基于RNA-Seq分析挖掘唾液腺多形性腺瘤核心基因及通路

doi:10.19438/j.cjoms.2019.05.003

中国口腔颌面外科杂志 ›› 2019, Vol. 17 ›› Issue (5): 397-402.doi: 10.19438/j.cjoms.2019.05.003

基于RNA-Seq分析挖掘唾液腺多形性腺瘤核心基因及通路

汪洋^1,*, 夏亮^2,*, 胡宇华¹, 张春叶¹, 王丽珍¹, 李江¹, 田臻¹

1. 上海交通大学医学院附属第九人民医院·口腔医学院口腔病理科上海 200011;
2.口腔颅颌面科,国家口腔疾病临床医学研究中心,上海市口腔医学重点实验室,上海市口腔医学研究所,上海 200011

收稿日期:2018-12-26 出版日期:2019-09-20 发布日期:2020-03-11
通讯作者: 田臻,E-mail：tian0304_cn@163.com
作者简介:汪洋（1989-）,男,硕士,E-mail：cmfuyangwang@126.com;夏亮（1990-）,男,硕士,住院医师,E-mail：anglexialiang@126.com。*并列第一作者
基金资助:
上海市自然科学基金（18ZR1422200）

Identification of core differentially expressed genes and pathways of salivary gland pleomorphic adenoma based on RNA-Seq

WANG Yang¹, XIA Liang², HU Yu-hua¹, ZHANG Chun-ye¹, WANG Li-zhen¹, LI Jiang¹, TIAN Zhen¹

1. Department of Oral Pathology Shanghai 200011, China;
2. Department of Oral and Craniomaxillofacial Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology. Shanghai 200011, China

Received:2018-12-26 Online:2019-09-20 Published:2020-03-11

摘要/Abstract

摘要： 目的：筛选多形性腺瘤（pleomorphic adenoma,PA）与瘤旁唾液腺腺体间的差异表达基因,挖掘PA形成过程中的核心基因及通路。方法：采用RNA-Seq技术,检测5例PA患者的配对肿瘤与瘤旁唾液腺腺体,筛选2组间差异基因。运用蛋白互作数据库STRING分析预测差异基因所编码蛋白间的相互作用。筛选互作网络中的核心模块及核心基因,分析核心模块中激活的信号通路,预测上述模块与PLAG1可能的相互作用关系。RT-PCR验证核心基因在20例PA患者的配对肿瘤组织及瘤旁唾液腺中的表达。采用SPSS 20.0软件包对数据进行统计学分析。结果：共测得3810个差异基因,其中2021个下调,1789个上调。核心模块中存在PI3K-AKT信号通路、ER受体信号通路、Rap1信号通路、cGMP-PKG信号通路的激活。PLAG1可能通过PHLPP1、LRRK2、β-catenin蛋白与核心模块发生作用。RT-PCR显示,核心基因在20例PA样本及其瘤旁唾液腺组织中的差异趋势与测序结果一致,且具有统计学意义（P<0.0001）。结论：核心基因ADCY3、 ADCY5、 ADORA1、 APLN、 APP、 C5、 CCL28、 DRD2、 FPR3、 GABBR1可能在PA发生、发展过程中起着重要作用,可为预防PA复发及预后标志物筛选提供思路。PLAG1可能通过PHLPP1、LRRK2、β-catenin间接激活PI3K-AKT信号通路、ER受体信号通路、Rap1信号通路、cGMP-PKG信号通路,从而诱发PA形成。

