175
Views
1
CrossRef citations to date
0
Altmetric
Original Research

Identification of Novel Kinase–Transcription Factor–mRNA–miRNA Regulatory Network in Nasopharyngeal Carcinoma by Bioinformatics Analysis

, &
Pages 7453-7469 | Published online: 30 Oct 2021

References

  • Wei WI, Sham JST. Nasopharyngeal carcinoma. Lancet (London, England). 2005;365(9476):2041–2054. doi:10.1016/S0140-6736(05)66698-6
  • Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424. doi:10.3322/caac.21492
  • Chen Y-P, Chan ATC, Le Q-T, Blanchard P, Sun Y, Ma J. Nasopharyngeal carcinoma. Lancet (London, England). 2019;394(10192):64–80. doi:10.1016/S0140-6736(19)30956-0
  • Tian Y, Tang L, Yi P, et al. MiRNAs in radiotherapy resistance of nasopharyngeal carcinoma. J Cancer. 2020;11(13):3976–3985. doi:10.7150/jca.42734
  • Chou J, Lin Y-C, Kim J, et al. Nasopharyngeal carcinoma–review of the molecular mechanisms of tumorigenesis. Head Neck. 2008;30(7):946–963. doi:10.1002/hed.20833
  • Liu J-P, Cassar L, Pinto A, Li H. Mechanisms of cell immortalization mediated by EB viral activation of telomerase in nasopharyngeal carcinoma. Cell Res. 2006;16(10):809–817. doi:10.1038/sj.cr.7310098
  • Zeng Z, Huang H, Huang L, et al. Regulation network and expression profiles of Epstein-Barr virus-encoded microRNAs and their potential target host genes in nasopharyngeal carcinomas. Sci China Life Sci. 2014;57(3):315–326. doi:10.1007/s11427-013-4577-y
  • Carroll PA, Freie BW, Mathsyaraja H, Eisenman RN. The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis. Front Med. 2018;12(4):412–425. doi:10.1007/s11684-018-0650-z
  • Lahiry P, Torkamani A, Schork NJ, Hegele RA. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet. 2010;11(1):60–74. doi:10.1038/nrg2707
  • Chen H-C, Chen G-H, Chen Y-H, et al. MicroRNA deregulation and pathway alterations in nasopharyngeal carcinoma. Br J Cancer. 2009;100(6):1002–1011. doi:10.1038/sj.bjc.6604948
  • Razak ARA, Siu LL, Liu F-F, Ito E, O’Sullivan B, Chan K. Nasopharyngeal carcinoma: the next challenges. Eur J Cancer. 2010;46(11):1967–1978. doi:10.1016/j.ejca.2010.04.004
  • Mastrogamvraki N, Zaravinos A. Signatures of co-deregulated genes and their transcriptional regulators in colorectal cancer. NPJ Syst Biol Appl. 2020;6(1):23. doi:10.1038/s41540-020-00144-8
  • Martinez NJ, Walhout AJM. The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays. 2009;31(4):435–445. doi:10.1002/bies.200800212
  • Lou Y, Jiang H, Cui Z, Wang X, Wang L, Han Y. Gene microarray analysis of lncRNA and mRNA expression profiles in patients with high-grade ovarian serous cancer. Int J Mol Med. 2018;42(1):91–104. doi:10.3892/ijmm.2018.3588
  • Jiang X, Feng L, Dai B, Li L, Lu W. Identification of key genes involved in nasopharyngeal carcinoma. Braz J Otorhinolaryngol. 2017;83(6):670–676. doi:10.1016/j.bjorl.2016.09.003
  • Zhang J-Z, Wu Z-H, Cheng Q. Screening and identification of key biomarkers in nasopharyngeal carcinoma: evidence from bioinformatic analysis. Medicine (Baltimore). 2019;98(48):e17997. doi:10.1097/MD.0000000000017997
  • Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. jvenn: an interactive Venn diagram viewer. BMC Bioinform. 2014;15(1):293. doi:10.1186/1471-2105-15-293
  • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–29. doi:10.1038/75556
