Co-expressed functional module-related genes in ovarian cancer stem cells represent novel prognostic biomarkers in ovarian cancer

References

• Aguirre-Gamboa R, Gomez-Rueda H, Martı´nez-Ledesma E. 2013. SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis. PLoS One. 8:e74250. doi:10.1371/journal.pone.0074250.
   PubMed Web of Science ®Google Scholar
• Ahmed N, Stenvers K. 2013. Getting to know ovarian cancer ascites: opportunities for targeted therapy-based translational research. Front Oncol. 3:256. doi:10.3389/fonc.2013.00256.
   PubMedGoogle Scholar
• Ayyildiz D, Gov E, Sinha R, Arga KY. 2017. Ovarian cancer differential interactome and network entropy analysis reveal new candidate biomarkers. OMICS. 21(5):285–294. doi:10.1089/omi.2017.0010.
   PubMed Web of Science ®Google Scholar
• Bareiss PM, Paczulla A, Wang H, Schairer R, Wiehr S, Kohlhofer U, Rothfuss OC, Fischer A, Perner S, Staebler A, et al. 2013. SOX2 expression associates with stem cell state in human ovarian carcinoma. Cancer Res. 73(17):5544–5555. doi:10.1158/0008-5472.CAN-12-4177.
   PubMed Web of Science ®Google Scholar
• Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al. 2013. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 41:D991–D995. doi:10.1093/nar/gks1193.
   PubMed Web of Science ®Google Scholar
• Batlle E, Clevers H. 2017. Cancer stem cells revisited. Nat Med. 23:1124. doi:10.1038/nm.4409.
   PubMed Web of Science ®Google Scholar
• Bilandzic M, Chu S, Farnworth PG, Harrison C, Nicholls P, Wang Y, Escalona RM, Fuller PJ, Findlay JK, Stenvers KL. 2009. Loss of betaglycan contributes to the malignant properties of human granulosa tumor cells. Mol Endocrinol. 23(4):539–548. doi:10.1210/me.2008-0300.
   PubMed Web of Science ®Google Scholar
• Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi M-B, Harpole D, Lancaster JM, Berchuck A, et al. 2006. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 439(7074):353. doi:10.1038/nature04296.
   PubMed Web of Science ®Google Scholar
• Bolstad BM, Irizarry RA, Åstrand M, Speed TP. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19:185–193. doi:10.1093/bioinformatics/19.2.185.
   PubMed Web of Science ®Google Scholar
• Byron SA, Gartside MG, Wellens CL, Goodfellow PJ, Birrer MJ, Campbell IG, Pollock PM. 2010. FGFR2 mutations are rare across histologic subtypes of ovarian cancer. Gynecol Oncol. 117(1):125–129. doi:10.1016/j.ygyno.2009.12.002.
   PubMed Web of Science ®Google Scholar
• Cai W, Song B, Ai H. 2019. Combined inhibition of FGFR and mTOR pathways is effective in suppressing ovarian cancer. Am J Transl Res. 11(3):1616.
   PubMed Web of Science ®Google Scholar
• Chen Z, Fadiel A, Feng Y, Ohtani K, Rutherford T, Naftolin F. 2001. Ovarian epithelial carcinoma tyrosine phosphorylation, cell proliferation, and ezrin translocation are stimulated by interleukin 1α and epidermal growth factor. Cancer. 92(12):3068–3075. doi:10.1002/1097-0142(20011215)92:12<3068::AID-CNCR10149>3.0.CO;2-5.
   PubMed Web of Science ®Google Scholar
• Clevers H. 2011. The cancer stem cell: premises, promises and challenges. Nat Med. 17:313. doi:10.1038/nm.2304.
   PubMed Web of Science ®Google Scholar
• Cline MS, Smoot M, Cerami E. 2007. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2:2366–2382. doi:10.1038/nprot.2007.324.
   PubMed Web of Science ®Google Scholar
• Cole C, Lau S, Backen A, Clamp A, Rushton G, Dive C, Hodgkinson C, McVey R, Kitchener H, Jayson GC 2010. Inhibition of FGFR2 and FGFR1 increases cisplatin sensitivity in ovarian cancer. Cancer Biol Ther. 10(5):495–504. doi:10.4161/cbt.10.5.12585.
