基于mRNA高通量测序的胆囊癌发病机制生物信息学研究

doi:10.3877/cma.j.issn.2095-3232.2021.02.020

目的

基于mRNA高通量测序和生物信息学分析探讨胆囊癌发病机制。

方法

本研究选取2017年1月至2018年10月在上海东方肝胆外科医院就诊的10例胆囊癌患者。对其胆囊癌组织及癌旁正常组织进行mRNA高通量测序，并进行生物信息学分析。

结果

肿瘤组织与对应的癌旁正常组织相比，共鉴定出1 704个差异表达基因（DEGs），其中523个DEGs上调，1 181个DEGs下调。其中有674个DEGs显著富集到46个信号通路，包括PI3K-Akt、MAPK、Ras、Wnt等癌症相关信号通路，以及细胞运动相关通路，其中最显著的途径是神经活性配体- 受体相互作用信号途径，45个基因显著富集到钙信号通路。

结论

基于高通量mRNA测序和生物信息学技术分析显示胆囊癌和癌旁正常组织存在DEGs, 神经活性的配体- 受体相互作用信号通路改变最为显著，钙信号传导途径异常揭示了慢性结石性胆囊炎向胆囊癌转变的重要信号通路。

关键词: 胆囊肿瘤, 高通量核苷酸测序, RNA, 信使

Objective

To explore the pathogenesis of gallbladder carcinoma base on high-throughput mRNA sequencing and bioinformatics analysis.

Methods

10 patients with gallbladder carcinoma admitted to Shanghai Eastern Hepatobiliary Surgery Hospital from January 2017 to October 2018 were recruited in this study. High-throughput mRNA sequencing and bioinformatics analysis were performed on the gallbladder carcinoma and paracancerous normal tissues.

Results

1 704 differentially-expressed genes (DEGs) were identified from tumor tissues and adjacent normal tissues, including 523 DEGs were up-regulated and 1 181 DEGs were down-regulated. Among them, 674 DEGs were significantly enriched on 46 signaling pathways, including PI3K-Akt, MAPK, Ras, Wnt and other cancer-related signaling pathways as well as cell movement-related signaling pathways, among which the most significant pathway was neuroactive ligand-receptor interaction signaling pathway, and 45 DEGs were significantly enriched on the calcium signaling pathway.

Conclusions

High-throughput mRNA sequencing and bioinformatics analysis demonstrate that DEGs exist in gallbladder cancer and adjacent normal tissues. The most significant changes are noted on the neuroactive ligand-receptor interaction signaling pathway. Abnormal calcium signaling pathway is noted as a critical signaling pathway for progression from chronic calculous cholecystitis to gallbladder cancer.

Key words: Gallbladder neoplasms, High-throughput nucleotide sequencing, RNA, messenger

