Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma

PeerJ

article

Shusen Zhang¹  Ruoyan Cao¹  Qiulan Li³  Mianfeng Yao⁴  Yu Chen¹  Hongbo Zhou¹ 

[1] Department of Prosthodontics, Xiangya Stomatological Hospital & School of Stomatology, Central South University;Department of Stomatology, Hunan University of Medicine;Department of Stomatology, The Second Xiangya Hospital, Central South University;Department of Stomatology, Xiangya Hospital, Central South University

关键词: Tongue squamous cell carcinoma;    Long noncoding RNA;    Prognosis;    Competing endogenous RNA network;   

DOI  :  10.7717/peerj.6397

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundIncreasing evidence has demonstrated that long non-coding RNAs (lncRNAs) play an important role in the competitive endogenous RNA (ceRNA) networks in that they regulate protein-coding gene expression by sponging microRNAs (miRNAs). However, the understanding of the ceRNA network in tongue squamous cell carcinoma (TSCC) remains limited.MethodsExpression profile data regarding mRNAs, miRNAs and lncRNAs as well as clinical information on 122 TSCC tissues and 15 normal controls from The Cancer Genome Atlas (TCGA) database were collected. We used the edgR package to identify differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and miRNAs (DEmiRNAs) between TSCC samples and normal samples. In order to explore the functions of DEmRNAs, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed. Subsequently, a ceRNA network was established based on the identified DElncRNAs–DEmiRNAs and DEmiRNAs–DEmRNAs interactions. The RNAs within the ceRNA network were analyzed for their correlation with overall disease survival. Finally, lncRNAs were specifically analyzed for their correlation with clinical features in the included TSCC patient samples.ResultsA total of 1867 mRNAs, 828 lncRNAs and 81 miRNAs were identified as differentially expressed in TSCC tissues (—log 2fold change— ≥ 2; adjusted P value <0.01). The resulting ceRNA network included 16 mRNAs, 56 lncRNAs and 6 miRNAs. Ten out of the 56 lncRNAs were found to be associated with the overall survival in TSCC patients (P < 0.05); 10 lncRNAs were correlated with TSCC progression (P < 0.05).ConclusionOur study deepens the understanding of ceRNA network regulatory mechanisms in TSCC. Furthermore, we identified ten lncRNAs (PART1, LINC00261, AL163952.1, C2orf48, FAM87A, LINC00052, LINC00472, STEAP3-AS1, TSPEAR-AS1 and ERVH48-1) as novel, potential prognostic biomarkers and therapeutic targets for TSCC.

【 授权许可】

CC BY