   PubMed Web of Science ®Google Scholar
• Crijns AP, Fehrmann RS, de Jong S, Gerbens F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, van der Zee AG. 2009. Survival-related profile. Pathways, and transcription factors in ovarian cancer PloS Medicine. 6(2):e1000024.
   Web of Science ®Google Scholar
• Cui J, Sun W, Hao X, Wei M, Su X, Zhang Y, Su L, Liu X. 2015. EHMT2 inhibitor BIX01294 induces apoptosis through PMAIP1-USP9X-MCL1 axis in human bladder cancer cells. Cancer Cell Int. 15(1):4. doi:10.1186/s12935-014-0149-x.
   PubMedGoogle Scholar
• Gao Q, Geng L, Kvalheim G, Gaudernack G, Suo Z. 2009. Identification of cancer stem-like side population cells in ovarian cancer cell line OVCAR-3. Ultrastruct Pathol. 33(4):175–181. doi:10.3109/01913120903086072.
   PubMed Web of Science ®Google Scholar
• Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5(10):80. doi:10.1186/gb-2004-5-10-r80.
   PubMed Web of Science ®Google Scholar
• Gov E, Arga KY. 2016. Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network. IET Syst Biol. 10(6):219–228. doi:10.1049/iet-syb.2016.0001.
   PubMed Web of Science ®Google Scholar
• Gov E, Arga KY. 2017. Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancer. Sci Rep. 7(1):4996. doi:10.1038/s41598-017-05298-w.
   PubMedGoogle Scholar
• Gov E, Kori M, Arga KY. 2017a. Multiomics analysis of tumor microenvironment reveals Gata2 and miRNA-124-3p as potential novel biomarkers in ovarian cancer. OMICS. 21(10):603–615. doi:10.1089/omi.2017.0115.
   PubMed Web of Science ®Google Scholar
• Gov E, Kori M, Arga KY. 2017b. RNA-based ovarian cancer research from ‘a gene to systems biomedicine’perspective. Syst Biol Reprod Med. 63(4):219 238. doi:10.1080/19396368.2017.1330368.
   PubMed Web of Science ®Google Scholar
• Hempel N, How T, Dong M, Murphy SK, Fields TA, Blobe GC. 2007. Loss of betaglycan expression in ovarian cancer: role in motility and invasion. Cancer Res. 67(11):5231 5238. doi:10.1158/0008-5472.CAN-07-0035.
   Web of Science ®Google Scholar
• Hippisley-Cox J, Coupland C. 2012. Identifying women with suspected ovarian cancer in primary care: derivation and validation of algorithm. Bmj. 344:d8009. doi:10.1136/bmj.d8009.
   Web of Science ®Google Scholar
• Hover LD, Young CD, Bhola NE, Wilson AJ, Khabele D, Hong CC, Moses HL, Owens P 2015. Small molecule inhibitor of the bone morphogenetic protein pathway DMH1 reduces ovarian cancer cell growth. Cancer Lett. 368(1):79–87. doi:10.1016/j.canlet.2015.07.032.
   PubMed Web of Science ®Google Scholar
• Hsu CL, Juan HF, Huang HC. 2015. Functional analysis and characterization of differential coexpression networks. Sci Rep. 5:13295. doi:10.1038/srep13295.
   PubMed Web of Science ®Google Scholar
• Hu L, McArthur C, Jaffe RB. 2010. Ovarian cancer stem-like side-population cells are tumourigenic and chemoresistant. Br J Cancer. 102(8):1276. doi:10.1038/sj.bjc.6605626.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37:1–13. doi:10.1093/nar/gkn923.
   PubMed Web of Science ®Google Scholar
• Ideker T, Krogan NJ. 2012. Differential network biology. Mol Syst Biol. 8:565. doi:10.1038/msb.2011.99.
   PubMed Web of Science ®Google Scholar
• Janzen DM, Tiourin E, Salehi JA, Paik DY, Lu J, Pellegrini M, Memarzadeh S. 2015. An apoptosis-enhancing drug overcomes platinum resistance in a tumour-initiating subpopulation of ovarian cancer. Nat Commun. 6:7956. doi:10.1038/ncomms8956.