图1 十例胆囊癌患者胆囊癌和癌旁组织差异表达基因火山图

表1 十例胆囊癌组织和癌旁正常组织的差异表达基因

序号	基因	log₂ （fold change）	P值	校正后 P值	变化
1	ADIPOQ	-13.509	2.35E-27	4.16E-23	下调
2	TUSC5	-10.122	9.29E-18	5.75E-14	下调
3	PLP1	-5.923	9.73E-18	5.75E-14	下调
4	NRXN1	-4.928	8.73E-17	3.63E-13	下调
5	FABP4	-6.390	1.02E-16	3.63E-13	下调
6	CBLN4	-6.226	3.33E-16	9.85E-13	下调
7	PI16	-6.425	7.63E-16	1.93E-12	下调
8	PMP2	-6.949	1.31E-15	2.91E-12	下调
9	SCRG1	-3.738	1.69E-15	3.32E-12	下调
10	PLAC9	-3.409	4.04E-15	7.17E-12	下调
11	CHRDL1	-4.935	1.42E-14	2.30E-11	下调
12	PLIN1	-6.880	4.63E-14	6.84E-11	下调
13	GRIK3	-5.246	8.73E-14	1.19E-10	下调
14	FAM180B	-6.128	2.61E-13	3.20E-10	下调
15	C2orf40	-4.997	2.71E-13	3.20E-10	下调
16	………
17	………
18	………
……	………
1692	………
1693	………
1694	………
1695	PNPLA3	1.859	0.008 757	0.049 212	上调
1696	GPM6B	-1.291	0.008 766	0.049 229	下调
1697	TRIM72	1.996	0.008 771	0.049 230	上调
1698	P2RY8	-1.104	0.008 804	0.049 335	下调
1699	VSTM2B	-2.950	0.008 807	0.049 341	下调
1700	SNED1	-1.077	0.008 813	0.049 359	下调
1701	C4BPB	1.636	0.008 943	0.049 824	上调
1702	LAMA1	1.744	0.008 955	0.049 854	上调
1703	HP	2.201	0.008 958	0.049 854	上调
1704	OVCH1	-1.554	0.008 984	0.049 954	下调

表1 十例胆囊癌组织和癌旁正常组织的差异表达基因

序号	基因	log₂ （fold change）	P值	校正后 P值	变化
1	ADIPOQ	-13.509	2.35E-27	4.16E-23	下调
2	TUSC5	-10.122	9.29E-18	5.75E-14	下调
3	PLP1	-5.923	9.73E-18	5.75E-14	下调
4	NRXN1	-4.928	8.73E-17	3.63E-13	下调
5	FABP4	-6.390	1.02E-16	3.63E-13	下调
6	CBLN4	-6.226	3.33E-16	9.85E-13	下调
7	PI16	-6.425	7.63E-16	1.93E-12	下调
8	PMP2	-6.949	1.31E-15	2.91E-12	下调
9	SCRG1	-3.738	1.69E-15	3.32E-12	下调
10	PLAC9	-3.409	4.04E-15	7.17E-12	下调
11	CHRDL1	-4.935	1.42E-14	2.30E-11	下调
12	PLIN1	-6.880	4.63E-14	6.84E-11	下调
13	GRIK3	-5.246	8.73E-14	1.19E-10	下调
14	FAM180B	-6.128	2.61E-13	3.20E-10	下调
15	C2orf40	-4.997	2.71E-13	3.20E-10	下调
16	………
17	………
18	………
……	………
1692	………
1693	………
1694	………
1695	PNPLA3	1.859	0.008 757	0.049 212	上调
1696	GPM6B	-1.291	0.008 766	0.049 229	下调
1697	TRIM72	1.996	0.008 771	0.049 230	上调
1698	P2RY8	-1.104	0.008 804	0.049 335	下调
1699	VSTM2B	-2.950	0.008 807	0.049 341	下调
1700	SNED1	-1.077	0.008 813	0.049 359	下调
1701	C4BPB	1.636	0.008 943	0.049 824	上调
1702	LAMA1	1.744	0.008 955	0.049 854	上调
1703	HP	2.201	0.008 958	0.049 854	上调
1704	OVCH1	-1.554	0.008 984	0.049 954	下调

