The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

被引：134

作者：

Han, Leng ^{[1
]}

Yuan, Yuan ^{[1
,2
]}

Zheng, Siyuan ^{[1
]}

Yang, Yang ^{[1
,3
]}

Li, Jun ^{[1
]}

Edgerton, Mary E. ^{[4
]}

Diao, Lixia ^{[1
]}

Xu, Yanxun ^{[1
]}

Verhaak, Roeland G. W. ^{[1
]}

Liang, Han ^{[1
,2
]}

机构：

[1] Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA

[2] Baylor Coll Med, Grad Program Struct & Computat Biol & Mol Biophys, Houston, TX 77030 USA

[3] Univ Texas Hlth Sci Ctr Houston, Sch Publ Hlth, Div Biostat, Houston, TX 77030 USA

[4] Univ Texas MD Anderson Canc Ctr, Dept Pathol, Houston, TX 77030 USA

来源：

NATURE COMMUNICATIONS | 2014年 / 5卷

基金：

美国国家卫生研究院;

关键词：

TARGETS; GENE;

D O I：

10.1038/ncomms4963

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Although individual pseudogenes have been implicated in tumour biology, the biomedical significance and clinical relevance of pseudogene expression have not been assessed in a systematic way. Here we generate pseudogene expression profiles in 2,808 patient samples of seven cancer types from The Cancer Genome Atlas RNA-seq data using a newly developed computational pipeline. Supervised analysis reveals a significant number of pseudogenes differentially expressed among established tumour subtypes and pseudogene expression alone can accurately classify the major histological subtypes of endometrial cancer. Across cancer types, the tumour subtypes revealed by pseudogene expression show extensive and strong concordance with the subtypes defined by other molecular data. Strikingly, in kidney cancer, the pseudogene expression subtypes not only significantly correlate with patient survival, but also help stratify patients in combination with clinical variables. Our study highlights the potential of pseudogene expression analysis as a new paradigm for investigating cancer mechanisms and discovering prognostic biomarkers.

引用

页数：9

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