Development and Validation of a Prognostic Model of RNA-Binding Proteins in Colon Adenocarcinoma: A Study Based on TCGA and GEO Databases

References

• Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68:394–424. doi:10.3322/caac.2149230207593
   PubMed Web of Science ®Google Scholar
• Sugarbaker PH. Improving oncologic outcomes for colorectal cancer at high risk for local-regional recurrence with novel surgical techniques. Expert Rev Gastroenterol Hepatol. 2016;10:205–213. doi:10.1586/17474124.2016.111001926643935
   PubMed Web of Science ®Google Scholar
• Symeonidis D, Christodoulidis G, Koukoulis G, Spyridakis M, Tepetes K. Colorectal cancer surgery in the elderly: limitations and drawbacks. Tech Coloproctol. 2011;15 Suppl 1:S47–S50. doi:10.1007/s10151-011-0751-z21887559
   PubMed Web of Science ®Google Scholar
• Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins, nature reviews. Genetics. 2014;15:829–845. doi:10.1038/nrg381325365966
   PubMed Web of Science ®Google Scholar
• Brinegar AE, Cooper TA. Roles for RNA-binding proteins in development and disease. Brain Res. 2016;1647:1–8. doi:10.1016/j.brainres.2016.02.05026972534
   PubMed Web of Science ®Google Scholar
• Protter DSW, Parker R. Principles and properties of stress granules. Trends Cell Biol. 2016;26(9):668–679. doi:10.1586/17474124.2016.111001927289443
   PubMed Web of Science ®Google Scholar
• de Bruin RG, Rabelink TJ, van Zonneveld AJ, van der Veer EP. Emerging roles for RNA-binding proteins as effectors and regulators of cardiovascular disease. Eur Heart J. 2017;38:1380–1388. doi:10.1093/eurheartj/ehw56728064149
   PubMed Web of Science ®Google Scholar
• Pereira B, Billaud M, Almeida R. RNA-binding proteins in cancer: old players and new actors. Trends Cancer. 2017;3:506–528. doi:10.1016/j.trecan.2017.05.00328718405
   PubMed Web of Science ®Google Scholar
• Chatterji P, Rustgi AK. RNA binding proteins in intestinal epithelial biology and colorectal cancer. Trends Mol Med. 2018;24:490–506. doi:10.1016/j.molmed.2018.03.00829627433
   PubMed Web of Science ®Google Scholar
• Xie M, Ma T, Xue J, et al. The long intergenic non-protein coding RNA 707 promotes proliferation and metastasis of gastric cancer by interacting with mRNA stabilizing protein HuR. Cancer Lett. 2019;443:67–79. doi:10.1016/j.canlet.2018.11.03230502359
   PubMed Web of Science ®Google Scholar
• Zhang H, Wang Y, Dou J, et al. Acetylation of AGO2 promotes cancer progression by increasing oncogenic miR-19b biogenesis. Oncogene. 2019;38:1410–1431. doi:10.1038/s41388-018-0530-730305728
   PubMed Web of Science ®Google Scholar
• Zong F-Y, Fu X, Wei W-J, et al. The RNA-binding protein QKI suppresses cancer-associated aberrant splicing. PLoS Genet. 2014;10:e1004289. doi:10.1371/journal.pgen.100428924722255
   PubMed Web of Science ®Google Scholar
• Jeong HM, Han J, Lee SH, et al. Correction: ESRP1 is overexpressed in ovarian cancer and promotes switching from mesenchymal to epithelial phenotype in ovarian cancer cells. Oncogenesis. 2019;8:47. doi:10.1038/s41389-019-0155-x31467265
   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;25:25–29. doi:10.1038/7555610802651
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44:D457–D462. doi:10.1093/nar/gkv107026476454
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45:D362–D368. doi:10.1093/nar/gkw93727924014
   PubMed Web of Science ®Google Scholar
• Bader GD, Hogue CWV. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 2003;4:2. doi:10.1186/1471-2105-4-2
   PubMed Web of Science ®Google Scholar