图2 胆囊癌患者样本中差异表达基因的无监督分层聚类热图

图3 胆囊癌患者样本中差异表达基因KEGG富集分析

[1]	Lazcano-Ponce EC, Miquel JF, Muñoz N, et al. Epidemiology and molecular pathology of gallbladder carcinoma[J]. CA Cancer J Clin, 2001, 51(6):349-364.
[2]	Boutros C, Gary M, Baldwin K, et al. Gallbladder carcinoma: past, present and an uncertain future[J]. Surg Oncol, 2012, 21(4):e183-191.
[3]	Zhu AX, Hong TS, Hezel AF, et al. Current management of gallbladder carcinoma[J]. Oncologist, 2010, 15(2):168-181.
[4]	Chen W, Zheng R, Baade PD, et al. Cancer statistics in China, 2015[J]. CA Cancer J Clin, 2016, 66(2):115-132.
[5]	Levy AD, Murakata LA, Rohrmann CA. Gallbladder carcinoma: radiologic-pathologic correlation[J]. Radiographics, 2001, 21(2): 295-314.
[6]	Hundal R, Shaffer EA. Gallbladder carcinoma: epidemiology and outcome[J]. Clin Epidemiol, 2014(6):99-109.
[7]	Li Y, Zhang J, Ma H. Chronic inflammation and gallbladder carcinoma[J]. Cancer Lett, 2014, 345(2):242-248.
[8]	Ferkingstad E, Oddsson A, Gretarsdottir S, et al. Genome-wide association meta-analysis yields 20 loci associated with gallstone disease[J]. Nat Commun, 2018, 9(1):5101.
[9]	Goldin RD, Roa JC. Gallbladder carcinoma: a morphological andmolecular update[J]. Histopathology, 2009, 55(2):218-229.
[10]	Agrawal V, Goel A, Krishnani N, et al. P53, carcinoembryonic antigen and carbohydrate antigen 19.9 expression in gallbladder cancer, precursor epithelial lesions and xanthogranulomatous cholecystitis[J]. J Postgrad Med, 2010(56):262-266.
[11]	Wistuba II, Gazdar AF. Gallbladder carcinoma: lessons from a rare tumour[J]. Nat Rev Cancer, 2004, 4(9):695-706.
[12]	Li M, Zhang Z, Li X, et al. Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway[J]. Nat Genet, 2014, 46(8):872-876.
[13]	Gu X, Li B, Jiang M, et al. RNA sequencing reveals differentially expressed genes as potential diagnostic and prognostic indicators of gallbladder carcinoma[J]. Oncotarget, 2015(6):20661-20671.
[14]	Ryu S, Chang Y, Yun K, et al. Gallstones and the risk of gallbladder carcinoma mortality: a cohort study[J]. Am J Gastroenterol, 2016(111):1476-1487.
[15]	Sharma RK, Sonkar K, Sinha N, et al. Gallstones: a worldwide multifaceted disease and its correlations with gallbladder carcinoma[J]. PLoS One, 2016, 11(11):e0166351.
[16]	Kong Y, Liang X, Liu L, et al. High throughput sequencing identifies microRNAs mediatingα-synuclein toxicity by targeting neuroactive-ligand receptor interaction pathway in early stage of Drosophila Parkinson's disease model[J]. PLoS One, 2015(10):e0137432.
[17]	Lammert F, Gurusamy K, Ko CW, et al. Gallstones[J]. Nat Rev Dis Primers, 2016(2):16024.
[18]	Yang B, Liu B, Bi P, et al. An integrated analysis of differential miRNA and mRNA expressions in human gallstones[J]. Mol Biosyst, 2015, 11(4):1004-1011.
[19]	Mishra SK, Kumari N, Krishnani N. Molecular pathogenesis of gallbladder carcinoma: an update[J]. Mutat Res, 2019:816-818.
[20]	Zuo M, Rashid A, Wang Y, et al. RNA sequencing-based analysis of gallbladder carcinoma reveals the importance of the liver X receptor and lipid metabolism in gallbladder cancer[J]. Oncotarget, 2016, 7(23):35302-35312.

