Identification of significant genes and therapeutic agents for breast cancer by integrated genomics

References

• Nyblade L, Stockton M, Travasso S, et al. A qualitative exploration of cervical and breast cancer stigma in Karnataka, India. BMC Womens Health. 2017;17(1):58.
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature.2012;490(7418):61–70.
   Google Scholar
• Hess KR, Pusztai L, Buzdar AU, et al. Estrogen receptors and distinct patterns of breast cancer relapse. Breast Cancer Res Treat. 2003;78(1):105–18. .
   PubMed Web of Science ®Google Scholar
• Andre F, Job B, Dessen P, et al. Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Clin Cancer Res. 2009;15(2):441–51.
   PubMed Web of Science ®Google Scholar
• Cocco S, Piezzo M, Calabrese A, et al. Biomarkers in triple-negative breast cancer: state-of-the-art and future perspectives. Int J Mol Sci. 2020;21(13):13. .
   Web of Science ®Google Scholar
• Piezzo M, Cocco S, Caputo R, et al. Targeting cell cycle in breast cancer: CDK4/6 INHIBITORS. Int J Mol Sci. 2020;21(18):18.
   Web of Science ®Google Scholar
• Fu CH, Lin R-J, Yu J, et al. A novel oncogenic role of inositol phosphatase SHIP2 in ER-negative breast cancer stem cells: involvement of JNK/vimentin activation. Stem Cells. 2014;32(8):2048–60.
   PubMed Web of Science ®Google Scholar
• Sirinian C, Papanastasiou AD, Schizas M, et al. RANK-c attenuates aggressive properties of ER-negative breast cancer by inhibiting NF-kappaB activation and EGFR signaling. Oncogene. 2018;37(37):5101–5114.
   PubMed Web of Science ®Google Scholar
• Gao S, Ge A, Xu S, et al. PSAT1 is regulated by ATF4 and enhances cell proliferation via the GSK3beta/beta-catenin/cyclin D1 signaling pathway in ER-negative breast cancer. J Exp Clin Cancer Res. 2017;36(1):179.
   PubMed Web of Science ®Google Scholar
• Nb S, Cd, M, S, B, et al. An azaspirane derivative suppresses growth and induces apoptosis of ER-positive and ER-negative breast cancer cells through the modulation of JAK2/STAT3 signaling pathway. Int J Oncol. 2016;49(3):1221–9.
   Google Scholar
• Sp H, Py, L, Cj, K, et al. The Gαh-PLCδ1 signaling axis drives metastatic progression in triple-negative breast cancer. J Hematol Oncol. 2017;10(1):114.
   Google Scholar
• Cj H, Yl H, Yf H, et al. Molecular mechanisms of anticancer effects of phytoestrogens in breast cancer. Breast cancer research and treatment. 2018;19(3):323–332.
   Google Scholar
• Espinal AC, Buas MF, Wang D, et al. FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women? Breast Cancer Res Treat. 2017;166(2):559–568.
   PubMed Web of Science ®Google Scholar
• Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6(2):95–108.
   PubMed Web of Science ®Google Scholar
• Greene CS, Krishnan A, Wong AK, et al. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet. 2015;47(6):569–76.
   PubMed Web of Science ®Google Scholar
• Wang J, Zheng J, Wang Z, et al. Inferring gene-disease association by an integrative analysis of eQTL genome-wide association study and protein-protein interaction data. Hum Hered. 2018;83(3):117–129.
   PubMed Web of Science ®Google Scholar
• Song A, Yan J, Kim S, et al. Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts. BioData Min. 2016;9(1):3.
   PubMed Web of Science ®Google Scholar
• Ma C, Gu C, Huo Y, et al. The integrated landscape of causal genes and pathways in schizophrenia. Transl Psychiatry. 2018;8(1):67.
   PubMed Web of Science ®Google Scholar
• Sudlow C, Gallacher J, Allen N, et al. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 2015;12(3):e1001779.
   PubMed Web of Science ®Google Scholar
• Hammerschlag AR, Stringer S. Genome-wide association analysis of insomnia complaints identifies risk genes and genetic overlap with psychiatric and metabolic traits. Nat Genet. 2017;49(11):1584–1592.
   Google Scholar
• Canela-Xandri O, Rawlik K, Tenesa A. An atlas of genetic associations in UK Biobank. Nat Genet. 2018;50(11):1593–1599.