• Chen H-Y, Yu S-L, Chen C-H, et al. A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med. 2007;356:11–20. doi:10.1056/NEJMoa06009617202451
   PubMed Web of Science ®Google Scholar
• Wu M, Li X, Zhang T, Liu Z, Zhao Y. Identification of a nine-gene signature and establishment of a prognostic nomogram predicting overall survival of pancreatic cancer. Front Oncol. 2019;9:996. doi:10.3389/fonc.2019.0099631612115
   PubMed Web of Science ®Google Scholar
• Heagerty PJ, Lumley T, Pepe MS. Time-dependent ROC curves for censored survival data and a diagnostic marker. Biometrics. 2000;56:337–344. doi:10.1111/j.0006-341X.2000.00337.x10877287
   PubMed Web of Science ®Google Scholar
• Thul PJ, Åkesson L, Wiking M, et al. A subcellular map of the human proteome. Science. 2017;356:eaal3321. doi:10.1126/science.aal332128495876
   PubMed Web of Science ®Google Scholar
• Wu Y, Chen H, Chen Y, et al. HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif. Aging (Albany NY). 2019;11:2430–2446. doi:10.18632/aging.10192731039132
   PubMedGoogle Scholar
• Li Y, Sahni N, Pancsa R, et al. Revealing the determinants of widespread alternative splicing perturbation in cancer. Cell Rep. 2017;21:798–812. doi:10.1016/j.celrep.2017.09.07129045845
   PubMed Web of Science ®Google Scholar
• Li S, Hu Z, Zhao Y, Huang S, He X. Transcriptome-wide analysis reveals the landscape of aberrant alternative splicing events in liver cancer. Hepatology (Baltimore, Md). 2019;69:359–375. doi:10.1002/hep.30158
   PubMed Web of Science ®Google Scholar
• Li Y, McGrail DJ, Xu J, et al. MERIT: systematic analysis and characterization of mutational effect on RNA interactome topology. Hepatology (Baltimore, Md). 2019;70:532–546. doi:10.1002/hep.30242
   PubMed Web of Science ®Google Scholar
• Lan Y, Xiao X, He Z, et al. Long noncoding RNA OCC-1 suppresses cell growth through destabilizing HuR protein in colorectal cancer. Nucleic Acids Res. 2018;46:5809–5821. doi:10.1093/nar/gky21429931370
   PubMed Web of Science ®Google Scholar
• Li K, Huang F, Li Y, et al. Stabilization of oncogenic transcripts by the IGF2BP3/ELAVL1 complex promotes tumorigenicity in colorectal cancer. Am J Cancer Res. 2020;10:2480–2494.32905413
   PubMed Web of Science ®Google Scholar
• Gao C, Han C, Yu Q, et al. Downregulation of Msi1 suppresses the growth of human colon cancer by targeting p21cip1. Int J Oncol. 2015;46:732–740. doi:10.3892/ijo.2014.274925394506
   PubMed Web of Science ®Google Scholar
• Goudarzi KM, Lindström MS. Role of ribosomal protein mutations in tumor development (review). Int J Oncol. 2016;48:1313–1324. doi:10.3892/ijo.2016.338726892688
   PubMed Web of Science ®Google Scholar
• Stålberg P, Grimfjärd P, Santesson M, et al. Transfection of the multiple endocrine neoplasia type 1 gene to a human endocrine pancreatic tumor cell line inhibits cell growth and affects expression of JunD, delta-like protein 1/preadipocyte factor-1, proliferating cell nuclear antigen, and QM/Jif-1. J Clin Endocrinol Metab. 2004;89:2326–2337. doi:10.1210/jc.2003-03122815126560
   PubMed Web of Science ®Google Scholar
• Altinok G, Powell IJ, Che M, et al. Reduction of QM protein expression correlates with tumor grade in prostatic adenocarcinoma. Prostate Cancer Prostatic Dis. 2006;9:77–82. doi:10.1038/sj.pcan.450084816331298
   PubMed Web of Science ®Google Scholar
• Rohozinski J, Anderson ML, Broaddus RE, Edwards CL, Bishop CE. Spermatogenesis associated retrogenes are expressed in the human ovary and ovarian cancers. PLoS One. 2009;4:e5064. doi:10.1371/journal.pone.000506419333399
   PubMed Web of Science ®Google Scholar
