Identification Of key prognostic genes in ovarian cancer using WGCNA and LASSO analysis

References

• Bi G, Chen Z, Yang X, Liang J, Hu Z, Bian Y, Sui Q, Li R, Zhan C, Fan H. 2020. Identification and validation of tumor environment phenotypes in lung adenocarcinoma by integrative genome-scale analysis. Cancer Immunol Immunother. 69(7):1293–1305.
   PubMed Web of Science ®Google Scholar
• Binnewies M, Roberts EW, Kersten K, Chan V, Fearon DF, Merad M, Coussens LM, Gabrilovich DI, Ostrand-Rosenberg S, Hedrick CC, et al. 2018. Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med. 24(5):541–550.
   PubMed Web of Science ®Google Scholar
• Bommer GT, Jäger C, Dürr EM, Baehs S, Eichhorst ST, Brabletz T, Hu G, Fröhlich T, Arnold G, Kress DC, et al. 2005. DRO1, a gene down-regulated by oncogenes, mediates growth inhibition in colon and pancreatic cancer cells. J Biol Chem. 280(9):7962–7975.
   PubMed Web of Science ®Google Scholar
• Cenciarelli C, Chiaur DS, Guardavaccaro D, Parks W, Vidal M, Pagano M. 1999. Identification of a family of human F-box proteins. Curr Biol. 9(20):1177–1179.
   PubMed Web of Science ®Google Scholar
• Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 4(1):s13742–015.
   Google Scholar
• Cheng H, Ma Y, Ni X, Jiang M, Guo L, Jin W, Xu W, Cao G, Ji C, Yin K, et al. 2002. cDNA cloning and expression analysis of a novel human F-box only protein. Mol Cells. 14(1):56–59.
   PubMed Web of Science ®Google Scholar
• Choi JH, Sohn GS, Chay DB, Cho HB, Kim JH. 2018. Preoperative serum levels of cancer antigen 125 and carcinoembryonic antigen ratio can improve differentiation between mucinous ovarian carcinoma and other epithelial ovarian carcinomas. Obstet Gynecol Sci. 61(3):344–351.
   PubMedGoogle Scholar
• Ferlay J, Colombet M, Soerjomataram I, Mathers C, Parkin DM, Piñeros M, Znaor A, Bray F. 2019. Estimating the global cancer incidence and mortality in 2018: GLOBOCAN sources and methods. Int J Cancer. 144(8):1941–1953.
   PubMed Web of Science ®Google Scholar
• Ferragud J, Avivar-Valderas A, Pla A, De Las Rivas J, de Mora J. F. 2011. Transcriptional repression of the tumor suppressor DRO1 by AIB1. FEBS Lett. 585(19):3041–3046.
   PubMed Web of Science ®Google Scholar
• Ferraro A, Schepis F, Leone V, Federico A, Borbone E, Pallante P, Berlingieri MT, Chiappetta G, Monaco M, Palmieri D, et al. 2013. Tumor suppressor role of the CL2/DRO1/CCDC80 gene in thyroid carcinogenesis. J Clin Endocrinol Metab. 98(7):2834–2843.
   PubMed Web of Science ®Google Scholar
• Fialová A, Partlová S, Sojka L, Hromádková H, Brtnický T, Fučíková J, Kocián P, Rob L, Bartůňková J, Spíšek R. 2013. Dynamics of T-cell infiltration during the course of ovarian cancer: the gradual shift from a Th17 effector cell response to a predominant infiltration by regulatory T-cells. Int J Cancer. 132(5):1070–1079.
   PubMed Web of Science ®Google Scholar
• Gadducci A, Guarneri V, Peccatori FA, Ronzino G, Scandurra G, Zamagni C, Zola P, Salutari V. 2019. Current strategies for the targeted treatment of high-grade serous epithelial ovarian cancer and relevance of BRCA mutational status. J Ovarian Res. 12(1):1–8.
