The identification of key genes and pathways in glioblastoma by bioinformatics analysis

References

• Van Meir EG, Hadjipanayis CG, Norden AD, Shu HK, Wen PY, Olson JJ. Exciting new advances in neuro‐oncology: the avenue to a cure for malignant glioma. CA Cancer J Clin. 2010;60(3):166–14. doi:10.3322/caac.20069.
   PubMed Web of Science ®Google Scholar
• Brat DJ, Prayson RA, Ryken TC, Olson JJ. Diagnosis of malignant glioma: role of neuropathology. J Neurooncol. 2008;89(3):287–311. doi:10.1007/s11060-008-9618-1.
   PubMed Web of Science ®Google Scholar
• Gallego O. Nonsurgical treatment of recurrent glioblastoma. Curr Oncol. 2015;22(4):273–281. doi:10.3747/co.22.2436.
   PubMed Web of Science ®Google Scholar
• Griesinger AM, Birks DK, Donson AM, Amani V, Hoffman LM, Waziri A, Wang M, Handler MH, Foreman NK. Characterization of distinct immunophenotypes across pediatric brain tumor types. J Immunol. 2013;191(9):4880–4888. doi:10.4049/jimmunol.1301966.
   PubMed Web of Science ®Google Scholar
• Gusev Y, Bhuvaneshwar K, Song L, Zenklusen J-C, Fine H, Madhavan S. The REMBRANDT study, a large collection of genomic data from brain cancer patients. Sci Data. 2018;5(1):158. doi:10.1038/sdata.2018.158.
   Google Scholar
• Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva N, Pyysalo S, et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51(D1):D638–D646. doi:10.1093/nar/gkac1000.
   PubMed Web of Science ®Google Scholar
• Chaudhary RK, Khanal P, Mateti UV, Shastry CS, Shetty J. Identification of hub genes involved in cisplatin resistance in head and neck cancer. J Genet Eng Biotechnol. 2023;21(1):1–17. doi:10.1186/s43141-023-00468-y.
   PubMed Web of Science ®Google Scholar
• Chin C-H, Chen S-H, Wu H-H, Ho C-W, Ko M-T, Lin C-Y. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(4):S11. doi:10.1186/1752-0509-8-S4-S11.
   PubMedGoogle Scholar
• Freshour SL, Kiwala S, Cotto KC, Coffman AC, McMichael JF, Song JJ, Griffith M, Griffith O, Wagner AH. Integration of the drug–gene interaction database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Res. 2020;49(D1):D1144–D1151. doi:10.1093/nar/gkaa1084.
   Web of Science ®Google Scholar
• Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–W102. doi:10.1093/nar/gkx247.
   PubMed Web of Science ®Google Scholar
• Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma’ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 2013;14(1):1471–2105. doi:10.1186/1471-2105-14-128.
   Google Scholar
• Yang L, Zhang Y-H, Huang F, Li Z, Huang T, Cai Y-D. Identification of protein–protein interaction associated functions based on gene ontology and KEGG pathway. Front Genet. 2022;13:1011659. doi:10.3389/fgene.2022.1011659.
   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. doi:10.1093/nar/28.1.27.
   PubMed Web of Science ®Google Scholar
• Feng Y, Wang Q, Wang T. Drug target protein-protein interaction networks: a systematic perspective. BioMed Res Int. 2017;2017. doi:10.1155/2017/1289259.
   Web of Science ®Google Scholar
• Malumbres M, Barbacid M. Cell cycle, CDKs and cancer: a changing paradigm. Nature reviews cancer. Nat Rev Cancer. 2009;9(3):153–166. doi:10.1038/nrc2602.
   PubMed Web of Science ®Google Scholar
• Zhou Y, Yang L, Zhang X, Chen R, Chen X, Tang W, Zhang M. Identification of potential biomarkers in glioblastoma through bioinformatic analysis and evaluating their prognostic value. BioMed Res Int. 2019;2019:1–13. doi:10.1155/2019/6581576.