关键词: 转录组测序, 唾液腺, 多形性腺瘤, 蛋白相互作用网络

Abstract: PURPOSE: The aim of this study was to identify the core differentially expressed genes (DEGs) signatures during pleomorphic adenoma (PA) and identified the key pathways and genes in PA. METHODS: The mRNA expression of 5 cases of PA and salivary gland was detected by RNA-Seq. Then the differentially expressed genes (DEGs) were screened. Protein-protein interaction (PPI) network of the DEGs was constructed and the core modules and hub genes were screened. The activated pathways associated with the core modules was analyzed, and the possible interaction between them and PLAG1 was predicted. Furthermore, the hub genes expression was validated by RT-PCR in 20 pairs of PA and normal salivary tissues. Statistical analysis was performed using SPSS 20.0 software package. RESULTS: In total, 3810 DEGs were identified in PA, including 2021 down-regulated genes and 1789 up-regulated genes. PI3K-AKT signaling pathway, ER receptor signaling pathway, Rap1 signaling pathway and cGMP-PKG signaling pathway were activated in the core modules. PLAG1 may interact with the core modules through PHLPP1, LRRK2, and beta-catenin proteins. The expression of the hub genes in 20 pairs of PA and normal salivary tissues were validated by RT-PCR, the expression trend was in accordance with the mRNA sequencing (P<0.0001). CONCLUSIONS: Hub genes including ADCY3, ADCY5, ADORA1, APLN, APP, C5, CCL28, DRD2, FPR3, GABBR1 may play important roles in the oncogenesis and development of PA, which can provide ideas for preventing recurrence and screening prognostic markers of PA. PLAG1 may induce oncogenesis of PA by interacting with PHLPP1, LRRK2, and beta-catenin proteins,which indirectly activate the PI3K-AKT signal pathway, ER receptor signal pathway, Rap1 signal pathway, and cGMP-PKG signal pathway.

Key words: RNA-Seq, Salivary gland, Pleomorphic adenoma, PPI network

中图分类号:

R739.8

汪洋, 夏亮, 胡宇华, 张春叶, 王丽珍, 李江, 田臻. 基于RNA-Seq分析挖掘唾液腺多形性腺瘤核心基因及通路[J]. 中国口腔颌面外科杂志, 2019, 17(5): 397-402.

WANG Yang, XIA Liang, HU Yu-hua, ZHANG Chun-ye, WANG Li-zhen, LI Jiang, TIAN Zhen. Identification of core differentially expressed genes and pathways of salivary gland pleomorphic adenoma based on RNA-Seq[J]. China J Oral Maxillofac Surg, 2019, 17(5): 397-402.