[1]	刘伟, 牛云峰, 安杰. LINC01232 通过miR-516a-5p/BCL9 轴促进三阴性乳腺癌的恶性进展[J/OL]. 中华乳腺病杂志(电子版), 2024, 18(06): 330-338.
[2]	刘政宏, 袁春銮. 乳腺癌患者血清外泌体中长链非编码RNA BC200的表达及临床意义[J/OL]. 中华乳腺病杂志(电子版), 2024, 18(04): 212-216.
[3]	于溟璇, 杜华, 张彩虹, 师迎旭. miRNA-192家族在乳腺癌中的作用机制及诊断价值[J/OL]. 中华乳腺病杂志(电子版), 2024, 18(04): 235-240.
[4]	何霞, 黄蓉, 祁文瑾. 胎膜早破孕妇胎盘与胎膜菌群丰度的高通量测序研究[J/OL]. 中华妇幼临床医学杂志(电子版), 2024, 20(05): 549-555.
[5]	白香妮, 孙巨军, 谢鹤, 李宏斌. 急性胰腺炎患者血清微小RNA-142-3p和磷脂酰肌醇3-激酶水平变化及对并发腹腔感染风险预测[J/OL]. 中华实验和临床感染病杂志(电子版), 2024, 18(04): 222-228.
[6]	安杰, 牛云峰, 刘伟. LINC00520 通过miR-519b-3p/HIF1A 轴促进胃癌的侵袭转移[J/OL]. 中华普通外科学文献(电子版), 2024, 18(06): 430-436.
[7]	马中正, 杨云川, 马翔, 周迟, 丁丁, 霍俊一, 徐楠, 崔培元, 周磊. 胰腺癌双硫死亡相关的lncRNA预后模型的构建及免疫反应研究[J/OL]. 中华普通外科学文献(电子版), 2024, 18(05): 368-376.
[8]	赵小欢, 尚志英, 段文超, 张晓燕, 孙东强. 无创通气治疗COPD 并发呼吸衰竭不同预后患者外周血MicroRNA及炎性因子水平分析[J/OL]. 中华肺部疾病杂志(电子版), 2024, 17(05): 777-780.
[9]	王向前, 李清峰, 陈磊, 丘文丹, 姚志成, 李熠, 吴荣焕. 姜黄素抑制肝细胞癌索拉非尼耐药作用及其调控机制[J/OL]. 中华肝脏外科手术学电子杂志, 2024, 13(05): 729-735.
[10]	张杰, 田广磊, 陈雄. 基于生物信息学分析探讨肝癌BRD4与预后关系及其ceRNA调控网络构建[J/OL]. 中华肝脏外科手术学电子杂志, 2024, 13(04): 568-576.
[11]	翟航, 张广权, 吴芳芳, 史宪杰. 非编码RNA调控胰腺纤维化研究进展[J/OL]. 中华肝脏外科手术学电子杂志, 2024, 13(04): 583-587.
[12]	董晓斌, 张静, 苏莎莎, 莎比亚·沙吾提, 盛好. 溃疡性结肠炎患者相关环状RNA 差异表达谱分析及功能研究[J/OL]. 中华结直肠疾病电子杂志, 2024, 13(06): 499-509.
[13]	张蔚林, 王哲学, 白峻阁, 黄忠诚, 肖志刚. 利用TCGA数据库构建基于miRNA的结直肠癌列线图预后模型[J/OL]. 中华结直肠疾病电子杂志, 2024, 13(05): 381-388.
[14]	李京, 牛博, 刘晓蓓, 魏新雪, 黄荣. circ-SESN2 沉默靶向调控miRNA-23a-5p/ULK1 在神经细胞氧化应激损伤中的作用机制研究[J/OL]. 中华神经创伤外科电子杂志, 2024, 10(05): 263-272.
[15]	王国强, 张纲, 唐建坡, 张玉国, 杨永江. LINC00839 调节miR-17-5p/WEE1 轴对结直肠癌细胞增殖、凋亡和迁移的影响[J/OL]. 中华消化病与影像杂志(电子版), 2024, 14(06): 491-499.

阅读次数

全文

摘要

选择文件类型/文献管理软件名称

选择包含的内容

Bioinformatics study of pathogenesis of gallbladder cancer base on high-throughput mRNA sequencing

模态框（Modal）标题

选择文件类型/文献管理软件名称

选择包含的内容

Bioinformatics study of pathogenesis of gallbladder cancer base on high-throughput mRNA sequencing