基于TCGA和GEO数据库的胃癌lncRNA筛选与ceRNA网络构建

doi:10.19586/j.2095-2341.2021.0042

生物技术进展 ›› 2022, Vol. 12 ›› Issue (1): 149-157.DOI: 10.19586/j.2095-2341.2021.0042

• 研究论文 • 上一篇

基于TCGA和GEO数据库的胃癌lncRNA筛选与ceRNA网络构建

雍嘉欣¹(), 韦权峰², 刘尚辉³()

^1.中国医科大学第二临床学院，沈阳 110122
^2.中国医科大学第一临床学院，沈阳 110122
^3.中国医科大学智能医学学院，沈阳 110122

收稿日期:2021-04-02 接受日期:2021-06-01 出版日期:2022-01-25 发布日期:2022-01-26
通讯作者: 刘尚辉
作者简介:雍嘉欣 E-mail：yongjiax@163.com；
基金资助:
2020年中国医科大学大学生创新创业训练计划（国家级）项目(202010159006)

Expression Profile Screening of lncRNA and ceRNA Network Construction in Gastric Cancer Based on TCGA and GEO Databases

Jiaxin YONG¹(), Quanfeng WEI², Shanghui LIU³()

^1.Second Clinical College，China Medical University，Shenyang 110122，China
^2.First Clinical College，China Medical University，Shenyang 110122，China
^3.School of Intelligent Medicine，China Medical University Shenyang 110122，China

Received:2021-04-02 Accepted:2021-06-01 Online:2022-01-25 Published:2022-01-26
Contact: Shanghui LIU

摘要/Abstract

摘要：

胃癌（gastric cancer，GC）是我国最常见的恶性肿瘤之一，严重危害人类健康。胃癌发病机制复杂，缺乏特异性预后生物标志物。长链非编码RNA（long non?coding RNA，lncRNA）可作为竞争性内源RNA（competing endogenous RNA，ceRNA），影响microRNA（miRNA）与mRNA的结合，从而影响胃癌的发生、发展。基于TCGA和GEO数据库的转录组数据，筛选GC中差异表达的lncRNAs，并构建基于6条lncRNAs（HAGLROS、TMEM92?AS1、LINC01745、HOXC?AS3、SEMA3B?AS1、FEZF1?AS1）的lncRNA?miRNA?mRNA网络。网络核心基因的KEGG/GO富集和蛋白质互作分析结果显示，lncRNA可能通过miRNA海绵吸附作用，调控胃癌的发生、发展与转移。AC011352.1、AC087636.1、AC093627.1、GAS1RR与胃癌患者的预后相关性具有统计学意义（P<0.05），并可能成为胃癌患者潜在的预后生物标志物。

关键词: 胃癌, 长链非编码RNA, 竞争性内源RNA网络, 预后生物标志物

Abstract:

Gastric cancer （GC） is one of the most malignant tumors in China， which seriously endangers human health. The tumorigenesis of GC is complicated and lacks specific prognostic biomarkers. Long non?coding RNA （lncRNA） can be used as competitive endogenous RNA （ceRNA） to affect the interaction of microRNA （miRNA） and mRNA， thereby affecting the carcinogenesis and development of GC. Based on the transcriptome data of the TCGA and GEO databases， this study screened the differentially expressed lncRNAs in GC. A lncRNA?miRNA?mRNA network based on six lncRNAs （HAGLROS， TMEM92?AS1， LINC01745， HOXC?AS3， SEMA3B?AS1， FEZF1?AS1） was constructed. The KEGG/GO enrichment and protein interaction analysis showed that lncRNA might regulate the occurrence， development， and metastasis of GC through the mechanism of microRNA sponge. AC011352.1， AC087636.1， AC093627.1， GAS1RR were significant related to the prognosis of GC patients （P<0.05）， which may become potential prognostic biomarkers for GC patients.

Key words: gastric cancer, long non?coding RNA, competing endogenous RNA network, prognostic biomarkers

中图分类号:

R735.2

雍嘉欣, 韦权峰, 刘尚辉. 基于TCGA和GEO数据库的胃癌lncRNA筛选与ceRNA网络构建[J]. 生物技术进展, 2022, 12(1): 149-157.