• Choucair N, Rajab M, Mégarbané A, Chouery E. Homozygous microdeletion of the ERI1 and MFHAS1 genes in a patient with intellectual disability, limb abnormalities, and cardiac malformation. Am J Med Genet. 2017;173:1955–1960. doi:10.1002/ajmg.a.3827128488351
   PubMed Web of Science ®Google Scholar
• Williams CS, Zhang B, Smith JJ, et al. BVES regulates EMT in human corneal and colon cancer cells and is silenced via promoter methylation in human colorectal carcinoma. J Clin Invest. 2011;121:4056–4069. doi:10.1172/JCI4422821911938
   PubMed Web of Science ®Google Scholar
• Ding Y, Xi Y, Chen T, et al. Caprin-2 enhances canonical Wnt signaling through regulating LRP5/6 phosphorylation. J Cell Biol. 2008;182:865–872. doi:10.1083/jcb.20080314718762581
   PubMed Web of Science ®Google Scholar
• Jia D, Dong R, Jing Y, et al. Exome sequencing of hepatoblastoma reveals novel mutations and cancer genes in the Wnt pathway and ubiquitin ligase complex. Hepatology (Baltimore, Md). 2014;60:1686–1696. doi:10.1002/hep.27243
   PubMed Web of Science ®Google Scholar
• Ai Y, Wu S, Zou C, Wei H. LINC00941 promotes oral squamous cell carcinoma progression via activating CAPRIN2 and canonical WNT/β-catenin signaling pathway. J Cell Mol Med. 2020;24:10512–10524. doi:10.1111/jcmm.1566732691935
   PubMed Web of Science ®Google Scholar
• Tan Y-Q, Tu C, Meng L, et al. Loss-of-function mutations in TDRD7 lead to a rare novel syndrome combining congenital cataract and nonobstructive azoospermia in humans. Genet Med. 2019;21:1209–1217. doi:10.1038/gim.2017.13031048812
   PubMed Web of Science ®Google Scholar
• Bracken CP, Wall SJ, Barré B, Panov KI, Ajuh PM, Perkins ND. Regulation of cyclin D1 RNA stability by SNIP1. Cancer Res. 2008;68:7621–7628. doi:10.1158/0008-5472.CAN-08-121718794151
   PubMed Web of Science ®Google Scholar
• Chen Y, Zhang W, Yan L, Zheng P, Li J. miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells. PeerJ. 2020;8:e10148. doi:10.7717/peerj.1014833150075
   PubMed Web of Science ®Google Scholar
• Jeon H-S, Choi YY, Fukuoka J, et al. High expression of SNIP1 correlates with poor prognosis in non-small cell lung cancer and SNIP1 interferes with the recruitment of HDAC1 to RB in vitro. Lung Cancer. 2013;82:24–30. doi:10.1016/j.lungcan.2013.07.01523932364
   PubMed Web of Science ®Google Scholar
• Xie Y, Deng H, Wei R, et al. Overexpression of miR-335 inhibits the migration and invasion of osteosarcoma by targeting SNIP1. Int J Biol Macromol. 2019;133:137–147. doi:10.1016/j.ijbiomac.2019.04.01630954590
   PubMed Web of Science ®Google Scholar
• Liang X, Zheng M, Jiang J, Zhu G, Yang J, Tang Y. Hypoxia-inducible factor-1 alpha, in association with TWIST2 and SNIP1, is a critical prognostic factor in patients with tongue squamous cell carcinoma. Oral Oncol. 2011;47:92–97. doi:10.1016/j.oraloncology.2010.11.01421167768
   PubMed Web of Science ®Google Scholar
• Lin J, Chen Y, Tang W-F, et al. rs3856806 C>T polymorphism increased the risk of colorectal cancer: a case-control study in eastern Chinese Han population. Front Oncol. 2019;9:63. doi:10.3389/fonc.2019.0006330838172
   PubMed Web of Science ®Google Scholar
• Vellinga TT, Borovski T, de Boer VCJ, et al. SIRT1/PGC1α-dependent increase in oxidative phosphorylation supports chemotherapy resistance of colon cancer. Clin Cancer Res. 2015;21:2870–2879. doi:10.1158/1078-0432.CCR-14-229025779952
   PubMed Web of Science ®Google Scholar
• Mootha VK, Lindgren CM, Eriksson K-F, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267–273. doi:10.1038/ng118012808457
   PubMed Web of Science ®Google Scholar