用的5mC图谱绘制方法——亚硫酸氢盐测序（BS-seq）的读数是5mC和5hmC水平的总和，这两种修饰的5mC/5hmC模式及其关系仍知之甚少。通过在单核苷酸分辨率下同时分析真实的5mC（经Tet辅助的BS-seq校正的BS-seq，即TAB-seq）和5hmC（TAB-seq）水平，我们在此证明，与匹配的正常组织相比，肾肿瘤中不存在5mC的整体缺失。相反，几乎所有肾肿瘤组织中的5hmC均整体缺失。肿瘤组织中的5hmC水平是肾癌的一个独立预后标志物，5hmC水平较低与总生存期较短相关。此外，我们证明，与匹配的正常组织相比，肿瘤中5hmC的缺失与高甲基化有关，尤其是在基因体区域。引人注目的是，基因体高甲基化与肿瘤相关基因的沉默显著相关。IDH1的下调被确定为肾癌中5hmC缺失的潜在机制。在异种移植模型中，恢复5hmC水平可减弱肿瘤细胞的侵袭能力并抑制肿瘤生长。总体而言，我们的结果表明，5hmC的缺失通过重塑DNA甲基化模式，既是肾癌的一个预后标志物，也是一个致癌事件。