   Web of Science ®Google Scholar
• Cayo M, Greenblatt DY, Kunnimalaiyaan M, Chen H. NOTCH1 (Notch homolog 1, translocation-associated (Drosophila)). Atlas Genet Cytogenet Oncol Haematol. 2008.
   Google Scholar
• Gaiano N, Nye JS, Fishell G. Radial glial identity is promoted by Notch1 signaling in the murine forebrain. Neuron. 2000;26(2):395–404. doi:10.1016/S0896-6273(00)81172-1.
   PubMed Web of Science ®Google Scholar
• Bazzoni R, Bentivegna A. Role of Notch signaling pathway in glioblastoma multiforme pathogenesis. Cancers. 2019;11(3):292. doi:10.3390/cancers11030292.
   PubMed Web of Science ®Google Scholar
• Gharaibeh L, Elmadany N, Alwosaibai K, Alshaer W. Notch1 in cancer therapy: possible clinical implications and challenges. Mol Pharmacol. 2020;98(5):559–576. doi:10.1124/molpharm.120.000006.
   PubMed Web of Science ®Google Scholar
• Dang CV. MYC on the path to cancer. cell. Cell. 2012;149(1):22–35. doi:10.1016/j.cell.2012.03.003.
   PubMed Web of Science ®Google Scholar
• Kim J-Y, Cho Y-E, Park J-H. The nucleolar protein GLTSCR2 is an upstream negative regulator of the oncogenic nucleophosmin-MYC axis. Am J Pathol. 2015;185(7):2061–2068. doi:10.1016/j.ajpath.2015.03.016.
   PubMed Web of Science ®Google Scholar
• Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W, Wang R, Green D, Tessarollo L, Casellas R, et al. C-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell. 2012;151(1):68–79. doi:10.1016/j.cell.2012.08.033.
   PubMed Web of Science ®Google Scholar
• Tateishi K, Iafrate AJ, Ho Q, Curry WT, Batchelor TT, Flaherty KT, Onozato ML, Lelic N, Sundaram S, Cahill DP, et al. Myc-driven Glycolysis is a therapeutic target in GlioblastomaTargeting Glycolysis for MYC-Driven glioblastoma. Clin Cancer Res. 2016;22(17):4452–4465. doi:10.1158/1078-0432.CCR-15-2274.
   PubMed Web of Science ®Google Scholar
• Uusküla-Reimand L, Wilson MD. Untangling the roles of TOP2A and TOP2B in transcription and cancer. Sci Adv. 2022;8(44):eadd4920. doi:10.1126/sciadv.add4920.
   PubMed Web of Science ®Google Scholar
• Zhou T, Wang Y, Qian D, Liang Q, Wang B. Over-expression of TOP2A as a prognostic biomarker in patients with glioma. Int J Clin Exp Pathol. 2018;11(3):1228.
   PubMed Web of Science ®Google Scholar
• Gorantla S, Gorantla G, Saha RN, Singhvi G. CD44 receptor-targeted novel drug delivery strategies for rheumatoid arthritis therapy. Expert Opin Drug Deliv. 2021;18(11):1553–1557. doi:10.1080/17425247.2021.1950686.
   PubMed Web of Science ®Google Scholar
• Mooney KL, Choy W, Sidhu S, Pelargos P, Bui TT, Voth B, Barnette N, Yang I. The role of CD44 in glioblastoma multiforme. J Clin Neurosci. 2016;34:1–5. doi:10.1016/j.jocn.2016.05.012.
   PubMed Web of Science ®Google Scholar
• Woods EL, Grigorieva IV, Midgley AC, Brown CVM, Lu Y-A, Phillips AO, Bowen T, Meran S, Steadman R. CD147 mediates the CD44s-dependent differentiation of myofibroblasts driven by transforming growth factor-β1. J Biol Chem. 2021;297(3):100987. doi:10.1016/j.jbc.2021.100987.