   PubMed Web of Science ®Google Scholar
• Otasek D, Morris JH, Bouças J, et al. Cytoscape Automation: empowering workflow-based network analysis. Genome Biol. 2019;20(1):185.
   PubMed Web of Science ®Google Scholar
• Bindea G, Galon J, Mlecnik B. CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics. 2013;29(5):661–3.
   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(D1):D447–52. Database issue.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D.  Morris J H, Cook H, et al. The STRING database in 2017: quality-controlled protein-protein association networks. made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362–d368.
   Google Scholar
• Y, Z, Y Z, Y F, et al. Identification of biomarkers, pathways and potential therapeutic agents for white adipocyte insulin resistance using bioinformatics analysis. Adipocyte. 2019;8(1):318–329.
   Google Scholar
• Z, T, C L, B K,  et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(null):W98–W102.
   Google Scholar
• Ponten F, Jirstrom K, Uhlen M. The human protein atlas–a tool for pathology. J Pathol. 2008;216(4):387–93.
   PubMed Web of Science ®Google Scholar
• Uhlen M, Zhang C, Lee S, et al. A pathology atlas of the human cancer transcriptome. Science. 2017;357(6352):6352.
   Web of Science ®Google Scholar
• Thul PJ, Åkesson L, Wiking M, et al. A subcellular map of the human proteome. Science. 2017;356(6340):6340.
   Web of Science ®Google Scholar
• Goswami CP, Nakshatri H. PROGgeneV2: enhancements on the existing database. BMC Cancer. 2014;14(1):970.
   PubMed Web of Science ®Google Scholar
• Lamb J, et al. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929–35.
   PubMed Web of Science ®Google Scholar
• Musa A, Ghoraie LS, Zhang S-D, et al. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2018;19(3):506–523.
   PubMed Web of Science ®Google Scholar
• Raghavan R, Hyter S, Pathak HB, et al. Drug discovery using clinical outcome-based connectivity mapping: application to ovarian cancer. BMC Genomics. 2016;17(1):811.
   PubMed Web of Science ®Google Scholar
• North CM, Christiani DC. Women and lung cancer: what is new? Semin Thorac Cardiovasc Surg. 2013;25(2):87–94.
   PubMedGoogle Scholar
• Woolston C. Breast cancer. Nature. 2015;527(7578):S101.
   PubMed Web of Science ®Google Scholar
• Tsikouras P, Zervoudis S, Manav B, et al. Cervical cancer: screening, diagnosis and staging. J Buon. 2016;21(2):320–5.
   PubMed Web of Science ®Google Scholar
• Anastasiadi Z, Lianos GD, Ignatiadou E, et al. Breast cancer in young women: an overview. Updates Surg. 2017;69(3):313–317. .
   PubMed Web of Science ®Google Scholar
• Musselwhite LW, Oliveira CM, Kwaramba T, et al. Racial/ethnic disparities in cervical cancer screening and outcomes. Acta Cytol. 2016;60(6):518–526. .
   PubMed Web of Science ®Google Scholar
• Kossai M, Leary A, Scoazec J-Y, et al. Ovarian Cancer: a heterogeneous disease. Pathobiology. 2018;85(1–2):41–49.
   PubMed Web of Science ®Google Scholar
• Bernardi M, Logullo A, Pasini F, et al. Prognostic significance of CD24 and claudin-7 immunoexpression in ductal invasive breast cancer. Oncol Rep. 2012;27(1):28–38.
   Google Scholar
• Guo X, Lin W, Bao J, et al. A Comprehensive cis-eQTL analysis revealed target genes in breast cancer susceptibility loci identified in genome-wide association studies. Am J Hum Genet. 2018;102(5):890–903.
   PubMed Web of Science ®Google Scholar
• Bauer D, Mazzio E, Soliman KFA. Whole transcriptomic analysis of apigenin on TNFα immuno-activated MDA-MB-231 breast cancer cells. Cancer Genomics Proteomics. 2019;16(6):421–431.
   PubMed Web of Science ®Google Scholar
• Fu R, Han C, Ni T, et al. A ZEB1/p53 signaling axis in stromal fibroblasts promotes mammary epithelial tumours. Nat Commun. 2019;10(1):3210.
   Google Scholar
• Zhu Y, Yang L, Chong Q-Y, et al. Long noncoding RNA Linc00460 promotes breast cancer progression by regulating the miR-489-5p/FGF7/AKT axis. Cancer Management and Research. 2019;11(p):5983–6001.
