Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma

References

• Fabian ID, Abdallah E, Abdullahi SU, et al. Global Retinoblastoma Study G. Global retinoblastoma presentation and analysis by national income level. JAMA Oncol. 2020;6:685–695.
   PubMed Web of Science ®Google Scholar
• Chawla B, Hasan F, Azad R, et al. Clinical presentation and survival of retinoblastoma in Indian children. Br J Ophthalmol. 2016;100(2):172–178.
   PubMed Web of Science ®Google Scholar
• Munier FL, Beck-Popovic M, Chantada GL, et al. Conservative management of retinoblastoma: challenging orthodoxy without compromising the state of metastatic grace. “Alive, with good vision and no comorbidity”. Prog Retin Eye Res. 2019;73:100764.
   PubMed Web of Science ®Google Scholar
• Lin FY, Chintagumpala MM. Neonatal retinoblastoma. Clin Perinatol. 2021;48(1):53–70.
   PubMed Web of Science ®Google Scholar
• Stransky B, Barrera J, Ohno-Machado L, et al. Modeling cancer: integration of “omics” information in dynamic systems. J Bioinform Comput Biol. 2007;5(4):977–986.
   PubMedGoogle Scholar
• Tao Z, Shi A, Li R, et al. Microarray bioinformatics in cancer- a review. J BUON. 2017;22:838–843.
   PubMed Web of Science ®Google Scholar
• Wu C, Shang XQ, You ZP, et al. TRIM59 promotes retinoblastoma progression by activating the p38-MAPK signaling pathway. Invest Ophthalmol Vis Sci. 2020;61(10):2.
   PubMed Web of Science ®Google Scholar
• Xu Y, Fu Z, Gao X, et al. Long non-coding RNA XIST promotes retinoblastoma cell proliferation, migration, and invasion by modulating microRNA-191-5p/brain derived neurotrophic factor. Bioengineered. 2021;12(1):1587–1598.
   PubMed Web of Science ®Google Scholar
• Guo L, Bai Y, Ni T, et al. MicroRNA1533p suppresses retinoblastoma cell growth and invasion via targeting the IGF1R/Raf/MEK and IGF1R/PI3K/AKT signaling pathways. Int J Oncol. 2021;59(1). DOI:10.3892/ijo.2021.5227.
   Web of Science ®Google Scholar
• Zeng Q, Wang S, Tan J, et al. The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study. PeerJ. 2021;9:e10830.
   PubMed Web of Science ®Google Scholar
• Sun Z, Zhang A, Hou M, et al. Circular RNA hsa_circ_0000034 promotes the progression of retinoblastoma via sponging microRNA-361-3p. Bioengineered. 2020;11(1):949–957.
   PubMed Web of Science ®Google Scholar
• Martinez-Sanchez M, Hernandez-Monge J, Rangel M, et al. Retinoblastoma: from discovery to clinical management. FEBS J. 2021. DOI:10.1111/febs.16035
   PubMed Web of Science ®Google Scholar
• Nalini V, Segu R, Deepa PR, et al. Molecular insights on post-chemotherapy retinoblastoma by microarray gene expression analysis. Bioinform Biol Insights. 2013;7:289–306.
   PubMedGoogle Scholar
• Hudson LE, Mendoza P, Hudson WH, et al. Distinct gene expression profiles define anaplastic grade in retinoblastoma. Am J Pathol. 2018;188(10):2328–2338.
   PubMed Web of Science ®Google Scholar
• Danda R, Ganapathy K, Sathe G, et al. Membrane proteome of invasive retinoblastoma: differential proteins and biomarkers. Proteomics Clin Appl. 2018;12(5):e1700101.
   PubMed Web of Science ®Google Scholar
• Liberzon A, Birger C, Thorvaldsdottir H, et al. The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425.
   PubMed Web of Science ®Google Scholar
• Goldman MJ, Craft B, Hastie M, et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol. 2020;38(6):675–678.
   PubMed Web of Science ®Google Scholar
• Gautier L, Cope L, Bolstad BM, et al. affy–analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20(3):307–315.
   PubMed Web of Science ®Google Scholar
• Leek JT, Johnson WE, Parker HS, et al. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28(6):882–883.
   PubMed Web of Science ®Google Scholar
• Ligges U, Mächler M. scatterplot3d- an R package for visualizing multivariate data. J Stat Softw. 2003;8(11):1–20.
   Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
   PubMed Web of Science ®Google Scholar
• Khomtchouk BB, Van Booven DJ, Wahlestedt C. HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. Source Code Biol Med. 2014;9(1):30.
   PubMedGoogle 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
• Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Walter W, Sanchez-Cabo F, Ricote M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics. 2015;31(17):2912–2914.
   PubMed Web of Science ®Google Scholar
• Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14(1):7.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D13.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003;4(1):2.
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, et al. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11.
   PubMed Web of Science ®Google Scholar
• Reinhold WC, Sunshine M, Liu H, et al. CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Res. 2012;72(14):3499–3511.