   PubMed Web of Science ®Google Scholar
• Charbonneau H, Tonks NK, Walsh KA, Fischer EH. The leukocyte common antigen (CD45): a putative receptor-linked protein tyrosine phosphatase. Proc Natl Acad Sci USA. 1988;85(19):7182–7186. doi:10.1073/pnas.85.19.7182.
   PubMed Web of Science ®Google Scholar
• Holmes N. CD45: all is not yet crystal clear. Immunology. 2006;117(2):145–155. doi:10.1111/j.1365-2567.2005.02265.x.
   PubMed Web of Science ®Google Scholar
• Wei J, Fang D, Zhou W. CCR2 and PTPRC are regulators of tumor microenvironment and potential prognostic biomarkers of lung adenocarcinoma. Ann Transl Med. 2021;9(18):1419–1419. doi:10.21037/atm-21-3301.
   PubMed Web of Science ®Google Scholar
• Navis AC, van den Eijnden M, Schepens JTG, Hooft van Huijsduijnen R, Wesseling P, Hendriks WJAJ. Protein tyrosine phosphatases in glioma biology. Acta Neuropathol. 2010;119(2):157–175. doi:10.1007/s00401-009-0614-0.
   PubMed Web of Science ®Google Scholar
• Poonan P, Agoni C, Ibrahim MA, Soliman ME. Glioma-targeted therapeutics: computer-aided drug design prospective. Protein J. 2021;40:601–655. doi:10.1007/s10930-021-10021.
   PubMed Web of Science ®Google Scholar
• Jia S, Guo B, Wang L, Peng L, Zhang L. The Current status of SSRP1 in cancer: tribulation and road ahead. J Healthc Eng. 2022;2022:1–9. doi:10.1155/2022/3528786.
   Web of Science ®Google Scholar
• Cai L, Qin X, Xu Z, Song Y, Jiang H, Wu Y, Ruan H, Chen J. Comparison of cytotoxicity evaluation of anticancer drugs between real-time cell analysis and CCK-8 method. ACS Omega. 2019;4(7):12036–12042. doi:10.1021/acsomega.9b01142.
   PubMed Web of Science ®Google Scholar
• Liao J, Tao X, Ding Q, Liu J, Yang X, Yuan F-E, Yang J-A, Liu B, Xiang G-A, Chen Q, et al. SSRP1 silencing inhibits the proliferation and malignancy of human glioma cells via the MAPK signaling pathway. Oncol Rep. 2017;38(5):2667–2676. doi:10.3892/or.2017.5982.
   PubMed Web of Science ®Google Scholar
• Bronner SM, Merrick KA, Murray J, Salphati L, Moffat JG, Pang J, Sneeringer CJ, Dompe N, Cyr P, Purkey H, et al. Design of a brain-penetrant CDK4/6 inhibitor for glioblastoma. Bioorg Med Chem Lett. 2019;29(16):2294–2301. doi:10.1016/j.bmcl.2019.06.021.
   PubMed Web of Science ®Google Scholar
• Wang C, Meier UT. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. EMBO J. 2004;23(8):1857–1867. doi:10.1038/sj.emboj.7600181.
   PubMed Web of Science ®Google Scholar
• Knight S, Heiss NS, Vulliamy TJ, Greschner S, Stavrides G, Pai GS, Lestringant G, Varma N, Mason PJ, Dokal I, et al. X-linked dyskeratosis congenita is predominantly caused by missense mutations in the DKC1 gene. Am J Hum Genet. 1999;65(1):50–58. doi:10.1086/302446.
   PubMed Web of Science ®Google Scholar
• Sieron P, Hader C, Hatina J, Engers R, Wlazlinski A, Müller M, Schulz WA. DKC1 overexpression associated with prostate cancer progression. Br J Cancer. 2009;101(8):1410–1416. doi:10.1038/sj.bjc.6605299.