   PubMed Web of Science ®Google Scholar
• Morel AP, Ginestier C, Pommier RM, et al. A stemness-related ZEB1-MSRB3 axis governs cellular pliancy and breast cancer genome stability. Nat Med. 2017;23(5):568–578.
   PubMed Web of Science ®Google Scholar
• Lin Q, He Y, Wang X, et al. Targeting pyruvate carboxylase by a small molecule suppresses breast cancer progression. Adv Sci (Weinh). 2020;7(9):1903483.
   Google Scholar
• Khawaled S, Nigita G, Distefano R, et al. Pleiotropic tumor suppressor functions of WWOX antagonize metastasis. Signal Transduction and Targeted Therapy. 2020;5(1):43. .
   PubMed Web of Science ®Google Scholar
• Eyre R, Alférez DG, Santiago-Gómez A, et al. Microenvironmental IL1β promotes breast cancer metastatic colonisation in the bone via activation of Wnt signalling. Nature Communications. 2019;10(1):5016. .
   PubMed Web of Science ®Google Scholar
• Cougot N, Daguenet É, Baguet A, et al. Overexpression of MLN51 triggers P-body disassembly and formation of a new type of RNA granules. J Cell Sci. 2014;127(21):4692–701. .
   PubMed Web of Science ®Google Scholar
• A, K, V LN, N N, et al. Benzo[b]furan derivatives induces apoptosis by targeting the PI3K/Akt/mTOR signaling pathway in human breast cancer cells. chemistry SRNJB. 2016;66(undefined):124–131.
   Google Scholar
• Kl W, JR A, JC L, et al. Ras signaling is a key determinant for metastatic dissemination and poor survival of luminal breast cancer patients. Cancer Res. 2015;75(22):4960–72.
   Google Scholar
• W, C, J L, Q H, et al. AMP-activated protein kinase: a potential therapeutic target for triple-negative breast cancer. Breast Cancer Res. 2019;21(1):29.
   Google Scholar
• Alao J, Stavropoulou A, Lam E, et al. Histone deacetylase inhibitor, trichostatin A induces ubiquitin-dependent cyclin D1 degradation in MCF-7 breast cancer cells. Mol Cancer. 2006;5(p):8.
   Google Scholar
• Jang E, Lim S, Lee E, et al. The histone deacetylase inhibitor trichostatin A sensitizes estrogen receptor alpha-negative breast cancer cells to tamoxifen. Oncogene. 2004;23(9):1724–36.
   Google Scholar
• Zheng L,  Ren J, Li H, et al. Downregulation of wild-type p53 protein by HER-2/neu mediated PI3K pathway activation in human breast cancer cells: its effect on cell proliferation and implication for therapy. Cell Res. 2004;14(6):497–506.
   Google Scholar
• Dong C,  Chen Y, Ma J, et al. Econazole nitrate reversed the resistance of breast cancer cells to Adriamycin through inhibiting the PI3K/AKT signaling pathway. Am J Cancer Res. 2020;10(1):263–274.
   Google Scholar
• Palmieri D, Lockman P, Thomas F, et al. Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks. Clinical cancer res. 2009;15(19):6148–57.
   Google Scholar
• Yang N, Zhou T, Lei X, et al. Inhibition of sonic hedgehog signaling pathway by thiazole antibiotic thiostrepton attenuates the CD44+/CD24-stem-like population and sphere-forming capacity in triple-negative breast cancer. Cell Physiol Biochem. 2016;38(3):1157–70.
   Google Scholar
• Kwok J, Myatt S, Marson C, et al. Thiostrepton selectively targets breast cancer cells through inhibition of forkhead box M1 expression. Mol Cancer Ther. 2008;7(7):2022–32.
   Google Scholar
• Xu X, Zhang J, Zhang Z, et al. Systems pharmacology in combination with proteomics reveals underlying mechanisms of Xihuang pill against triple-negative breast cancer. Bioengineered. 2020;11(1):1170–1188. .
   PubMed Web of Science ®Google Scholar
• Ye Q, Han X, Wu Z. Bioinformatics analysis to screen key prognostic genes in the breast cancer tumor microenvironment. Bioengineered. 2020;11(1):1280–1300.
   PubMed Web of Science ®Google Scholar
• Yan S, Xu J, Liu B, et al. Long non-coding RNA BCAR4 aggravated proliferation and migration in esophageal squamous cell carcinoma by negatively regulating p53/p21 signaling pathway. Bioengineered. 2021;12(1):682–696.
   PubMed Web of Science ®Google Scholar