Identification of potential hub genes and therapeutic drugs in ovarian cancer via bioinformatics analysis

References

• Acevedogadea C, Hatzis C, Chung G, Fishbach N, Lezongeyda K, Zelterman D, Digiovanna MP, Harris L, Abukhalaf MM. 2015. Trastuzumab, sirolimus, HER2. Breast Cancer. 150:157–167.
   Google Scholar
• Agarwal A, Tressel SL, Kaimal R, Balla M, Lam FH, Covic L, Kuliopulos A. 2010. Identification of a metalloprotease-chemokine signaling system in the ovarian cancer microenvironment: implications for antiangiogenic therapy. Cancer Res. 70(14):5880–5890. doi: 10.1158/0008-5472.CAN-09-4341.
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25(1):25–29. doi: 10.1038/75556.
   PubMed Web of Science ®Google Scholar
• Au KK, Peterson N, Truesdell P, Reid-Schachter G, Khalaj K, Ren R, Francis J-A, Graham CH, Craig AW, Koti M. 2017. CXCL10 alters the tumour immune microenvironment and disease progression in a syngeneic murine model of high-grade serous ovarian cancer. Gynecol Oncol. 145(1):436–445. doi: 10.1016/j.ygyno.2017.03.007.
   PubMedGoogle Scholar
• Bader GD, Hogue CW. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 4(1):2. doi: 10.1186/1471-2105-4-2.
   PubMed Web of Science ®Google Scholar
• Bland JM, Altman DG. 1998. Statistics notes: survival probabilities (the Kaplan-Meier method). Br Med J. 317(7172):1572–1580. doi: 10.1136/bmj.317.7172.1572.
   PubMed Web of Science ®Google Scholar
• Brackmann M, Stasenko M, Uppal S, Erba J, Reynolds RK, McLean K. 2018. Comparison of first-line chemotherapy regimens for ovarian2 carcinosarcoma: a single institution case series and review of the literature. BMC Cancer. 18(1):172. doi: 10.1186/s12885-018-4082-6.
   PubMedGoogle Scholar
• Bronger H, Singer J, Windmüller C, Reuning U, Zech D, Delbridge C, Dorn J, Kiechle M, Schmalfeldt B, Schmitt M. 2016. CXCL9 and CXCL10 predict survival and are regulated by cyclooxygenase inhibition in advanced serous ovarian cancer. Br J Cancer. 115(5):553–563. doi: 10.1038/bjc.2016.172.
   PubMed Web of Science ®Google Scholar
• Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O’Donnell L, Oster S, Theesfeld C, Sellam A. 2017. The BioGRID interaction database: 2017 update. Nucleic Acids Res. 45(D1):D369–D379. doi: 10.1093/nar/gkw1102.
   PubMed Web of Science ®Google Scholar
• Chatterjee M, Hurley LC, Tainsky MA. 2017. Paraneoplastic antigens as biomarkers for early diagnosis of ovarian cancer. Gynecol Oncol Rep. 21:37–44. doi: 10.1016/j.gore.2017.06.006.
   PubMedGoogle Scholar
• Chen M-W, Yang S-T, Chien M-H, Hua K-T, Wu C-J, Hsiao SM, Lin H, Hsiao M, Su J-L, Wei L-H. 2017. The STAT3-miRNA-92-Wnt signaling pathway regulates spheroid formation and malignant progression in ovarian cancer. Cancer Res. 77(8):1955–1967. doi: 10.1158/0008-5472.CAN-16-1115.
   PubMed Web of Science ®Google Scholar
• Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B. 2009. Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics. 25(11):1422–1423. doi: 10.1093/bioinformatics/btp163.
   PubMed Web of Science ®Google Scholar
• Cotto KC, Wagner AH, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL, Griffith M. 2018. DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. Nucleic Acids Res. 46(D1):D1068–D1073. doi: 10.1093/nar/gkx1143.
