Identification of novel biomarkers in breast cancer via integrated bioinformatics analysis and experimental validation

References

• Yanovich G, Agmon H, Harel M, et al. Clinical proteomics of breast cancer reveals a novel layer of breast cancer classification. Cancer Res. 2018;78(20):6001–6010.
   PubMed Web of Science ®Google Scholar
• DeSantis CE, Ma J, Goding Sauer A, et al. Breast cancer statistics, 2017, racial disparity in mortality by state. CA. 2017;67(6):439–448.
   Google Scholar
• Tang J, Ma W, Zeng Q, et al. Identification of miRNA-based signature as a novel potential prognostic biomarker in patients with breast cancer. Dis Markers. 2019;2019:3815952.
   PubMed Web of Science ®Google Scholar
• Figueroa-Magalhães MC, Jelovac D, Connolly R, et al. Treatment of HER2-positive breast cancer. Breast. 2014;23(2):128–136.
   PubMed Web of Science ®Google Scholar
• Li J, Liang R, Song C, et al. Prognostic value of Ki-67/MIB-1 expression in meningioma patients: a meta-analysis. Crit Rev Eukaryot Gene Expr. 2019;29(2):141–150.
   PubMed Web of Science ®Google Scholar
• Pan D, Wei K, Ling Y, et al. The prognostic role of Ki-67/MIB-1 in cervical cancer: a systematic review with meta-analysis. Med Sci Monit. 2015;21::882–889.
   Web of Science ®Google Scholar
• Martinez-Gutierrez AD, Cantú de León D, Millan-Catalan O, et al. Identification of miRNA master regulators in breast cancer. Cells. 2020;9(7):1610.
   PubMed Web of Science ®Google Scholar
• Yerukala Sathipati S, Ho SY. Identifying a miRNA signature for predicting the stage of breast cancer. Sci Rep. 2018;8(1):16138.
   PubMedGoogle Scholar
• Vogelstein B, Papadopoulos N, Velculescu VE, et al. Cancer genome landscapes. Science (New York, NY). 2013;339(6127):1546–1558.
   Google Scholar
• Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BIOCONDUCTOR. Bioinformatics. 2007;23(14):1846–1847.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Ogata H, Goto S, Sato K, et al. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999;27(1):29–34.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Tan Q, et al. The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007;8(9):R183.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43( Database issue):D447–452.
   PubMed Web of Science ®Google Scholar
• Smoot ME, Ono K, Ruscheinski J, et al. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432.
   PubMed Web of Science ®Google Scholar
• Li L, Lei Q, Zhang S, et al. Screening and identification of key biomarkers in hepatocellular carcinoma: evidence from bioinformatic analysis. Oncol Rep. 2017;38(5):2607–2618.
   PubMed Web of Science ®Google Scholar
• Ma L, Deng C. Identification of a novel four-lncRNA signature as a prognostic indicator in cirrhotic hepatocellular carcinoma. PeerJ. 2019;7:e7413.
   PubMed Web of Science ®Google Scholar
• Jézéquel P, Frénel JS, Campion L, et al. bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses. Database. 2013;2013:bas060.
   PubMedGoogle Scholar
• Jézéquel P, Gouraud W, Ben Azzouz F, et al. bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses. Database. 2021;2021:1–10
   Google Scholar
• Jiang C, Jiang L, Li Q, et al. Acrolein induces NLRP3 inflammasome-mediated pyroptosis and suppresses migration via ROS-dependent autophagy in vascular endothelial cells. Toxicology. 2018;410::26–40.
   Web of Science ®Google Scholar
• Takeshita F, Patrawala L, Osaki M, et al. Systemic delivery of synthetic microRNA-16 inhibits the growth of metastatic prostate tumors via downregulation of multiple cell-cycle genes. Mol Ther. 2010;18(1):181–187.
   PubMed Web of Science ®Google Scholar
• Cheng S, Castillo V, Sliva D. CDC20 associated with cancer metastasis and novel mushroom‑derived CDC20 inhibitors with antimetastatic activity. Int J Oncol. 2019;54(6):2250–2256.
   PubMed Web of Science ®Google Scholar
• Udhaya Kumar S, Thirumal Kumar D, Bithia R, et al. Analysis of differentially expressed genes and molecular pathways in familial hypercholesterolemia involved in atherosclerosis: a systematic and bioinformatics approach. Front Genet. 2020;11:734.
   PubMed Web of Science ®Google Scholar
• Udhaya Kumar S, Madhana Priya N, Thirumal Kumar D, et al. An integrative analysis to distinguish between emphysema (EML) and alpha-1 antitrypsin deficiency-related emphysema (ADL)-A systems biology approach. Adv Protein Chem Struct Biol. 2021;127:315–342.
   PubMed Web of Science ®Google Scholar
• Wan J, Jiang S, Jiang Y, et al. Data mining and expression analysis of differential lncRNA ADAMTS9-AS1 in prostate cancer. Front Genet. 2019;10:1377.
   PubMed Web of Science ®Google Scholar
• Fu D, Zhang B, Yang L, et al. Development of an immune-related risk signature for predicting prognosis in lung squamous cell carcinoma. Front Genet. 2020;11:978.