Jiaxin YONG, Quanfeng WEI, Shanghui LIU. Expression Profile Screening of lncRNA and ceRNA Network Construction in Gastric Cancer Based on TCGA and GEO Databases[J]. Current Biotechnology, 2022, 12(1): 149-157.

图/表 9

参考文献 17

1	SUNG H, FERLAY J, SIEGEL R L, et al.. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries[J]. CA Cancer J. Clin., 2021, 71(3): 209-249.
2	POLISENO L, SALMENA L, ZHANG J, et al.. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology[J]. Nature, 2010, 465(7301): 1033-1038.
3	WANG Y, HOU J, HE D, et al.. The emerging function and mechanism of cernas in cancer[J]. Trends Genet., 2016, 32(4): 211-224.
4	GUO X, LV X, RU Y, et al.. Circulating exosomal gastric cancer-associated long noncoding RNA1 as a biomarker for early detection and monitoring progression of gastric cancer: a multiphase study[J]. JAMA Surg., 2020, 155(7): 572-579.
5	YANG X Z, CHENG T T, HE Q J, et al.. LINC01133 as ceRNA inhibits gastric cancer progression by sponging miR-106a-3p to regulate APC expression and the Wnt/β-catenin pathway[J/OL]. Mol. Cancer., 2018, 17(1): 126[2021-11-02]. .
6	YUAN L, XU Z Y, RUAN S M, et al.. Long non-coding RNAs towards precision medicine in gastric cancer: early diagnosis, treatment, and drug resistance[J/OL]. Mol. Cancer, 2020, 19(1): 96[2021-11-02]. .
7	WANG C J, ZHU C C, XU J, et al.. The lncRNA UCA1 promotes proliferation, migration, immune escape and inhibits apoptosis in gastric cancer by sponging anti-tumor miRNAs[J]. Mol. Cancer, 2019, 18(1):115.
8	THRIFT A P, EL-SERAG H B. Burden of gastric cancer[J]. Clin. Gastroenterol. Hepatol., 2020, 18(3): 534-542.
9	ZHANG E, HE X, ZHANG C, et al.. A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1[J/OL]. Genome Biol., 2018, 19(1):154[2021-11-02]. .
10	ZHUO W, LIU Y, LI S, et al.. Long noncoding RNA GMAN, up-regulated in gastric cancer tissues, is associated with metastasis in patients and promotes translation of ephrin A1 by competitively binding GMAN-AS[J]. Gastroenterology, 2019, 156(3): 676-691.
11	NECULA L, MATEI L, DRAGU D, et al.. Recent advances in gastric cancer early diagnosis[J]. World J. Gastroenterol., 2019, 25(17): 2029-2044.
12	SHUAI Y, MA Z, LIU W, et al.. TEAD4 modulated LncRNA MNX1-AS1 contributes to gastric cancer progression partly through suppressing BTG2 and activating BCL2[J/OL]. Mol. Cancer., 2020, 19(1): 6[2021-11-02]. .
13	XU W, ZHOU G, WANG H, et al.. Circulating lncRNA SNHG11 as a novel biomarker for early diagnosis and prognosis of colorectal cancer[J]. Int. J. Cancer., 2020, 146(10): 2901-2912.
14	GU J, LI Y, FAN L, et al.. Identification of aberrantly expressed long non-coding RNAs in stomach adenocarcinoma[J]. Oncotarget, 2017, 8(30): 49201-49216.
15	LIU Y W, XIA R, LU K, et al. LincRNAFEZF1-AS1 represses p21 expression to promote gastric cancer proliferation through LSD1-mediated H3K4me2 demethylation[J/OL]. Mol. Cancer, 2017, 16(1): 39[2021-11-02]. .
16	SONG J, LIU Y, WANG T, et al.. MiR-17-5p promotes cellular proliferation and invasiveness by targeting RUNX3 in gastric cancer[J/OL]. Biomed. Pharmacother., 2020, 128: 110246[2021-11-02]. .
17	HUANG S, ZHANG X, GUAN B, et al.. A novel circular RNA hsa_circ_0008035 contributes to gastric cancer tumorigenesis through targeting the miR-375/YBX1 axis[J]. Am. J. Transl. Res., 2019, 11(4): 2455-2462.

