Tags

Type your tag names separated by a space and hit enter

Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma.
PeerJ. 2019; 7:e6397.P

Abstract

Background

Increasing 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.

Methods

Expression 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.

Results

A 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).

Conclusion

Our 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.

Authors+Show Affiliations

Department of Prosthodontics, Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha, China. Department of Stomatology, Hunan University of Medicine, Hunan, China.Department of Prosthodontics, Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha, China.Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China.Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China.Department of Prosthodontics, Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha, China.Department of Prosthodontics, Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha, China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30755833

Citation

Zhang, Shusen, et al. "Comprehensive Analysis of lncRNA-associated Competing Endogenous RNA Network in Tongue Squamous Cell Carcinoma." PeerJ, vol. 7, 2019, pp. e6397.
Zhang S, Cao R, Li Q, et al. Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma. PeerJ. 2019;7:e6397.
Zhang, S., Cao, R., Li, Q., Yao, M., Chen, Y., & Zhou, H. (2019). Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma. PeerJ, 7, e6397. https://doi.org/10.7717/peerj.6397
Zhang S, et al. Comprehensive Analysis of lncRNA-associated Competing Endogenous RNA Network in Tongue Squamous Cell Carcinoma. PeerJ. 2019;7:e6397. PubMed PMID: 30755833.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma. AU - Zhang,Shusen, AU - Cao,Ruoyan, AU - Li,Qiulan, AU - Yao,Mianfeng, AU - Chen,Yu, AU - Zhou,Hongbo, Y1 - 2019/02/06/ PY - 2018/10/03/received PY - 2019/01/07/accepted PY - 2019/2/14/entrez PY - 2019/2/14/pubmed PY - 2019/2/14/medline KW - Competing endogenous RNA network KW - Long noncoding RNA KW - Prognosis KW - Tongue squamous cell carcinoma SP - e6397 EP - e6397 JF - PeerJ VL - 7 N2 - Background: Increasing 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. Methods: Expression 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. Results: A 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). Conclusion: Our 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. SN - 2167-8359 UR - https://www.unboundmedicine.com/medline/citation/30755833/Comprehensive_analysis_of_lncRNA_associated_competing_endogenous_RNA_network_in_tongue_squamous_cell_carcinoma_ L2 - https://doi.org/10.7717/peerj.6397 DB - PRIME DP - Unbound Medicine ER -
Try the Free App:
Prime PubMed app for iOS iPhone iPad
Prime PubMed app for Android
Prime PubMed is provided
free to individuals by:
Unbound Medicine.