   PubMed Web of Science ®Google Scholar
• Li JH, Liu S, Zhou H, et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(D1):D92–7.
   PubMed Web of Science ®Google Scholar
• Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48(D1):D127–D31.
   PubMed Web of Science ®Google Scholar
• Dweep H, Gretz N. miRWalk2.0: a comprehensive atlas of microRNA-target interactions. Nat Methods. 2015;12(8):697.
   PubMed Web of Science ®Google Scholar
• Keenan AB, Torre D, Lachmann A, et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 2019;47(W1):W212–W24.
   PubMed Web of Science ®Google Scholar
• Hu H, Miao YR, Jia LH, et al. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic Acids Res. 2019;47(D1):D33–D8.
   PubMed Web of Science ®Google Scholar
• Newman AM, Steen CB, Liu CL, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37(7):773–782.
   PubMed Web of Science ®Google Scholar
• Tang Z, Li C, Kang B, et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–W102.
   PubMed Web of Science ®Google Scholar
• Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6(269):l1.
   Web of Science ®Google Scholar
• You ZP, Zhang YL, Shi K, et al. Suppression of diabetic retinopathy with GLUT1 siRNA. Sci Rep. 2017;7(1):7437.
   PubMedGoogle Scholar
• Thorsson V, Gibbs DL, Brown SD, et al. The immune landscape of cancer. Immunity. 2018;48:812–30 e14.
   PubMed Web of Science ®Google Scholar
• Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell. 2011;146(3):353–358.
   PubMed Web of Science ®Google Scholar
• Dimaras H, Kimani K, Dimba EA, et al. Retinoblastoma. Lancet. 2012;379(9824):1436–1446.
   PubMed Web of Science ®Google Scholar
• Gunduz K, Muftuoglu O, Gunalp I, et al. Metastatic retinoblastoma clinical features, treatment, and prognosis. Ophthalmology. 2006;113(9):1558–1566.
   PubMed Web of Science ®Google Scholar
• de Carvalho IN, de Freitas RM, Vargas FR. Translating microRNAs into biomarkers: what is new for pediatric cancer? Med Oncol. 2016;33(5):49.
   PubMed Web of Science ®Google Scholar
• Golabchi K, Soleimani-Jelodar R, Aghadoost N, et al. MicroRNAs in retinoblastoma: potential diagnostic and therapeutic biomarkers. J Cell Physiol. 2018;233(4):3016–3023.
   PubMed Web of Science ®Google Scholar
• Marshall AE, Roes MV, Passos DT, et al. RB1 deletion in retinoblastoma protein pathway-disrupted cells results in DNA damage and cancer progression. Mol Cell Biol. 2019;39(16). DOI:10.1128/MCB.00105-19.
   Web of Science ®Google Scholar
• Manning AL, Dyson NJ. RB: mitotic implications of a tumour suppressor. Nat Rev Cancer. 2012;12(3):220–226.
   PubMed Web of Science ®Google Scholar
• Sikkema WK, Strikwerda A, Sharma M, et al. Regulation of mitotic cytoskeleton dynamics and cytokinesis by integrin-linked kinase in retinoblastoma cells. PLoS One. 2014;9(6):e98838.
   PubMed Web of Science ®Google Scholar
• Rodriguez CO Jr., Stellrecht CM, Gandhi V. Mechanisms for T-cell selective cytotoxicity of arabinosylguanine. Blood. 2003;102(5):1842–1848.
   PubMed Web of Science ®Google Scholar
• Hoyt MA, Totis L, Roberts BT. S. cerevisiae genes required for cell cycle arrest in response to loss of microtubule function. Cell. 1991;66(3):507–517.
   PubMed Web of Science ®Google Scholar
• Kim T, Gartner A. Bub1 kinase in the regulation of mitosis. Anim Cells Syst (Seoul). 2021;25(1):1–10.
   PubMed Web of Science ®Google Scholar
• Fujibayashi Y, Isa R, Nishiyama D, et al. Aberrant BUB1 overexpression promotes mitotic segregation errors and chromosomal instability in multiple Myeloma. Cancers (Basel). 2020;12(8):2206.
   PubMed Web of Science ®Google Scholar
• Nie C, Ma H, Gao Y, et al. RNA sequencing and bioinformatic analysis on retinoblastoma revealing that cell cycle deregulation is a key process in retinoblastoma tumorigenesis. Ophthalmologica. 2021;244:51–59.
   PubMed Web of Science ®Google Scholar
• Huang Z, Wang S, Wei H, et al. Inhibition of BUB1 suppresses tumorigenesis of osteosarcoma via blocking of PI3K/Akt and ERK pathways. J Cell Mol Med. 2021. DOI:10.1111/jcmm.16805.
   Web of Science ®Google Scholar
• Roskoski R Jr. Cyclin-dependent protein serine/threonine kinase inhibitors as anticancer drugs. Pharmacol Res. 2019;139:471–488.