  • Altermann E, Klaenhammer TR. PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. BMC Genomics. 2005;6:60. doi:10.1186/1471-2164-6-60
  • Liao Y, Wang J, Jaehnig EJ, Shi Z, Zhang B. WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 2019;47(W1):W199–W205. doi:10.1093/nar/gkz401
  • Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613. doi:10.1093/nar/gky1131
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.1239303
  • Han H, Cho J-W, Lee S, et al. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res. 2018;46(D1):D380–D386. doi:10.1093/nar/gkx1013
  • Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 2007;35(Database issue):D137–40. doi:10.1093/nar/gkl1041
  • Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma’ayan A. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics. 2012;28(1):105–111. doi:10.1093/bioinformatics/btr625
  • Dweep H, Sticht C, Pandey P, Gretz N. miRWalk–database: prediction of possible miRNA binding sites by “walking” the genes of three genomes. J Biomed Inform. 2011;44(5):839–847. doi:10.1016/j.jbi.2011.05.002
  • Dweep H, Gretz N, Sticht C. miRWalk database for miRNA-target interactions. Methods Mol Biol. 2014;1182:289–305. doi:10.1007/978-1-4939-1062-5_25
  • Rhodes DR, Yu J, Shanker K, et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004;6(1):1–6. doi:10.1016/s1476-5586(04)80047-2
  • Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929–1935. doi:10.1126/science.1132939
  • Chua MLK, Wee JTS, Hui EP, Chan ATC. Nasopharyngeal carcinoma. Lancet (London, England). 2016;387(10022):1012–1024. doi:10.1016/S0140-6736(15)00055-0
  • Cho WC-S. Nasopharyngeal carcinoma: molecular biomarker discovery and progress. Mol Cancer. 2007;6:1. doi:10.1186/1476-4598-6-1
  • Li X-J, Peng L-X, Shao J-Y, et al. As an independent unfavorable prognostic factor, IL-8 promotes metastasis of nasopharyngeal carcinoma through induction of epithelial-mesenchymal transition and activation of AKT signaling. Carcinogenesis. 2012;33(7):1302–1309. doi:10.1093/carcin/bgs181
  • Song L, Liu H, Ma L, Zhang X, Jiang Z, Jiang C. Inhibition of autophagy by 3-MA enhances endoplasmic reticulum stress-induced apoptosis in human nasopharyngeal carcinoma cells. Oncol Lett. 2013;6(4):1031–1038. doi:10.3892/ol.2013.1498
  • Hu H, Tang KF, Chua YN, et al. Expression of interleukin-18 by nasopharyngeal carcinoma cells: a factor that possibly initiates the massive leukocyte infiltration. Hum Pathol. 2004;35(6):722–728. doi:10.1016/j.humpath.2004.01.026
  • Peng T, Hu M, Wu -T-T, et al. Andrographolide suppresses proliferation of nasopharyngeal carcinoma cells via attenuating NF-κB pathway. Biomed Res Int. 2015;2015:735056. doi:10.1155/2015/735056
  • Guo C, Huang Y, Yu J, et al. The impacts of single nucleotide polymorphisms in genes of cell cycle and NF-kB pathways on the efficacy and acute toxicities of radiotherapy in patients with nasopharyngeal carcinoma. Oncotarget. 2017;8(15):25334–25344. doi:10.18632/oncotarget.15835
  • Zhao W, Ma N, Wang S, et al. RERG suppresses cell proliferation, migration and angiogenesis through ERK/NF-κB signaling pathway in nasopharyngeal carcinoma. J Exp Clin Cancer Res. 2017;36(1):88. doi:10.1186/s13046-017-0554-9
  • Caldwell RG, Wilson JB, Anderson SJ, Longnecker R. Epstein-Barr virus LMP2A drives B cell development and survival in the absence of normal B cell receptor signals. Immunity. 1998;9(3):405–411. doi:10.1016/s1074-7613(00)80623-8
