Screening of Potential Key Biomarkers for Ewing Sarcoma: Evidence from Gene Array Analysis

References

• Esiashvili N, Goodman M, Marcus RB Jr. Changes in incidence and survival of Ewing sarcoma patients over the past 3 decades: surveillance epidemiology and end results data. J Pediatr Hematol Oncol. 2008;30(6):425–430. PMID: 18525458. doi:10.1097/MPH.0b013e31816e22f3
   PubMed Web of Science ®Google Scholar
• Ward E, DeSantis C, Robbins A, Kohler B, Jemal A. Childhood and adolescent cancer statistics, 2014. CA Cancer J Clin. 2014;64(2):83–103. PMID: 24488779. doi:10.3322/caac.21219
   PubMed Web of Science ®Google Scholar
• Biermann JS, Chow W, Reed DR, et al. NCCN guidelines insights: bone cancer, version 2.2017. J Natl Compr Canc Netw. 2017;15(2):155–167. PMID: 28188186. doi:10.6004/jnccn.2017.0017
   PubMed Web of Science ®Google Scholar
• Mirabello L, Troisi RJ, Savage SA. Osteosarcoma incidence and survival rates from 1973 to 2004: data from the surveillance, epidemiology, and end results program. Cancer. 2009;115(7):1531–1543. PMID: 19197972; PMCID: PMCPMC2813207. doi:10.1002/cncr.24121
   PubMed Web of Science ®Google Scholar
• Delattre O, Zucman J, Melot T, et al. The Ewing family of tumors–a subgroup of small-round-cell tumors defined by specific chimeric transcripts. N Engl J Med. 1994;331(5):294–299. PMID: 8022439. doi:10.1056/nejm199408043310503
   PubMed Web of Science ®Google Scholar
• Jaffe R, Santamaria M, Yunis EJ, et al. The neuroectodermal tumor of bone. Am J Surg Pathol. 1984;8(12):885–898. PMID: 6083729. doi:10.1097/00000478-198412000-00001
   PubMed Web of Science ®Google Scholar
• Carlei F, Polak JM, Ceccamea A, et al. Neuronal and glial markers in tumours of neuroblastic origin. Virchows Arch a Pathol Anat Histopathol. 1984;404(3):313–324. PMID: 6149650. doi:10.1007/bf00694896
   PubMedGoogle Scholar
• Hashimoto H, Enjoji M, Nakajima T, Kiryu H, Daimaru Y. Malignant neuroepithelioma (peripheral neuroblastoma). A clinicopathologic study of 15 cases. Am J Surg Pathol. 1983;7(4):309–318. PMID: 6869663. doi:10.1097/00000478-198306000-00002
   PubMed Web of Science ®Google Scholar
• Bellan DG, Filho RJ, Garcia JG, et al. Ewing’s sarcoma: epidemiology and prognosis for patients treated at the pediatric oncology institute, iop-graacc-unifesP. Rev Bras Ortop. 2012;47(4):446–450. PMID: 27047848; PMCID: PMCPMC4799471. doi:10.1016/s2255-4971(15)30126-9
   PubMedGoogle Scholar
• Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: mining tens of millions of expression profiles–database and tools update. Nucleic Acids Res. 2007;35:D760–D765. PMID: 17099226; PMCID: PMCPMC1669752. doi:10.1093/nar/gkl887
   PubMed Web of Science ®Google Scholar
• Svoboda LK, Harris A, Bailey NJ, et al. Overexpression of HOX genes is prevalent in Ewing sarcoma and is associated with altered epigenetic regulation of developmental transcription programs. Epigenetics. 2014;9(12):1613–1625. PMID: 25625846; PMCID: PMCPMC4622732. doi:10.4161/15592294.2014.988048
   PubMed Web of Science ®Google Scholar
• Specht K, Sung YS, Zhang L, Richter GH, Fletcher CD, Antonescu CR. Distinct transcriptional signature and immunoprofile of CIC-DUX4 fusion-positive round cell tumors compared to EWSR1-rearranged Ewing sarcomas: further evidence toward distinct pathologic entities. Genes Chromosom Cancer. 2014;53(7):622–633. PMID: 24723486; PMCID: PMCPMC4108073. doi:10.1002/gcc.22172
   PubMed Web of Science ®Google Scholar
• Agelopoulos K, Richter GH, Schmidt E, et al. Deep sequencing in conjunction with expression and functional analyses reveals activation of FGFR1 in Ewing sarcoma. Clin Cancer Res. 2015;21(21):4935–4946. PMID: 26179511. doi:10.1158/1078-0432.Ccr-14-2744