参考文献

[1] 李江. 口腔颌面肿瘤病理学[M]. 上海: 世界图书出版公司, 2013.
[2] Dulguerov P, Todic J, Pusztaszeri M, et al.Why do parotid pleomorphic adenomas recur? A systematic review of pathological and surgical variables[J]. Front Surg, 2017, 4: 26.
[3] Iro H, Zenk J, Koch M, et al.Follow-up of parotid pleomorphic adenomas treated by extracapsular dissection[J]. Head Neck, 2013, 35(6): 788-793.
[4] Fehr A, Stenman G, Bullerdiek J, et al.Molecular markers in salivary gland tumors: their use in diagnostic and prognostic workup[J]. Pathologe, 2009, 30(6): 466-471.
[5] Zhao X, Ren W, Yang W, et al.Wnt pathway is involved in pleomorphic adenomas induced by overexpression of plag1 in transgenic mice[J]. Int J Cancer, 2006, 118(3): 643-648.
[6] Obtulovicova K, Starek I, Salzman R, et al.Recurrent salivary pleomorphic adenoma shows increased immunohistologic expression of bcl-2 oncoprotein[J]. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub, 2015, 159(3): 460-465.
[7] Glas AS, Hollema H, Nap RE, et al.Expression of estrogen receptor, progesterone receptor, and insulin-like growth factor receptor-1 and of mib-1 in patients with recurrent pleomorphic adenoma of the parotid gland[J]. Cancer, 2002, 94(8): 2211-2216.
[8] Roy S, Coldren C, Karunamurthy A, et al.Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: A joint recommendation of the association for molecular pathology and the college of american pathologists[J]. J Mol Diagn, 2018, 20(1): 4-27.
[9] Chamberlin MD, Bernhardt EB, Miller TW.Clinical implementation of novel targeted therapeutics in advanced breast cancer[J]. J Cell Biochem, 2016, 117(11): 2454-2463.
[10] Wang S, Zhang C, Zhang Z, et al.Transcriptome analysis in primary colorectal cancer tissues from patients with and without liver metastases using next-generation sequencing[J]. Cancer Med, 2017, 6(8): 1976-1987.
[11] Szklarczyk D, Morris J H, Cook H, et al.The string database in 2017: quality-controlled protein-protein association networks, made broadly accessible[J]. Nucleic Acids Res, 2017, 45(D1): D362-d368.
[12] Shannon P, Markiel A, Ozier O, et al.Cytoscape: a software environment for integrated models of biomolecular interaction networks[J]. Genome Res, 2003, 13(11): 2498-2504.
[13] Bader GD, Hogue CW.An automated method for finding molecular complexes in large protein interaction networks[J]. BMC Bioinformatics, 2003, 4: 2.
[14] Riquelme I, Tapia O, Espinoza JA, et al.The gene expression status of the pi3k/akt/mtor pathway in gastric cancer tissues and cell lines[J]. Pathol Oncol Res, 2016, 22(4): 797-805.
[15] Kumar D, Haldar S, Gorain M, et al.Epoxyazadiradione suppresses breast tumor growth through mitochondrial depolarization and caspase-dependent apoptosis by targeting PI3K/Akt pathway[J]. BMC Cancer, 2018, 18(1): 52.
[16] Can NT, Lingen MW, Mashek H, et al.Expression of hormone receptors and her-2 in benign and malignant salivary gland tumors[J]. Head Neck Pathol, 2018, 12(1): 95-104.
[17] Li W, Jin B, Cornelius LA, et al.Inhibitory effects of rap1gap overexpression on proliferation and migration of endothelial cells via erk and akt pathways[J]. J Huazhong Univ Sci Technolog Med Sci, 2011, 31(6): 721-727.
[18] Ding L, Zhang C, Masood A, et al.Protective effects of phosphodiesterase 2 inhibitor on depression- and anxiety-like behaviors: Involvement of antioxidant and anti-apoptotic mechanisms[J]. Behav Brain Res, 2014, 268: 150-158.
[19] Wang Y, Shang W, Lei X, et al.Opposing functions of plag1 in pleomorphic adenoma: A microarray analysis of plag1 transgenic mice[J]. Biotechnol Lett, 2013, 35(9): 1377-1385.
[20] Hong SH, Goh SH, Lee SJ, et al.Upregulation of adenylate cyclase 3 (adcy3) increases the tumorigenic potential of cells by activating the creb pathway[J]. Oncotarget, 2013, 4(10): 1791-1803.
[21] Dastjerdi MN, Valiani A, Mardani M, et al.Adenosine a1 receptor modifies p53 expression and apoptosis in breast cancer cell line mcf-7[J]. Bratisl Lek Listy, 2016, 117(4): 242-246.
[22] Gholipour N, Ohradanova-Repic A, Ahangari G.A novel report of mir-4301 induces cell apoptosis by negatively regulating drd2 expression in human breast cancer cells[J]. J Cell Biochem, 2018, 119(8): 6408-6417.
[23] Prevete N, Liotti F, Visciano C, et al.The formyl peptide receptor 1 exerts a tumor suppressor function in human gastric cancer by inhibiting angiogenesis[J]. Oncogene, 2015, 34(29): 3826-3838.
[24] Solorzano SR, Imaz-Rosshandler I, Camacho-Arroyo I, et al.Gaba promotes gastrin-releasing peptide secretion in NE/NE-like cells: Contribution to prostate cancer progression[J]. Sci Rep, 2018, 8(1): 10272.
[25] Heo K, Kim YH, Sung HJ, et al.Hypoxia-induced up-regulation of apelin is associated with a poor prognosis in oral squamous cell carcinoma patients[J]. Oral Oncol, 2012, 48(6): 500-506.
[26] Nitta H, Murakami Y, Wada Y, et al.Cancer cells release anaphylatoxin C5a from C5 by serine protease to enhance invasiveness[J]. Oncol Rep, 2014, 32(4): 1715-1719.
[27] Tegowski M, Santos C, Baldwin A.Abstract 3316: The effects of dopamine receptor 2 on breast cancer tumor initiating cells[J]. Cancer Res, 2016, 76(14 Supplement): 3316.
[28] Markiewski MM, DeAngelis RA, Benencia F, et al. Modulation of the antitumor immune response by complement[J]. Nat Immunol, 2008, 9(11): 1225-1235.

基于RNA-Seq分析挖掘唾液腺多形性腺瘤核心基因及通路

Identification of core differentially expressed genes and pathways of salivary gland pleomorphic adenoma based on RNA-Seq

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