   PubMedGoogle Scholar
• Guo J, Yang WL, Pak D, Celestino J, Lu KH, Ning J, Lokshin AE, Cheng Z, Lu Z, Bast RC, Jr. 2019. Osteopontin, macrophage migration inhibitory factor and anti-interleukin-8 autoantibodies complement CA125 for detection of early stage ovarian cancer. Cancers (Basel). 11(5):596.
   PubMed Web of Science ®Google Scholar
• Gutiérrez-Castañeda LD, Tovar-Parra D, Quintero G, Amezquita L, Guerrero C, Sanabria D. 2020. Isolation and phenotypic characterization of tumor cells of patients with a diagnosis of ovarian cancer. J Cell Physiol. 235(4):3320–3328.
   PubMed Web of Science ®Google Scholar
• Hänzelmann S, Castelo R, Guinney J. 2013. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 14(1):1–15.
   PubMedGoogle Scholar
• Hilliard TS. 2018. The impact of mesothelin in the ovarian cancer tumor microenvironment. Cancers (Basel). 10(9):277.
   PubMed Web of Science ®Google Scholar
• Hou P, Kapoor A, Zhang Q, Li J, Wu CJ, Li J, Lan Z, Tang M, Ma X, Ackroyd JJ, et al. 2020. Tumor microenvironment remodeling enables bypass of oncogenic KRAS dependency in pancreatic cancer. Cancer Discov. 10(7):1058–1077.
   PubMed Web of Science ®Google Scholar
• Ichimura T, Abe H, Morikawa T, Yamashita H, Ishikawa S, Ushiku T, Seto Y, Fukayama M. 2016. Low density of CD204-positive M2-type tumor-associated macrophages in epstein-barr virus-associated gastric cancer: a clinicopathologic study with digital image analysis. Hum Pathol. 56:74–80.
   PubMed Web of Science ®Google Scholar
• Khan M, Muzumdar D, Shiras A. 2019. Attenuation of tumor suppressive function of FBXO16 ubiquitin ligase activates Wnt signaling In glioblastoma. Neoplasia. 21(1):106–116.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 9:559.
   PubMed Web of Science ®Google Scholar
• Leone V, Ferraro A, Schepis F, Federico A, Sepe R, Arra C, Langella C, Palma G, De Lorenzo C, Troncone G, et al. 2015. The cl2/dro1/ccdc80 null mice develop thyroid and ovarian neoplasias. Cancer Lett. 357(2):535–541.
   PubMed Web of Science ®Google Scholar
• Liang L, Jiang Y, Chen JS, Niu N, Piao J, Ning J, Zu Y, Zhang J, Liu J. 2016. B7-H4 expression in ovarian serous carcinoma: a study of 306 cases. Hum Pathol. 57:1–6.
   PubMed Web of Science ®Google Scholar
• Lin Y, Wang S, Chappell RJ. 2013. Lasso tree for cancer staging with survival data. Biostatistics. 14(2):327–339.
   PubMed Web of Science ®Google Scholar
• Ma Y, Shurin GV, Peiyuan Z, Shurin MR. 2013. Dendritic cells in the cancer microenvironment. J Cancer. 4(1):36–44.
   PubMed Web of Science ®Google Scholar
• Malki K, Tosto MG, Jumabhoy I, Lourdusamy A, Sluyter F, Craig I, Uher R, McGuffin P, Schalkwyk LC. 2013. Integrative mouse and human mRNA studies using WGCNA nominates novel candidate genes involved in the pathogenesis of major depressive disorder. Pharmacogenomics. 14(16):1979–1990.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. 2015. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 12(5):453–457.
   PubMed Web of Science ®Google Scholar
• Paul D, Islam S, Manne RK, Dinesh US, Malonia SK, Maity B, Boppana R, Rapole S, Shetty PK, Santra MK. 2019. F-box protein FBXO16 functions as a tumor suppressor by attenuating nuclear β-catenin function. J Pathol. 248(3):266–279.
   PubMed Web of Science ®Google Scholar
• Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL. 2002. Hierarchical organization of modularity in metabolic networks. Science (New York, NY). 297(5586):1551–1555.