   PubMed Web of Science ®Google Scholar
• Jung JG, Shih IM, Park JT, Gerry E, Kim TH, Ayhan A, Handschuh K, Davidson B, Fader AN, Selleri L, et al. 2016. Ovarian cancer chemoresistance relies on the stem cell reprogramming factor PBX1. Cancer Res. 76(21):6351–6361. doi:10.1158/0008-5472.CAN-16-0980.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42:D199–D205. doi:10.1093/nar/gkt1076.
   PubMed Web of Science ®Google Scholar
• Karabudak AA, Hafner J, Shetty V, Chen S, Secord AA, Morse MA, Philip R. 2013. Autoantibody biomarkers identified by proteomics methods distinguish ovarian cancer from non-ovarian cancer with various CA-125 levels. J Cancer Res Clin Oncol. 139(10):1757–1770. doi:10.1007/s00432-013-1501-6.
   PubMed Web of Science ®Google Scholar
• Konstantinopoulos PA, Fountzilas E, Pillay K, Zerbini LF, Libermann TA, Cannistra SA, Spentzos D. 2008. Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer. BMC Med Genomics. 1(1):59. doi:10.1186/1755-8794-1-59.
   PubMedGoogle Scholar
• Kori M, Gov E, Arga KY. 2019. Novel genomic biomarker candidates for cervical cancer as identified by differential co-expression network analysis. OMICS. 23(5):261–273.
   PubMed Web of Science ®Google Scholar
• Liu DC, Yang ZL, Jiang S. 2011. Identification of PEG10 and TSG101 as carcinogenesis, progression, and poor-prognosis related biomarkers for gallbladder adenocarcinoma. Pathol Oncol Res. 17(4):859. doi:10.1007/s12253-011-9394-7.
   PubMed Web of Science ®Google Scholar
• Liu Z, Yang Z, Liu D, Li D, Zou Q, Yuan Y, Li J, Liang L, Chen M, Chen S. 2014. TSG101 and PEG10 are prognostic markers in squamous cell/adenosquamous carcinomas and adenocarcinoma of the gallbladder. Oncol Lett. 7(4):1128–1138. doi:10.3892/ol.2014.1886.
   PubMed Web of Science ®Google Scholar
• Ma X, Ren L, Zhang N, Liu C, Zhu Y, Xiao J. 2017. Knock-down of KHDRBS3 gene inhibits proliferation of human ovarian cancer CAOV-3 cells. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 33(8):1062–1066.
   PubMedGoogle Scholar
• Marchini S, Fruscio R, Clivio L, Beltrame L, Porcu L, Nerini IF, Cavalieri D, Chiorino G, Cattoretti G, Mangioni C, et al. 2013. Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer. Eur J Cancer. 49(2):520–530. doi:10.1016/j.ejca.2012.06.026.
   PubMed Web of Science ®Google Scholar
• Mythreye K, Blobe GC. 2009. The type III TGF-β receptor regulates epithelial and cancer cell migration through β-arrestin2-mediated activation of Cdc42. PNAS. 106(20):8221–8226. doi:10.1073/pnas.0812879106.
   PubMed Web of Science ®Google Scholar
• Osaki M, Okada F, Ochiya T. 2015. miRNA therapy targeting cancer stem cells: a new paradigm for cancer treatment and prevention of tumor recurrence. Ther Deliv. 6:323–337. doi:10.4155/tde.14.122.
   PubMed Web of Science ®Google Scholar
• Pils D, Wittinger M, Petz M, Gugerell A, Gregor W, Alfanz A, Horvat R, Braicu EI, Sehouli J, Zeillinger R, Mikulits W. 2010. BAMBI is overexpressed in ovarian cancer and co-translocates with Smads into the nucleus upon TGF-ß treatment. Gynecol Oncol. 117(2):189–197. doi:10.1016/j.ygyno.2009.12.034.
   PubMed Web of Science ®Google Scholar
• Saito R, Smoot ME, Ono K. 2012. A travel guide to Cytoscape plugins. Nat Methods. 9:1068–1076. doi:10.1038/nmeth.2212.
   Web of Science ®Google Scholar
• Siegel RL, Miller KD, Jemal A. 2016. (2016) Cancer statistics. CA Cancer J Clin. 66:7–30. doi:10.3322/caac.21332.
   PubMed Web of Science ®Google Scholar
• Smyth GK. 2005. LIMMA: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and computational biology solutions using R and bioconductor. NY: Springer; p. 397–420.