   PubMedGoogle Scholar
• Fang WB, Jokar I, Zou A, Lambert D, Dendukuri P, Cheng N. 2012. CCL2/CCR2 chemokine signaling coordinates survival and motility of breast cancer cells through Smad3 protein- and p42/44 mitogen-activated protein kinase (MAPK)-dependent mechanisms. J Biol Chem. 287(43):36593–36608. doi: 10.1074/jbc.M112.365999.
   PubMed Web of Science ®Google Scholar
• Fu LJ, Wang B. 2013. Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis. J Ovarian Res. 6(1):92. doi: 10.1186/1757-2215-6-92.
   PubMedGoogle Scholar
• Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, et al. 2020. Visualizing and interpreting cancer genomics data via the xena platform. Nat Biotechnol. 38(6):675–678. doi: 10.1038/s41587-020-0546-8.
   PubMed Web of Science ®Google Scholar
• Griner SE, Joshi JP, Nahta R. 2013. Growth differentiation factor 15 stimulates rapamycin-sensitive ovarian cancer cell growth and invasion. Biochem Pharmacol. 85(1):46–58. doi: 10.1016/j.bcp.2012.10.007.
   PubMed Web of Science ®Google Scholar
• Grisaru D, Hauspy J, Prasad M, Albert M, Murphy KJ, Covens A, Macgregor PF, Rosen B. 2007. Microarray expression identification of differentially expressed genes in serous epithelial ovarian cancer compared with bulk normal ovarian tissue and ovarian surface scrapings. Oncol Rep. 18:1347–1356.
   PubMed Web of Science ®Google Scholar
• Halari CD, Zheng M, Lala PK. 2021. Roles of two small leucine-rich proteoglycans decorin and biglycan in pregnancy and pregnancy-associated diseases. Int J Mol Sci. 22(19):10584. doi: 10.3390/ijms221910584.
   PubMed Web of Science ®Google Scholar
• Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S. 2012. GENCODE: the reference human genome annotation for The ENCODE project. Genome Res. 22(9):1760–1774. doi: 10.1101/gr.135350.111.
   PubMed Web of Science ®Google Scholar
• Holschneider CH, Berek JS. 2000. Ovarian cancer: epidemiology, biology, and prognostic factors. Semin Surg Oncol. 19(1):3–10. doi: 10.1002/1098-2388(200007/08)19:1<3::AID-SSU2>3.0.CO;2-S.
   PubMedGoogle Scholar
• Javdan P, Reiisi S, Mohammadi Nejad P. 2018. Overexpression of TRAF4 gene in ovarian cancer samples and association with metastasis and poor prognosis in patients. J Arak Uni Med Sci. 21:21–30.
   Google Scholar
• Jiang H, Feng Y. 2004. Inhibition of hypoxia-inducible factor 1alpha expression and tumor growth in SKOV3 ovarian cancer model by sirolimus. Zhonghua fu Chan ke za zhi. 39:474–477.
   PubMedGoogle Scholar
• Jiang Y-P, Wu X-H, Shi B, Wu W-X, Yin G-R. 2006. Expression of chemokine CXCL12 and its receptor CXCR4 in human epithelial ovarian cancer: an independent prognostic factor for tumor progression. Gynecol Oncol. 103(1):226–233. doi: 10.1016/j.ygyno.2006.02.036.
   PubMed Web of Science ®Google Scholar
• Jiang Z, Xu Y, Cai S. 2010. CXCL10 expression and prognostic significance in stage II and III colorectal cancer. Mol Biol Rep. 37(6):3029–3036. doi: 10.1007/s11033-009-9873-z.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1):27–30. doi: 10.1093/nar/28.1.27.
   PubMed Web of Science ®Google Scholar
• Koop G. 2017. Bayesian methods for empirical macroeconomics with big data. Rev Economic Anal. 9(1):33–56. doi: 10.15353/rea.v9i1.1434.
   Google Scholar
• Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH. 2017. A scored human protein–protein interaction network to catalyze genomic interpretation. Nat Meth. 14(1):61–64. doi: 10.1038/nmeth.4083.