   Google Scholar
• Reles A, Wen WH, Schmider A, Gee C, Runnebaum IB, Kilian U, Jones LA, El-Naggar A, Minguillon C, Schönborn I, et al. 2001. Correlation of p53 mutations with resistance to platinum-based chemotherapy and shortened survival in ovarian cancer. Clin Cancer Res. 7(10):2984–2997.
   PubMed Web of Science ®Google Scholar
• Ribbing J, Nyberg J, Caster O, Jonsson EN. 2007. The lasso–a novel method for predictive covariate model building in nonlinear mixed effects models. J Pharmacokinet Pharmacodyn. 34(4):485–517.
   PubMed Web of Science ®Google Scholar
• Sarvaria A, Madrigal JA, Saudemont A. 2017. B cell regulation in cancer and anti-tumor immunity. Cell Mol Immunol. 14(8):662–674.
   PubMed Web of Science ®Google Scholar
• Shih KK, Chi DS, Barakat RR, Leitao MM. 2010. Tertiary cytoreduction in patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer: an updated series. Gynecol Oncol. 117(2):330–335.
   PubMed Web of Science ®Google Scholar
• Terabe M, Matsui S, Noben-Trauth N, Chen H, Watson C, Donaldson DD, Carbone DP, Paul WE, Berzofsky JA. 2000. NKT cell-mediated repression of tumor immunosurveillance by IL-13 and the IL-4R-STAT6 pathway. Nat Immunol. 1(6):515–520.
   PubMed Web of Science ®Google Scholar
• Udyavar AR, Hoeksema MD, Clark JE, Zou Y, Tang Z, Li Z, Li M, Chen H, Statnikov A, Shyr Y, et al. 2013. Co-expression network analysis identifies spleen tyrosine kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. BMC Syst Biol. 7(5):1–16.
   PubMedGoogle Scholar
• Urban N, Hawley S, Janes H, Karlan BY, Berg CD, Drescher CW, Manson JE, Palomares MR, Daly MB, Wactawski-Wende J, et al. 2015. Identifying post-menopausal women at elevated risk for epithelial ovarian cancer. Gynecol Oncol. 139(2):253–260.
   PubMed Web of Science ®Google Scholar
• van Zyl B, Tang D, Bowden NA. 2018. Biomarkers of platinum resistance in ovarian cancer: what can we use to improve treatment. Endocr Relat Cancer. 25(5):R303–r318.
   PubMed Web of Science ®Google Scholar
• Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, et al. 2015. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature. 518(7540):495–501.
   PubMed Web of Science ®Google Scholar
• Wan J, Shi F, Xu Z, Zhao M. 2015. Knockdown of eIF4E suppresses cell proliferation, invasion and enhances cisplatin cytotoxicity in human ovarian cancer cells. Int J Oncol. 47(6):2217–2225.
   PubMed Web of Science ®Google Scholar
• Wei SU, Li H, Zhang B. 2016. The diagnostic value of serum HE4 and CA-125 and ROMA index in ovarian cancer. Biomed Rep. 5(1):41–44.
   PubMed Web of Science ®Google Scholar
• Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, Bindal N, Beare D, Smith JA, Thompson IR, et al. 2013. Genomics of drug sensitivity in cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res. 41:D955–D961.
   PubMed Web of Science ®Google Scholar
• Yang-Hartwich Y, Soteras MG, Lin ZP, Holmberg J, Sumi N, Craveiro V, Liang M, Romanoff E, Bingham J, Garofalo F, et al. 2015. P53 protein aggregation promotes platinum resistance in ovarian cancer. Oncogene. 34(27):3605–3616.
   PubMed Web of Science ®Google Scholar
• Zhang YJ, Cao LY, Fu ZZ, Wang YJ, Wang GX, Gu T. 2015. Clinical significance of plasma lysophosphatidic acid levels in the differential diagnosis of ovarian cancer. J Cancer Res Ther. 11(2):375–380.
   PubMed Web of Science ®Google Scholar