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SFTA1P、LINC00968、GATA6-AS1、TBX5-AS1和FEZF1-AS1是与肺鳞状细胞癌预后相关的关键长链非编码RNA。

SFTA1P, LINC00968, GATA6-AS1, TBX5-AS1, and FEZF1-AS1 are crucial long non-coding RNAs associated with the prognosis of lung squamous cell carcinoma.

作者信息

Xiong Youwen, Zhang Xinyi, Lin Zhuohui, Xiong Aizhen, Xie Shanshan, Liang Jia, Zhang Weifang

机构信息

Department of Pharmacy/Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China.

Testing Room 3, Jiangxi Supervision and Inspection Center for Medical Devices, Nanchang, Jiangxi 330029, P.R. China.

出版信息

Oncol Lett. 2019 Oct;18(4):3985-3993. doi: 10.3892/ol.2019.10744. Epub 2019 Aug 14.

DOI:10.3892/ol.2019.10744
PMID:31579094
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6757264/
Abstract

Lung cancer has high incidence and mortality rates, and lung squamous cell carcinoma (LUSC) is a common form of non-small-cell lung carcinoma (NSCLC). The aim of our study was to discover long non-coding RNAs (lncRNAs) associated with LUSC prognosis. RNA-sequencing data obtained from LUSC samples were extracted from The Cancer Genome Atlas database. Using the limma package, differentially expressed genes (DEGs; including differentially expressed lncRNA genes (DELs), coding genes (DECs), and other genes (DEOs)) between LUSC and control samples were analyzed. Using Kaplan-Meier survival analysis, prognosis-associated lncRNAs were further selected. Following the calculation of Pearson's correlation coefficients between DELs and other DEGs, the DEL-DEG co-expression network was visualized using Cytoscape software. Using the clusterProfiler package, potential functions for DECs co-expressed with DELs were predicted. There were 1,305 DEGs in LUSC samples, including 153 DELs, 1,109 DECs, and 43 DEOs. Based on survival analysis, 22 prognosis-associated lncRNAs (including surfactant associated 1, pseudogene (SFTA1P), long intergenic non-protein coding RNA 968 (LINC00968), GATA6 antisense RNA 1, (GATA6-AS1) TBX5 antisense RNA 1 (TBX5-AS1) and FEZF1 antisense RNA 1 (FEZF1-AS1)) in LUSC were selected from these DELs, and the associated abnormal expression levels were also verified in LUSC clinical samples. A DEL-DEG co-expression network was constructed, which involved 93 DELs. Co-expressed DECs were enriched for only 8 prognosis-associated DELs, including LINC00968, SFTA1P, and TBX5-AS1. Specifically, mitogen-activated protein kinase (MAPK) signaling pathway-associated genes were enriched in DECs co-expressed with LINC00968, SFTA1P, GATA6-AS1, TBX5-AS1 and FEZF1-AS1, which may be prognosis-associated lncRNAs in LUSC. In addition, LINC00968 may affect the outcome of patients with LUSC via the MAPK signaling pathway.

摘要

肺癌具有较高的发病率和死亡率，肺鳞状细胞癌（LUSC）是非小细胞肺癌（NSCLC）的一种常见形式。我们研究的目的是发现与LUSC预后相关的长链非编码RNA（lncRNA）。从癌症基因组图谱数据库中提取了从LUSC样本获得的RNA测序数据。使用limma软件包，分析了LUSC样本与对照样本之间的差异表达基因（DEG；包括差异表达的lncRNA基因（DEL）、编码基因（DEC）和其他基因（DEO））。使用Kaplan-Meier生存分析，进一步筛选出与预后相关的lncRNA。计算DEL与其他DEG之间的Pearson相关系数后，使用Cytoscape软件可视化DEL-DEG共表达网络。使用clusterProfiler软件包，预测了与DEL共表达的DEC的潜在功能。LUSC样本中有1305个DEG，包括153个DEL、1109个DEC和43个DEO。基于生存分析，从这些DEL中筛选出22个与LUSC预后相关的lncRNA（包括表面活性剂相关1假基因（SFTA1P）、长链基因间非编码RNA 968（LINC00968）、GATA6反义RNA 1（GATA6-AS1）、TBX5反义RNA 1（TBX5-AS1）和FEZF1反义RNA 1（FEZF1-AS1）），并在LUSC临床样本中验证了相关的异常表达水平。构建了一个包含93个DEL的DEL-DEG共表达网络。共表达的DEC仅富集了8个与预后相关的DEL，包括LINC00968、SFTA1P和TBX5-AS1。具体而言，丝裂原活化蛋白激酶（MAPK）信号通路相关基因在与LINC00968、SFTA1P、GATA6-AS1、TBX5-AS1和FEZF1-AS1共表达的DEC中富集，这些可能是LUSC中与预后相关的lncRNA。此外，LINC00968可能通过MAPK信号通路影响LUSC患者的预后。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/1992ea0a3c0f/ol-18-04-3985-g07.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/8e5b0c850627/ol-18-04-3985-g00.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/f58ecfb2cd30/ol-18-04-3985-g04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/5133dcac01f8/ol-18-04-3985-g05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/bd4d277ee966/ol-18-04-3985-g06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/1992ea0a3c0f/ol-18-04-3985-g07.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/8e5b0c850627/ol-18-04-3985-g00.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/412d0db2dd4f/ol-18-04-3985-g01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/82299a51bc26/ol-18-04-3985-g02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/d3d5516b12f1/ol-18-04-3985-g03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/f58ecfb2cd30/ol-18-04-3985-g04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/5133dcac01f8/ol-18-04-3985-g05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/bd4d277ee966/ol-18-04-3985-g06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7fb4/6757264/1992ea0a3c0f/ol-18-04-3985-g07.jpg

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