  • Young LS, Dawson CW. Epstein-Barr virus and nasopharyngeal carcinoma. Chin J Cancer. 2014;33(12):581–590. doi:10.5732/cjc.014.10197
  • Trifan OC, Hla T. Cyclooxygenase-2 modulates cellular growth and promotes tumorigenesis. J Cell Mol Med. 2003;7(3):207–222. doi:10.1111/j.1582-4934.2003.tb00222.x
  • Li Z-L, Ye S-B, OuYang L-Y, et al. COX-2 promotes metastasis in nasopharyngeal carcinoma by mediating interactions between cancer cells and myeloid-derived suppressor cells. Oncoimmunology. 2015;4(11):e1044712. doi:10.1080/2162402X.2015.1044712
  • Tan K-B, Putti TC. Cyclooxygenase 2 expression in nasopharyngeal carcinoma: immunohistochemical findings and potential implications. J Clin Pathol. 2005;58(5):535–538. doi:10.1136/jcp.2004.021923
  • Zhong Q, Wang Z, Liao X, Wu R, Guo X. LncRNA GAS5/miR-4465 axis regulates the malignant potential of nasopharyngeal carcinoma by targeting COX2. Cell Cycle. 2020;19(22):3004–3017. doi:10.1080/15384101.2020.1816280
  • Wilson CB, Leopard J, Cheresh DA, Nakamura RM. Extracellular matrix and integrin composition of the normal bladder wall. World J Urol. 1996;14(Suppl 1):S30–7. doi:10.1007/BF00182062
  • Ma L-J, Lee S-W, Lin L-C, et al. Fibronectin overexpression is associated with latent membrane protein 1 expression and has independent prognostic value for nasopharyngeal carcinoma. Tumour Biol. 2014;35(2):1703–1712. doi:10.1007/s13277-013-1235-8
  • Wang J, Deng L, Huang J, et al. High expression of Fibronectin 1 suppresses apoptosis through the NF-κB pathway and is associated with migration in nasopharyngeal carcinoma. Am J Transl Res. 2017;9(10):4502–4511.
  • Song L, Liu H, Liu Q. Matrix metalloproteinase 1 promotes tumorigenesis and inhibits the sensitivity to 5-fluorouracil of nasopharyngeal carcinoma. Biomed Pharmacother. 2019;118:109120. doi:10.1016/j.biopha.2019.109120
  • Lee DCW, Chua DTT, Wei WI, Sham JST, Lau ASY. Induction of matrix metalloproteinases by Epstein-Barr virus latent membrane protein 1 isolated from nasopharyngeal carcinoma. Biomed Pharmacother. 2007;61(9):520–526. doi:10.1016/j.biopha.2007.08.007
  • Wang M-H, Zhou X-M, Zhang M-Y, et al. BMP2 promotes proliferation and invasion of nasopharyngeal carcinoma cells via mTORC1 pathway. Aging (Albany NY). 2017;9(4):1326–1340. doi:10.18632/aging.101230
  • Xu T, Huang Z, Su B, et al. Prognostic significance of circulating CD19+ B lymphocytes in EBV-associated nasopharyngeal carcinoma. Med Oncol. 2014;31(10):198. doi:10.1007/s12032-014-0198-y
  • Qi X, Li X, Sun X. Reduced expression of polymeric immunoglobulin receptor (pIgR) in nasopharyngeal carcinoma and its correlation with prognosis. Tumour Biol. 2016;37(8):11099–11104. doi:10.1007/s13277-016-4791-x
  • Ai C, Zhang J, Lian S, et al. FOXM1 functions collaboratively with PLAU to promote gastric cancer progression. J Cancer. 2020;11(4):788–794. doi:10.7150/jca.37323
  • Xiao M, Zhang L, Zhu X, et al. Genetic polymorphisms of MDM2 and TP53 genes are associated with risk of nasopharyngeal carcinoma in a Chinese population. BMC Cancer. 2010;10:147. doi:10.1186/1471-2407-10-147
  • Chung GT-Y, Lou WP-K, Chow C, et al. Constitutive activation of distinct NF-κB signals in EBV-associated nasopharyngeal carcinoma. J Pathol. 2013;231(3):311–322. doi:10.1002/path.4239
