结直肠癌发病相关关键lncRNA的筛选和鉴定：基于肿瘤基因图谱数据库的生物信息学分析

徐丞; 刘占国; 罗育其; 张一方

doi:10.12122/j.issn.1674-4500.2019.01.14

结直肠癌发病相关关键lncRNA的筛选和鉴定：基于肿瘤基因图谱数据库的生物信息学分析

doi: 10.12122/j.issn.1674-4500.2019.01.14

徐丞^1,2,,
刘占国^1, ,,
罗育其³,
张一方⁴

1.
南方医科大学珠江医院重症医学科，广东广州 510280
2.
中国人民解放军南部战区总医院干部病房五科，广东广州 510010
3.
广州市第一人民医院南沙医院普通外科，广东广州 511457
4.
广东省人民医院南海医院普通外科，广东佛山 528251

基金项目: 广东省自然科学基金（2015A030310021）；华南理工大学中央高校基本科研业务费专项基金（2018MS21）

详细信息

作者简介:
徐丞：徐丞，主治医师，E-mail: 52696468@qq.com

通讯作者:
刘占国，教授，主任医师，E-mail: zhguoliu@163.com

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- 被引次数: 0
出版历程
- 收稿日期: 2018-10-22
- 刊出日期: 2019-01-01

Screening and identification of key lncRNA associate with carcinogenesis and development of CRC: a bioinformatic analysis of TCGA

Cheng XU^{1,2
,},
Zhanguo LIU^{1
, ,},
Yuqi LUO³,
Yifang ZHANG⁴

1.
Department of Critical Care, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
2.
Ward of Cadres, General Hospital of Southern Theater Command, PLA, Guangzhou 510010, China
3.
Department of General Surgery, Nansha Hospital of Guangzhou First People’s Hospital, Guangzhou 511457, China
4.
Department of General Surgery, Nanhai Hospital, Guangdong Province People’s Hospital, Foshan 528251, China

摘要

摘要: 目的探讨长链非编码RNA（lncRNA）在结直肠癌（CRC）中的表达特征及其对患者生存预后判断的潜在价值。方法下载肿瘤基因图谱（TCGA）中CRC相关的RNA序列（RNA-seq）数据，进行lncRNA表达差异、功能、通路富集、调控网络及lncRNA-mRNA共表达分析，同时分析lncRNA差异表达对CRC患者预后的影响。结果对TCGA 453个CRC临床样本数据进行分析，提示有119个lncRNA存在差异性表达，lncRNA和编码基因存在共表达关系，对基因富集性分析发现，lncRNA参与细胞的多个生物学行为；16个lncRNA对患者生存预后显著相关，其中3个lncRNA BVES-AS1、HAND2-AS1和MAMDC2-AS1为关键lncRNA，可作为预后判断的标志物，同时与miRNA、coding gene存在紧密的调控网络。结论 lncRNA在CRC中存在差异性表达，起着重要的调控作用，在CRC患者诊断、靶向治疗及预后判断方面具有潜在的应用价值。
- 长链非编码RNA /
- 生物信息学分析 /
- 结直肠癌 /
- 肿瘤基因图谱
Abstract: Objective To expore the lncRNA expression profiles and features in CRC tissues and their potential value associated with prognosis assessment. Methods The differential expression, functional and pathway enrichment, interaction network and lncRNA-mRNA co-expression of lncRNA wereanalyzed using RNA-seq data from TCGA. The prognosis changes of CRC patients induced by the differential expression level of lncRNA wereanalyzed . Results TCGA RNA-seq data from 453 specimens of CRC patients showed that there were 119 lncRNA which expressed differentially. lncRNA and coding gene had the relation of co-expression. lncRNA played various roles in biological features of cells. There existed lncRNA-miRNA-mRNA regulatory network. 16 of these lncRNA had potential value on the prognosis of CRC patients, 3 of them were key lncRNA, which were BVES-AS1, HAND2-AS1 and MAMDC2-AS1. They could be seemed as the biomarkers for prognosis of CRC patients. They also had close relations with the miRNA and coding gene. Conclusion lncRNA express differently in CRC tissues, and play an important role in biological feature of CRC cells, which have potential value in diagnosis, targeted therapy and prognosis of CRC patients.
- lncRNA /
- bioinformatics analysis /
- colorectal cancer /
- TCGA

HTML全文

图 1 lncRNA-coding gene共表达网络

红色代表显著差异表达上调，绿色代表显著差异表达下调，圆形表示coding gene，三角形表示lncRNA.

下载: 全尺寸图片幻灯片

图 2 lncRNA的GO功能富集结果（A）和KEGG pathway富集结果（B）

下载: 全尺寸图片幻灯片

图 3 BVES-AS1 （A）、HAND2-AS1 （B）、MAMDC2-AS1 （C）的生存曲线及其与miRNA、coding gene的调控网络（D）

三角形为lncRNA，菱形为miRNA，圆形为coding gene.

下载: 全尺寸图片幻灯片

表 1 差异表达基因统计结果

Item	UP	DOWN	Total
lncRNA	97	27	119
Coding gene	504	352	856
Total	601	379	975

下载: 导出CSV

表 2 与预后相关的lncRNA信息

Gene name	Ensembl ID	Chromosomal Location	log₂FC	FDR
AC079612.1	ENSG00000196758	chr2:240499995-240507788	3.69	2.22E-17
MAMDC2-AS1	ENSG00000204706	chr9:72648837-72790804	–3.63	2.69E-73
LINC01555	ENSG00000180869	chr1:85093913-85100703	3.01	2.68E-17
BVES-AS1	ENSG00000203808	chr6:105584183-105617820	–3.511	1.14E-41
LINC00922	ENSG00000261742	chr16:65318402-65610203	3.15	2.25E-16
WT1-AS	ENSG00000183242	chr11:32457064-32480315	3.59	1.59E-08
HOTAIR	ENSG00000228630	chr12:54356092-54368740	4.16	1.87E-08
RP11-353N14.4	ENSG00000262188	chr17:77893156-77899261	3.76	3.05E-28
LL22NC03-N64E9.	ENSG00000271127	chr22:16179617-16181004	3.54	2.40E-13
PGM5-AS1	ENSG00000224958	chr9:70970105-70972768	–4.59	3.02E-43
RP11-141J13.5	ENSG00000261863	chr17:4513744-4520945	4.7	8.91E-19
AC006262.5	ENSG00000268621	chr19:46692423-46706340	6.88	1.54E-17
HAND2-AS1	ENSG00000237125	chr4:174448421-174512475	–4.72	1.13E-55
MIR31HG	ENSG00000171889	chr9:21455641-21559668	3.3	4.31E-09
RP11-10A14.5	ENSG00000248538	chr8:9046521-9060364	4.62	6.34E-18
CTC-529P8.1	ENSG00000250072	chr5:148442880-148489350	3.32	1.29E-18

下载: 导出CSV

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