Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in laryngeal squamous cell carcinoma

Kexing Lyu; Yun Li; Yang Xu; Huijun Yue; Yihui Wen; Tesi Liu; Siyu Chen; Qihong Liu; Weiqiang Yang; Xiaolin Zhu; Zhangfeng Wang; Liping Chai; Weiping Wen; Chunwei Li; Wenbin Lei

doi:10.1080/15476286.2020.1741282

Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in laryngeal squamous cell carcinoma

RNA Biol. 2020 Jul;17(7):977-989. doi: 10.1080/15476286.2020.1741282. Epub 2020 Mar 30.

Authors

Kexing Lyu¹, Yun Li¹, Yang Xu¹, Huijun Yue¹, Yihui Wen¹, Tesi Liu¹, Siyu Chen¹, Qihong Liu², Weiqiang Yang³, Xiaolin Zhu¹, Zhangfeng Wang¹, Liping Chai¹, Weiping Wen¹, Chunwei Li¹, Wenbin Lei¹

Affiliations

¹ Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China.
² Department of Otolaryngology, The Eighth Affiliated Hospital, Sun Yat-sen University , Shenzhen, Guangdong, P.R. China.
³ Department of Otolaryngology, Peking University Shenzhen Hospital , Shenzhen, Guangdong, P.R. China.

Abstract

Accumulating evidence indicates that lncRNAs can interact with miRNAs to regulate target mRNAs through competitive interactions. However, this mechanism remains largely unexplored in laryngeal squamous cell carcinoma (LSCC). In this study, transcriptome-wide RNA sequencing was performed on 3 pairs of LSCC tissues and adjacent normal tissues to investigate the expression profiles of lncRNAs, miRNAs and mRNAs, with differential expression of 171 lncRNAs, 36 miRNAs and 1709 mRNAs detected. Seven lncRNAs, eight mRNAs and three miRNAs were identified to be dysregulated in patients' tissues by using qRT-PCR. GO and KEGG pathway enrichment analyses were performed to elucidate the potential functions of these differentially expressed genes in LSCC. Subsequently, a ceRNA (lncRNA-miRNA-mRNA) network including 4631 ceRNA pairs was constructed based on predicted miRNAs shared by lncRNAs and mRNAs. Cis- and transregulatory lncRNAs were analysed by bioinformatics-based methods. Importantly, mRNA-related ceRNA networks (mRCNs) were further obtained based on potential cancer-related coding genes. Coexpression between lncRNAs and downstream mRNAs was used as a criterion for the validation of mRCNs, with the ZNF561-AS1-miR217-WNT5A and SATB1-AS1-miR1299-SAV1/CCNG2/SH3 KBP1/JADE1/HIPK2 ceRNA regulatory interactions determined, followed by experimental validation after siRNA transfection. Moreover, ceRNA activity analysis revealed that different activities of ceRNA modules existing in specific pathological environments may contribute to the tumorigenesis of LSCC. Consistently, both downregulated SATB1-AS1 and ZNF561-AS1 significantly promoted laryngeal cancer cell migration and invasion, indicating their important roles in LSCC via a ceRNA regulatory mechanism. Taken together, the results of this investigation uncovered and systemically characterized a lncRNA-related ceRNA regulatory network that may be valuable for the diagnosis and treatment of LSCC.

Keywords: CeRNA; RNA sequencing; laryngeal carcinoma; lncRNA; noncoding RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers, Tumor
Carcinoma, Squamous Cell / genetics*
Cell Movement / genetics
Computational Biology / methods
Gene Expression Profiling / methods
Gene Expression Regulation, Neoplastic*
Gene Regulatory Networks*
Humans
Laryngeal Neoplasms / genetics*
MicroRNAs / genetics
RNA Interference
RNA, Long Noncoding*
RNA, Messenger / genetics
Reproducibility of Results
Transcriptome

Substances

Biomarkers, Tumor
MicroRNAs
RNA, Long Noncoding
RNA, Messenger

Grants and funding

This work was supported by the Science and Technology Planning Project of Guangdong Province (China) (Grant No. 2017A050506018), National Natural Science Foundation of China (Grant No. 81972528) and Guangzhou Municipal Science and Technology Project (China) (Grant No. 201704020092). Assistance with the RNA sequencing technology was provided by GENE DENOVO (Guangzhou, China).