lncRNA	ENSG_ID	log₂FC	P值
AL499627.1	ENSG00000260542	9.443 963	1.16E⁃06
LINC00392	ENSG00000228295	8.611 667	2.37E⁃08
LINC02163	ENSG00000251026	7.361 286	2.45E⁃08
LINC02241	ENSG00000251629	7.182 590	2.54E⁃05
LINC00280	ENSG00000229643	7.071 880	1.94E⁃07
AL365255.1	ENSG00000236948	7.061 308	1.72E⁃06
AC106875.1	ENSG00000228496	6.929 041	1.67E⁃05
HOXC-AS3	ENSG00000251151	6.836 142	8.24E⁃11
AC105460.1	ENSG00000250920	6.744 219	7.94E⁃10
LINC02342	ENSG00000280580	6.613 304	2.69E⁃07
AL163974.1	ENSG00000258576	-6.157 410	3.74E⁃28
LINC02255	ENSG00000277718	-5.827 930	1.94E⁃26
AC005909.1	ENSG00000265425	-5.443 180	3.69E⁃34
LIVAR	ENSG00000266304	-5.309 590	4.98E⁃36
AC239803.2	ENSG00000232265	-5.042 440	1.89E⁃45
LINC01531	ENSG00000205786	-4.907 700	4.37E⁃34
AC007342.4	ENSG00000261804	-4.905 270	2.04E⁃54
AC009120.6	ENSG00000261404	-4.855 820	1.23E⁃34
CNTN4-AS2	ENSG00000227588	-4.830 330	3.62E⁃32
LINC02445	ENSG00000257750	-4.763 960	7.42E⁃30

lncRNA	ENSG_ID	log₂FC	P值
AL499627.1	ENSG00000260542	9.443 963	1.16E⁃06
LINC00392	ENSG00000228295	8.611 667	2.37E⁃08
LINC02163	ENSG00000251026	7.361 286	2.45E⁃08
LINC02241	ENSG00000251629	7.182 590	2.54E⁃05
LINC00280	ENSG00000229643	7.071 880	1.94E⁃07
AL365255.1	ENSG00000236948	7.061 308	1.72E⁃06
AC106875.1	ENSG00000228496	6.929 041	1.67E⁃05
HOXC-AS3	ENSG00000251151	6.836 142	8.24E⁃11
AC105460.1	ENSG00000250920	6.744 219	7.94E⁃10
LINC02342	ENSG00000280580	6.613 304	2.69E⁃07
AL163974.1	ENSG00000258576	-6.157 410	3.74E⁃28
LINC02255	ENSG00000277718	-5.827 930	1.94E⁃26
AC005909.1	ENSG00000265425	-5.443 180	3.69E⁃34
LIVAR	ENSG00000266304	-5.309 590	4.98E⁃36
AC239803.2	ENSG00000232265	-5.042 440	1.89E⁃45
LINC01531	ENSG00000205786	-4.907 700	4.37E⁃34
AC007342.4	ENSG00000261804	-4.905 270	2.04E⁃54
AC009120.6	ENSG00000261404	-4.855 820	1.23E⁃34
CNTN4-AS2	ENSG00000227588	-4.830 330	3.62E⁃32
LINC02445	ENSG00000257750	-4.763 960	7.42E⁃30

lncRNA	KM	HR	HR.95L	HR.95H	Cox P值
GAS1RR	2.25E⁃02	1.003 3	1.000 1	1.006 5	4.01E⁃02
AC087636.1	3.67E⁃02	1.077 8	1.020 9	1.137 8	6.75E⁃03
AC093627.1	5.68E⁃03	1.007 0	1.001 6	1.012 4	1.04E⁃02
AC011352.1	9.20E⁃03	1.012 5	1.001 7	1.023 4	2.34E⁃02

lncRNA	KM	HR	HR.95L	HR.95H	Cox P值
GAS1RR	2.25E⁃02	1.003 3	1.000 1	1.006 5	4.01E⁃02
AC087636.1	3.67E⁃02	1.077 8	1.020 9	1.137 8	6.75E⁃03
AC093627.1	5.68E⁃03	1.007 0	1.001 6	1.012 4	1.04E⁃02
AC011352.1	9.20E⁃03	1.012 5	1.001 7	1.023 4	2.34E⁃02

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基于TCGA和GEO数据库的胃癌lncRNA筛选与ceRNA网络构建

Expression Profile Screening of lncRNA and ceRNA Network Construction in Gastric Cancer Based on TCGA and GEO Databases

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