   PubMed Web of Science ®Google Scholar
• Majercikova Z, Dibdiakova K, Gala M, Horvath D, Murin R, Zoldak G, Hatok J. Different approaches for the profiling of cancer pathway-related genes in glioblastoma cells. Int J Mol Sci. 2022;23(18):10883. doi:10.3390/ijms231810883.
   PubMed Web of Science ®Google Scholar
• Kiledjian M, Dreyfuss G. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J. 1992;11(7):2655–2664. doi:10.1002/j.1460-2075.1992.tb05331.x.
   PubMed Web of Science ®Google Scholar
• Pavlyukov MS, Yu H, Bastola S, Minata M, Shender VO, Lee Y, Zhang S, Wang J, Komarova S, Wang J, et al. Apoptotic cell-derived extracellular vesicles promote malignancy of glioblastoma via intercellular transfer of splicing factors. Cancer Cell. 2018;34(1):119–135.e10. doi:10.1016/j.ccell.2018.05.012.
   PubMed Web of Science ®Google Scholar
• Deng J, Chen S, Wang F, Zhao H, Xie Z, Xu Z, Zhang Q, Liang P, Zhai X, Cheng Y, et al. Effects of hnRNP A2/B1 knockdown on inhibition of glioblastoma cell invasion, growth and survival. Mol Neurobiol. 2016;53(2):1132–1144. doi:10.1007/s12035-014-9080-3.
   PubMed Web of Science ®Google Scholar
• Vega F, Medeiros LJ, Bueso-Ramos CE, Arboleda P, Miranda RN. Hematolymphoid neoplasms associated with rearrangements of PDGFRA, PDGFRB, and FGFR1. Am J Clin Pathol. 2015;144(3):377–392. doi:10.1309/AJCPMORR5Z2IKCEM.
   PubMed Web of Science ®Google Scholar
• Peng G, Wang Y, Ge P, Bailey C, Zhang P, Zhang D, Meng Z, Qi C, Chen Q, Chen J, et al. The HIF1α-PDGFD-PDGFRα axis controls glioblastoma growth at normoxia/mild-hypoxia and confers sensitivity to targeted therapy by echinomycin. J Exp Clin Canc Res. 2021;40(1):1–16. doi:10.1186/s13046-021-02082-7.
   PubMed Web of Science ®Google Scholar
• Zhong S, Bai Y, Wu B, Ge J, Jiang S, Li W, Wang X, Ren J, Xu H, Chen Y, et al. Selected by gene co-expression network and molecular docking analyses, ENMD-2076 is highly effective in glioblastoma-bearing rats. Aging. 2019;11(21):9738–9766. doi:10.18632/aging.102422.
   PubMedGoogle Scholar
• Zhong S, Wu B, Dong X, Han Y, Jiang S, Zhang Y, Bai Y, Luo SX, Chen Y, Zhang H, et al. Identification of driver genes and key pathways of glioblastoma shows JNJ-7706621 as a novel antiglioblastoma drug. World Neurosurg. 2018;109:e329–e342. doi:10.1016/j.wneu.2017.09.176.
   PubMed Web of Science ®Google Scholar
• Recasens A, Humphrey SJ, Ellis M, Hoque M, Abbassi RH, Chen B, Longworth M, Needham EJ, James DE, Johns TG, et al. Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells. cell death discovery. Cell Death Discovery. 2021;7(1):81. doi:10.1038/s41420-021-00456-6.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Xia Q, Lin J. Identification of the potential oncogenes in glioblastoma based on bioinformatic analysis and elucidation of the underlying mechanisms. Oncol Rep. 2018;40(2):715–725. doi:10.3892/or.2018.6483.
   PubMed Web of Science ®Google Scholar
• Cui K, Chen J-H, Zou Y-F, Zhang S-Y, Wu B, Jing K, Li L-W, Xia L, Sun C, Dong Y-L, et al. Hub biomarkers for the diagnosis and treatment of glioblastoma based on microarray technology. Technol Cancer Res Treat. 2021;20:1533033821990368. doi:10.1177/1533033821990368.
   Google Scholar