Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in laryngeal squamous cell carcinoma
Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in laryngeal squamous cell carcinoma
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DOI：
10.1080/15476286.2020.1741282
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发表时间：
2020-07-02
期刊：
影响因子：
4.1
通讯作者：
Lei, Wenbin
中科院分区：
文献类型：
--
作者：
Lyu, Kexing;Li, Yun;Lei, Wenbin
越来越多的证据表明，lncRNAs可以与miRNAs相互作用，通过竞争性相互作用调节靶基因的表达。然而，这一机制在喉鳞状细胞癌（LSCC）中仍有待进一步研究。本研究通过对3对喉鳞癌组织及癌旁正常组织进行全转录组RNA测序，研究lncRNA、miRNAs和mRNAs的表达谱，共检测到171个lncRNA、36个miRNAs和1709个mRNAs的差异表达。通过使用qRT-PCR鉴定出7种lncRNA、8种mRNA和3种miRNA在患者组织中失调。通过GO和KEGG途径富集分析，阐明这些差异表达基因在喉鳞状细胞癌中的潜在功能。随后，基于lncRNA和mRNA共享的预测的miRNA构建了包括4631个ceRNA对的ceRNA（lncRNA-miRNA-mRNA）网络。通过基于生物信息学的方法分析顺式和反式调节lncRNA。重要的是，基于潜在的癌症相关编码基因，进一步获得了mRNA相关的ceRNA网络（mRCN）。lncRNA和下游mRNA之间的共表达被用作验证mRCN的标准，确定ZNF 561-AS 1-miR 217-WNT 5A和SATB 1-AS 1-miR 1299-SAV 1/CCNG 2/SH 3 KBP 1/JADE 1/HIPK 2 ceRNA调节相互作用，然后在siRNA转染后进行实验验证。此外，ceRNA活性分析显示，在特定的病理环境中，ceRNA模块的不同活性可能与喉鳞癌的发生有关。SATB 1-AS 1和ZNF 561-AS 1的表达下调均能显著促进喉癌细胞的迁移和侵袭，提示它们通过ceRNA调控机制在喉鳞状细胞癌中发挥重要作用。总之，本研究的结果揭示并系统表征了lncRNA相关的ceRNA调控网络，这可能对LSCC的诊断和治疗有价值。
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.