The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers

Shuaibin Lian; Liansheng Li; Yongjie Zhou; Zixiao Liu; Lei Wang

doi:10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers

PeerJ. 2019 Sep 17:7:e7696. doi: 10.7717/peerj.7696. eCollection 2019.

Authors

Shuaibin Lian^#¹, Liansheng Li^#², Yongjie Zhou¹, Zixiao Liu¹, Lei Wang²

Affiliations

¹ College of Physics and Electronic Engineering, XinYang Normal University, Xinyang, HeNan, China.
² College of Life Sciences, XinYang Normal University, Xinyang, HeNan, China.

^# Contributed equally.

Abstract

Background: RNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation.

Results: Here, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types-CHOL and KICH-is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively.

Conclusions: These results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic targets for patients with cancers at the N and M stages in two cancer types CHOL and KICH.

Keywords: Clinical TNM system; Co-expression networks; Differential expression; RNA-binding proteins (RBPs); Transcriptional factors; lncRNAs.

Grants and funding

This work was supported by the National Natural Science Foundation of China (Grant. 61501392) and the Nanhu Scholars Program for Young Scholars of XYNU (Xin Yang Normal University). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.