   PubMed Web of Science ®Google Scholar
• Nishida T, Matsushima T, Tsujimoto M, et al. Cyclin-dependent kinase activity correlates with the prognosis of patients who have gastrointestinal stromal tumors. Ann Surg Oncol. 2015;22(11):3565–3573.
   PubMed Web of Science ®Google Scholar
• Selvan LDN, Danda R, Madugundu AK, et al. Phosphoproteomics of retinoblastoma: a pilot study identifies aberrant kinases. Molecules. 2018;23(6):1454.
   PubMed Web of Science ®Google Scholar
• Voce DJ, Bernal GM, Cahill KE, et al. CDK1 is up-regulated by temozolomide in an NF-kappaB dependent manner in glioblastoma. Sci Rep. 2021;11(1):5665.
   PubMed Web of Science ®Google Scholar
• Lai F, Godley LA, Joslin J, et al. Transcript map and comparative analysis of the 1.5-Mb commonly deleted segment of human 5q31 in malignant myeloid diseases with a del(5q). Genomics. 2001;71(2):235–245.
   PubMed Web of Science ®Google Scholar
• Ren X, Chen X, Ji Y, et al. Upregulation of KIF20A promotes tumor proliferation and invasion in renal clear cell carcinoma and is associated with adverse clinical outcome. Aging (Albany NY). 2020;12(24):25878–25894.
   PubMedGoogle Scholar
• Zhang Q, Di J, Ji Z, et al. KIF20A predicts poor survival of patients and promotes colorectal cancer tumor progression through the JAK/STAT3 signaling pathway. Dis Markers. 2020;2020:2032679.
   PubMed Web of Science ®Google Scholar
• Gaudet S, Branton D, Lue RA. Characterization of PDZ-binding kinase, a mitotic kinase. Proc Natl Acad Sci U S A. 2000;97(10):5167–5172.
   PubMed Web of Science ®Google Scholar
• Yu WN, Lin HF, Lee YI, et al. PBK expression is associated with prognosis of patients with oral squamous cell carcinoma treated with radiotherapy: a retrospective study. Anticancer Res. 2021;41:2177–2182.
   PubMed Web of Science ®Google Scholar
• Ma H, Han F, Yan X, et al. PBK promotes aggressive phenotypes of cervical cancer through ERK/c-Myc signaling pathway. J Cell Physiol. 2021;236(4):2767–2781.
   PubMed Web of Science ®Google Scholar
• Kufer TA, Sillje HH, Korner R, et al. Human TPX2 is required for targeting Aurora-A kinase to the spindle. J Cell Biol. 2002;158(4):617–623.
   PubMed Web of Science ®Google Scholar
• Matson DR, Denu RA, Zasadil LM, et al. High nuclear TPX2 expression correlates with TP53 mutation and poor clinical behavior in a large breast cancer cohort, but is not an independent predictor of chromosomal instability. BMC Cancer. 2021;21(1):186.
   PubMed Web of Science ®Google Scholar
• Huang DH, Jian J, Li S, et al. TPX2 silencing exerts antitumor effects on hepatocellular carcinoma by regulating the PI3K/AKT signaling pathway. Int J Mol Med. 2019;44:2113–2122.
   PubMed Web of Science ®Google Scholar
• Rao CV, Yamada HY, Yao Y, et al. Enhanced genomic instabilities caused by deregulated microtubule dynamics and chromosome segregation: a perspective from genetic studies in mice. Carcinogenesis. 2009;30(9):1469–1474.
   PubMed Web of Science ®Google Scholar
• Hao X, Qu T. Expression of CENPE and its prognostic role in non-small cell lung cancer. Open Med (Wars). 2019;14(1):497–502.
   PubMedGoogle Scholar
• Anderson NM, Simon MC. The tumor microenvironment. Curr Biol. 2020;30(16):R921–R5.
   PubMed Web of Science ®Google Scholar
• Junttila MR, de Sauvage FJ. Influence of tumour micro-environment heterogeneity on therapeutic response. Nature. 2013;501(7467):346–354.
   PubMed Web of Science ®Google Scholar
• Friedmann-Morvinski D, Verma IM. Dedifferentiation and reprogramming: origins of cancer stem cells. EMBO Rep. 2014;15(3):244–253.
   PubMed Web of Science ®Google Scholar
• Miranda A, Hamilton PT, Zhang AW, et al. Cancer stemness, intratumoral heterogeneity, and immune response across cancers. Proc Natl Acad Sci U S A. 2019;116(18):9020–9029.
   PubMed Web of Science ®Google Scholar
• Jimenez-Avila CE, Villegas-Ruiz V, Zapata-Tarres M, et al. Centromere-associated protein E expresses a novel mRNA isoform in acute lymphoblastic leukemia. Int J Mol Epidemiol Genet. 2018;9:43–54.
   PubMed Web of Science ®Google Scholar