   PubMed Web of Science ®Google Scholar
• Zhang M, Chen H, Wang M, et al. Bioinformatics analysis of prognostic significance of COL10A1 in breast cancer. Biosci Rep. 2020;40:2.
   Web of Science ®Google Scholar
• Wang Q, Zhao S, Gan L, et al. Bioinformatics analysis of prognostic value of PITX1 gene in breast cancer. Biosci Rep. 2020;40:9.
   Web of Science ®Google Scholar
• Scully OJ, Bay BH, Yip G, et al. Breast cancer metastasis. Cancer Genomics Proteomics. 2012;9(5):311–320.
   PubMed Web of Science ®Google Scholar
• Nabet BY, Qiu Y, Shabason JE, et al. Exosome RNA unshielding couples stromal activation to pattern recognition receptor signaling in cancer. Cell. 2017;170(2):352–366.e313.
   PubMed Web of Science ®Google Scholar
• Ling L, Tan SK, Goh TH, et al. Targeting the heparin-binding domain of fibroblast growth factor receptor 1 as a potential cancer therapy. Mol Cancer. 2015;14:136.
   PubMed Web of Science ®Google Scholar
• Holt LJ, Tuch BB, Villén J, et al. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science (New York, NY). 2009;325(5948):1682–1686.
   Google Scholar
• Ravindran Menon D, Luo Y, Arcaroli JJ, et al. CDK1 interacts with Sox2 and promotes tumor initiation in human melanoma. Cancer Res. 2018;78(23):6561–6574.
   PubMed Web of Science ®Google Scholar
• Qian JY, Gao J, Sun X, et al. KIAA1429 acts as an oncogenic factor in breast cancer by regulating CDK1 in an N6-methyladenosine-independent manner. Oncogene. 2019;38(33):6123–6141.
   PubMed Web of Science ®Google Scholar
• Yamamura M, Sato Y, Takahashi K, et al. The cyclin‑dependent kinase pathway involving CDK1 is a potential therapeutic target for cholangiocarcinoma. Oncol Rep. 2020;43(1):306–317.
   PubMed Web of Science ®Google Scholar
• Bharadwaj R, Yu H. The spindle checkpoint, aneuploidy, and cancer. Oncogene. 2004;23(11):2016–2027.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Huang H, Liu A, et al. Cell division cycle 20 (CDC20) drives prostate cancer progression via stabilization of β-catenin in cancer stem-like cells. EBioMedicine. 2019;42::397–407.
   Web of Science ®Google Scholar
• Bavetsias V, Linardopoulos S. Aurora kinase inhibitors: current status and outlook. Front Oncol. 2015;5:278.
   PubMed Web of Science ®Google Scholar
• Marumoto T, Zhang D, Saya H. Aurora-A - a guardian of poles. Nat Rev Cancer. 2005;5(1):42–50.
   PubMed Web of Science ®Google Scholar
• Sakakura C, Hagiwara A, Yasuoka R, et al. Tumour-amplified kinase BTAK is amplified and overexpressed in gastric cancers with possible involvement in aneuploid formation. Br J Cancer. 2001;84(6):824–831.
   PubMed Web of Science ®Google Scholar
• Peng F, Xu J, Cui B, et al. Oncogenic AURKA-enhanced N(6)-methyladenosine modification increases DROSHA mRNA stability to transactivate STC1 in breast cancer stem-like cells. Cell Res. 2020;31(3):345–361.
   Web of Science ®Google Scholar
• Zhang W, Xia D, Li Z, et al. Aurora-A/ERK1/2/mTOR axis promotes tumor progression in triple-negative breast cancer and dual-targeting Aurora-A/mTOR shows synthetic lethality. Cell Death Dis. 2019;10(8):606.
   PubMedGoogle Scholar
• Forsburg SL. Eukaryotic MCM proteins: beyond replication initiation. Microbiol Mol Biol Rev. 2004;68(1):109–131.
   PubMed Web of Science ®Google Scholar
• Issac MSM, Yousef E, Tahir MR, et al. MCM2, MCM4, and MCM6 in breast cancer: clinical utility in diagnosis and prognosis. Neoplasia (New York, NY). 2019;21(10):1015–1035.
   PubMed Web of Science ®Google Scholar
• Kwok HF, Zhang SD, McCrudden CM, et al. Prognostic significance of minichromosome maintenance proteins in breast cancer. Am J Cancer Res. 2015;5(1):52–71.
   PubMed Web of Science ®Google Scholar
• Liu Z, Liang G, Tan L, et al. High-efficient screening method for identification of key genes in breast cancer through microarray and bioinformatics. Anticancer Res. 2017;37(8):4329–4335.
   PubMed Web of Science ®Google Scholar
• Hong Z, Wang Q, Hong C, et al. Identification of seven cell cycle-related genes with unfavorable prognosis and construction of their TF-miRNA-mRNA regulatory network in breast cancer. J Cancer. 2021;12(3):740–753.
   PubMed Web of Science ®Google Scholar