   PubMed Web of Science ®Google Scholar
• Liou J-T, Yuan H-B, Mao C-C, Lai Y-S, Day Y-J. 2012. Absence of C–C motif chemokine ligand 5 in mice leads to decreased local macrophage recruitment and behavioral hypersensitivity in a murine neuropathic pain model. Pain. 153(6):1283–1291. doi: 10.1016/j.pain.2012.03.008.
   PubMed Web of Science ®Google Scholar
• Long H, Xiang T, Qi W, Huang J, Chen J, He L, Liang Z, Guo B, Li Y, Xie R. 2015. CD133+ ovarian cancer stem-like cells promote non-stem cancer cell metastasis via CCL5 induced epithelial-mesenchymal transition. Oncotarget. 6(8):5846–5859. doi: 10.18632/oncotarget.3462.
   PubMedGoogle Scholar
• Long H, Xie R, Xiang T, Zhao Z, Lin S, Liang Z, Chen Z, Zhu B. 2012. Autocrine CCL5 signaling promotes invasion and migration of CD133+ ovarian cancer stem-like cells via NF-κB-mediated MMP-9 upregulation. Stem Cells. 30(10):2309–2319. doi: 10.1002/stem.1194.
   PubMed Web of Science ®Google Scholar
• Nash MA, Deavers MT, Freedman RS. 2002. The expression of decorin in human ovarian tumors. Clin Cancer Res. 8:1754–1760.
   PubMed Web of Science ®Google Scholar
• Norouzi-Barough L, Sarookhani MR, Sharifi M, Moghbelinejad S, Jangjoo S, Salehi R. 2018. Molecular mechanisms of drug resistance in ovarian cancer. J Cell Physiol. 233(6):4546–4562. doi: 10.1002/jcp.26289.
   PubMed Web of Science ®Google Scholar
• Obermajer N, Muthuswamy R, Odunsi K, Edwards RP, Kalinski P. 2011. PGE2-induced CXCL12 production and CXCR4 expression controls the accumulation of human MDSCs in ovarian cancer environment. Cancer Res. 71(24):7463–7470. doi: 10.1158/0008-5472.CAN-11-2449.
   PubMed Web of Science ®Google Scholar
• Pandis N. 2016. Linear regression. Am J Orthod Dentofacial Orthop. 149(3):431–434. doi:10.1016/j.ajodo.2015.11.019.
   PubMed Web of Science ®Google Scholar
• Pintoleite R, Botelho P, Ribeiro E, Oliveira PA, Santos L. 2009. Effect of sirolimus on urinary bladder cancer T24 cell line. J Exp Clin Cancer Res. 28(1):3–3. doi: 10.1186/1756-9966-28-3.
   PubMedGoogle Scholar
• Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ. 2015. DISEASES: text mining and data integration of disease–gene associations. Methods. 74:83–89. doi: 10.1016/j.ymeth.2014.11.020.
   PubMed Web of Science ®Google Scholar
• Rainczuk A, Rao JR, Gathercole JL, Fairweather NJ, Chu S, Masadah R, Jobling TW, Deb-Choudhury S, Dyer J, Stephens AN. 2014. Evidence for the antagonistic form of CXC-motif chemokine CXCL10 in serous epithelial ovarian tumours. Int J Cancer. 134(3):530–541. doi: 10.1002/ijc.28393.
   PubMed Web of Science ®Google Scholar
• Richardson A, Kaye SB. 2005. Drug resistance in ovarian cancer: the emerging importance of gene transcription and spatio-temporal regulation of resistance. Drug Resist Updates. 8(5):311–321. doi: 10.1016/j.drup.2005.09.001.
   PubMed Web of Science ®Google Scholar
• Righi E, Kashiwagi S, Yuan J, Santosuosso M, Leblanc P, Ingraham R, Forbes B, Edelblute B, Collette B, Xing D. 2011. CXCL12/CXCR4 blockade induces multimodal antitumor effects that prolong survival in an immunocompetent mouse model of ovarian cancer. Cancer Res. 71(16):5522–5534. doi: 10.1158/0008-5472.CAN-10-3143.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. 2015. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res . 43(7):e47. doi:10.1093/nar/gkv007.