   Google Scholar
• Song J, Fadiel A, Edusa V, Chen Z, So J, Sakamoto H, Fishman DA, Naftolin F. 2005. Estradiol-induced ezrin overexpression in ovarian cancer: a new signaling domain for estrogen. Cancer Lett. 220(1):57–65. doi:10.1016/j.canlet.2004.04.024.
   PubMed Web of Science ®Google Scholar
• Szotek PP, Pieretti-Vanmarcke R, Masiakos PT, Dinulescu DM, Connolly D, Foster R, Dombkowski D, Preffer F, MacLaughlin DT, Donahoe PK. 2006. Ovarian cancer side population defines cells with stem cell-like characteristics and mullerian inhibiting substance responsiveness. PNAS. 103(30):11154–11159. doi:10.1073/pnas.0603672103.
   PubMed Web of Science ®Google Scholar
• Tothill RW, Tinker AV, George J, Brown R, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Traficante N. 2008. Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome. Clin Cancer Res. 14(16):5198–5208. doi:10.1158/1078-0432.CCR-08-0196.
   PubMed Web of Science ®Google Scholar
• Vathipadiekal V, Saxena D, Mok SC, Hauschka PV, Ozbun L, Birrer MJ. 2012. Identification of a potential ovarian cancer stem cell gene expression profile from advanced stage papillary serous ovarian cancer. PLoS One. 7(1):e29079. doi:10.1371/journal.pone.0029079.
   PubMed Web of Science ®Google Scholar
• Wang L, Mezencev R, Bowen NJ, Matyunina LV, McDonald JF. 2012. Isolation and characterization of stem-like cells from a human ovarian cancer cell line. Mol Cell Biochem. 363(1–2):257–268. doi:10.1007/s11010-011-1178-6.
   PubMed Web of Science ®Google Scholar
• Yoshihara K, Tajima A, Adachi S, Quan J, Sekine M, Kase H, Yahata T, Inoue I, Tanaka K. 2011. Germline copy number variations in BRCA1-associated ovarian cancer patients. Genes Chromosomes Cancer. 50(3):167–177. doi:10.1002/gcc.20841.
   PubMed Web of Science ®Google Scholar
• Yoshihara K, Tsunoda T, Shigemizu D, Fujiwara H, Hatae M, Fujiwara H, Masuzaki H, Katabuchi H, Kawakami Y, Okamoto A, et al. 2012. High-risk ovarian cancer based on 126-gene expression signature is uniquely characterized by downregulation of antigen presentation pathway. Clin Cancer Res. 18(5):1374–1385. doi:10.1158/1078-0432.CCR-11-2725.
   PubMed Web of Science ®Google Scholar
• Zeimet AG, Reimer D, Sopper S, Boesch M, Martowicz A, Roessler J, Wiedemair AM, Rumpold H, Untergasser G, Concin N, et al. 2012. Ovarian cancer stem cells. Neoplasma. 59(6):747. doi:10.4149/neo_2012_094.
   PubMed Web of Science ®Google Scholar
• Zhan Q, Wang C, Ngai S. 2013. Ovarian cancer stem cells: a new target for cancer therapy. Biomed Res Int. 2013:916819. doi:10.1155/2013/916819.
   Web of Science ®Google Scholar
• Zhang T, Xu J, Deng S, Zhou F, Li J, Zhang L, Li L, Wang QE, Li F. 2018. Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data. PLoS One. 13(5):e0196351.
   Web of Science ®Google Scholar
• Zhao X, Liu X, Su L. 2014. Parthenolide induces apoptosis via TNFRSF10B and PMAIP1 pathways in human lung cancer cells. J Exp Clin Cancer Res. 33:3. doi:10.1186/1756-9966-33-3. https://www.ncbi.nlm.nih.gov/pubmed/24387758
   PubMed Web of Science ®Google Scholar
• Zhou Q, Chen A, Song H, Tao J, Yang H, Zuo M. 2015. Prognostic value of cancer stem cell marker CD133 in ovarian cancer: a meta-analysis. Int J Clin Exp Med. 8(3):3080.
   PubMed Web of Science ®Google Scholar
• Zou J, Yin F, Wang Q, Zhang W, Li L. 2015. Analysis of microarray-identified genes and microRNAs associated with drug resistance in ovarian cancer. Int J Clin Exp Pathol. 8(6):6847.
   PubMed Web of Science ®Google Scholar