Research Papers:

Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma

Zongcheng Li _, Yaowen Chen, Shuofeng Hu, Jian Zhang, Jiaqi Wu, Wu Ren, Ningsheng Shao and Xiaomin Ying

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Oncotarget. 2016; 7:82671-82685. https://doi.org/10.18632/oncotarget.12340

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Zongcheng Li1,2, Yaowen Chen1,3, Shuofeng Hu1, Jian Zhang1, Jiaqi Wu1, Wu Ren1,4, Ningsheng Shao1, Xiaomin Ying1

1Beijing Institute of Basic Medical Sciences, Beijing 100850, China

2Translational Medicine Center of Stem Cells, 307-Ivy Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing 100071, China

3Department of Obstetrics and Gynecology, Fuzhou General Hospital of Nanjing Military Command, Fuzhou, Fujian 350025, China

4Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jilin University, Changchun 130021, China

Correspondence to:

Xiaomin Ying, email: [email protected]; [email protected]

Keywords: subtyping, integrative analysis, transcriptome, ccRCC, non-coding RNAs

Received: May 23, 2016    Accepted: September 20, 2016    Published: September 29, 2016


Protein-coding genes and non-coding RNAs cooperate mutually in cells. Integrative analysis of protein-coding and non-coding RNAs may facilitate characterizing tumor heterogeneity. We introduced integrated consensus clustering (ICC) method to integrate mRNA, miRNA and lncRNA expression profiles of 431 primary clear cell renal cell carcinomas (ccRCCs). We identified one RCC subgroup easily misdiagnosed as ccRCC in clinic and four robust ccRCC subtypes associated with distinct clinicopathologic and molecular features. In subtype R1, AMPK signaling pathway is significantly upregulated, which may improve the oncologic-metabolic shift and partially account for its best prognosis. Subtype R2 has more chromosomal abnormities, higher expression of cell cycle genes and less expression of genes in various metabolism pathways, which may explain its more aggressive characteristic and the worst prognosis. Moreover, much more miRNAs and lncRNAs are significantly upregulated in R2 and R4 respectively, suggesting more important roles of miRNAs in R2 and lncRNAs in R4. Triple-color co-expression network analysis identified 28 differentially expressed modules, indicating the importance of cooperative regulation of mRNAs, miRNAs and lncRNAs in ccRCC. This study establishes an integrated transcriptomic classification which may contribute to understanding the heterogeneity and implicating the treatment of ccRCC.

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