   PubMed Web of Science ®Google Scholar
• Samuel P, Mulcahy LA, Furlong F, McCarthy HO, Brooks SA, Fabbri M, Pink RC, Carter DRF. 2018. Cisplatin induces the release of extracellular vesicles from ovarian cancer cells that can induce invasiveness and drug resistance in bystander cells. Philos Trans R Soc B. 373(1737):20170065. doi: 10.1098/rstb.2017.0065.
   PubMedGoogle Scholar
• Shah ED, Fisch BM, Arceci RJ, Buckley JD, Reaman GH, Sorensen PH, Triche TJ, Reynolds CP. 2014. Drugpath: a database for academic investigators to match oncology molecular targets with drugs in development. Cancer Chemother Pharmacol. 73(5):1089–1093. doi: 10.1007/s00280-014-2433-9.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11):2498–2504. doi: 10.1101/gr.1239303.
   PubMed Web of Science ®Google Scholar
• Stippel D, Kasper H, Schleimer K, Töx U, Bangard C, Hölscher A, Beckurts K. 2005. Successful use of sirolimus in a patient with bulky ovarian metastasis of hepatocellular carcinoma after liver transplantation. Transplant Proc. 37(5):2185–2187. doi: 10.1016/j.transproceed.2005.03.013.
   PubMed Web of Science ®Google Scholar
• Tang Z, Kang B, Li C, Chen T, Zhang Z. 2019. Structural and functional insight into the mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor. Nucleic Acids Res. 47(18):9934–9949. doi: 10.1093/nar/gkz724.
   PubMed Web of Science ®Google Scholar
• Torre LA, Trabert B, DeSantis CE, Miller KD, Samimi G, Runowicz CD, Gaudet MM, Jemal A, Siegel RL. 2018. Ovarian cancer statistics, 2018. CA Cancer J Clin. 68(4):284–296. doi:10.3322/caac.21456.
   PubMed Web of Science ®Google Scholar
• Türei D, Korcsmáros T, Saez-Rodriguez J. 2016. Omnipath: guidelines and gateway for literature-curated signaling pathway resources. Nat Meth. 13(12):966–967. doi: 10.1038/nmeth.4077.
   PubMed Web of Science ®Google Scholar
• Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A. 2015. Tissue-based map of the human proteome. Science. 347(6220):1260419. doi: 10.1126/science.1260419.
   PubMed Web of Science ®Google Scholar
• Wang Z, Jensen MA, Zenklusen JC. 2016. A practical guide to the cancer genome atlas (TCGA). Meth Mol Biol. 1418:111–141. doi:10.1007/978-1-4939-3578-9_6.
   PubMedGoogle Scholar
• Weitzenfeld P, Benbaruch A. 2014. The chemokine system, and its CCR5 and CXCR4 receptors, as potential targets for personalized therapy in cancer. Cancer Lett. 352(1):36–53. doi: 10.1016/j.canlet.2013.10.006.
   PubMed Web of Science ®Google Scholar
• Yaalhahoshen N, Shina S, Leidertrejo L, Barnea I, Shabtai E, Azenshtein E, Greenberg I, Keydar I, Benbaruch A. 2006. The chemokine CCL5 as a potential prognostic factor predicting disease progression in stage II breast cancer patients. Clin Cancer Res. 12(15):4474–4480. doi: 10.1158/1078-0432.CCR-06-0074.
   PubMed Web of Science ®Google Scholar
• Zhou B, Sun C, Li N, Shan W, Lu H, Guo L, Guo E, Xia M, Weng D, Meng L. 2016. Cisplatin-induced CCL5 secretion from CAFs promotes cisplatin-resistance in ovarian cancer via regulation of the STAT3 and PI3K/Akt signaling pathways. Int J Oncol. 48(5):2087–2097. doi: 10.3892/ijo.2016.3442.
   PubMed Web of Science ®Google Scholar
• Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK. 2019. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 10(1):1523. doi:10.1038/s41467-019-09234-6.
   PubMed Web of Science ®Google Scholar