  • Rao M, Zhu Y, Cong X, Li Q. Knockdown of CREB1 inhibits tumor growth of human gastric cancer in vitro and in vivo. Oncol Rep. 2017;37(6):3361–3368. doi:10.3892/or.2017.5636
  • Milde-Langosch K. The Fos family of transcription factors and their role in tumourigenesis. Eur J Cancer. 2005;41(16):2449–2461. doi:10.1016/j.ejca.2005.08.008
  • He S-W, Xu C, Li Y-Q, et al. AR-induced long non-coding RNA LINC01503 facilitates proliferation and metastasis via the SFPQ-FOSL1 axis in nasopharyngeal carcinoma. Oncogene. 2020;39(34):5616–5632. doi:10.1038/s41388-020-01388-8
  • Tulalamba W, Janvilisri T. Nasopharyngeal carcinoma signaling pathway: an update on molecular biomarkers. Int J Cell Biol. 2012;2012:594681. doi:10.1155/2012/594681
  • Hirota Y, Yamashita S, Kurihara Y, et al. Mitophagy is primarily due to alternative autophagy and requires the MAPK1 and MAPK14 signaling pathways. Autophagy. 2015;11(2):332–343. doi:10.1080/15548627.2015.1023047
  • Bonney EA. Mapping out p38MAPK. Am J Reprod Immunol. 2017;77:5. doi:10.1111/aji.12652
  • Li L, Guo L, Tao Y, et al. Latent membrane protein 1 of Epstein-Barr virus regulates p53 phosphorylation through MAP kinases. Cancer Lett. 2007;255(2):219–231. doi:10.1016/j.canlet.2007.04.014
  • Kockeritz L, Doble B, Patel S, Woodgett JR. Glycogen synthase kinase-3–an overview of an over-achieving protein kinase. Curr Drug Targets. 2006;7(11):1377–1388. doi:10.2174/1389450110607011377
  • Hu W, Xiao L, Cao C, Hua S, Wu D. UBE2T promotes nasopharyngeal carcinoma cell proliferation, invasion, and metastasis by activating the AKT/GSK3β/β-catenin pathway. Oncotarget. 2016;7(12):15161–15172. doi:10.18632/oncotarget.7805
  • Zhu H-M, Jiang X-S, Li H-Z, et al. miR-184 inhibits tumor invasion, migration and metastasis in nasopharyngeal carcinoma by targeting Notch2. Cell Physiol Biochem. 2018;49(4):1564–1576. doi:10.1159/000493459
  • Yan H-L, Li L, Li S-J, Zhang H-S, Xu W. miR-346 promotes migration and invasion of nasopharyngeal carcinoma cells via targeting BRMS1. J Biochem Mol Toxicol. 2016;30(12):602–607. doi:10.1002/jbt.21827
  • Blanchard P, Lee A, Marguet S, et al. Chemotherapy and radiotherapy in nasopharyngeal carcinoma: an update of the MAC-NPC meta-analysis. Lancet Oncol. 2015;16(6):645–655. doi:10.1016/S1470-2045(15)70126-9
  • Seelinger G, Merfort I, Schempp CM. Anti-oxidant, anti-inflammatory and anti-allergic activities of luteolin. Planta Med. 2008;74(14):1667–1677. doi:10.1055/s-0028-1088314
  • Ong C-S, Zhou J, Ong C-N, Shen H-M. Luteolin induces G1 arrest in human nasopharyngeal carcinoma cells via the Akt-GSK-3β-Cyclin D1 pathway. Cancer Lett. 2010;298(2):167–175. doi:10.1016/j.canlet.2010.07.001
  • Wu -C-C, Fang C-Y, Hsu H-Y, et al. EBV reactivation as a target of luteolin to repress NPC tumorigenesis. Oncotarget. 2016;7(14):18999–19017. doi:10.18632/oncotarget.7967
  • Khaiwa N, Maarouf NR, Darwish MH, et al. Camptothecin’s journey from discovery to WHO essential medicine: fifty years of promise. Eur J Med Chem. 2021;223:113639. doi:10.1016/j.ejmech.2021.113639
  • Li B-S, Huang J-Y, Guan J, Chen L-H. Camptothecin inhibits the progression of NPC by regulating TGF-β-induced activation of the PI3K/AKT signaling pathway. Oncol Lett. 2018;16(1):552–558. doi:10.3892/ol.2018.8688