   PubMed Web of Science ®Google Scholar
• Savola S, Klami A, Myllykangas S, et al. High expression of complement component 5 (C5) at tumor site associates with superior survival in Ewing’s sarcoma family of tumour patients. ISRN Oncol. 2011;2011:168712. PMID: 22084725; PMCID: PMCPMC3196920. doi:10.5402/2011/168712
   PubMedGoogle Scholar
• Skov V, Glintborg D, Knudsen S, et al. Reduced expression of nuclear-encoded genes involved in mitochondrial oxidative metabolism in skeletal muscle of insulin-resistant women with polycystic ovary syndrome. Diabetes. 2007;56(9):2349–2355. PMID: 17563058. doi:10.2337/db07-0275
   PubMed Web of Science ®Google Scholar
• Roth RB, Hevezi P, Lee J, et al. Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics. 2006;7(2):67–80. PMID: 16572319. doi:10.1007/s10048-006-0032-6
   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. PMID: 17784955; PMCID: PMCPMC2375021. doi:10.1186/gb-2007-8-9-r183
   PubMed Web of Science ®Google Scholar
• Kanehisa M. The KEGG database. Novartis Found Symp. 2002;247:91–101; discussion −3, 19–28, 244–52. PMID: 12539951.
   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. PMID: 10802651; PMCID: PMCPMC3037419. doi:10.1038/75556
   PubMed Web of Science ®Google Scholar
• Franceschini A, Szklarczyk D, Frankild S, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41:D808–D815. PMID: 23203871; PMCID: PMCPMC3531103. doi:10.1093/nar/gks1094
   PubMed Web of Science ®Google Scholar
• Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432. PMID: 21149340; PMCID: PMCPMC3031041. doi:10.1093/bioinformatics/btq675
   PubMed Web of Science ®Google Scholar
• Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 2003;4:2. PMID: 12525261; PMCID: PMCPMC149346. doi:10.1186/1471-2105-4-2
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl4):S11. PMID: 25521941; PMCID: PMCPMC4290687. doi:10.1186/1752-0509-8-s4-s11
   PubMed Web of Science ®Google Scholar
• Rhodes DR, Yu J, Shanker K, et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004;6(1):1–6. PMID: 15068665; PMCID: PMCPMC1635162. doi:10.1016/s1476-5586(04)80047-2
   PubMed Web of Science ®Google Scholar
• Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005;21(16):3448–3449. PMID: 15972284. doi:10.1093/bioinformatics/bti551
   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. PMID: 32444850; PMCID: PMCPMC7386072. doi:10.1038/s41587-020-0546-8
   PubMed Web of Science ®Google Scholar
• Li T, Fu J, Zeng Z, et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 2020;48(W1):W509–w14. PMID: 32442275; PMCID: PMCPMC7319575. doi:10.1093/nar/gkaa407
   PubMed Web of Science ®Google Scholar
• Li T, Fan J, Wang B, et al. TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells. Cancer Res. 2017;77(21):e108–e10. PMID: 29092952; PMCID: PMCPMC6042652. doi:10.1158/0008-5472.Can-17-0307
   PubMed Web of Science ®Google Scholar
• Li B, Severson E, Pignon JC, et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol. 2016;17(1):174. PMID: 27549193; PMCID: PMCPMC4993001. doi:10.1186/s13059-016-1028-7
   PubMed Web of Science ®Google Scholar
• Anaya J. OncoLnc: linking TCGA survival data to mRNAs, miRNAs, and lncRNAs. PeerJ Comput Sci. 2016;2:e67. doi:10.7717/peerj-cs.67
   Web of Science ®Google Scholar
• Brohl AS, Solomon DA, Chang W, et al. The genomic landscape of the Ewing sarcoma family of tumors reveals recurrent STAG2 mutation. PLoS Genet. 2014;10(7):e1004475. PMID: 25010205; PMCID: PMCPMC4091782. doi:10.1371/journal.pgen.1004475
   PubMed Web of Science ®Google Scholar
• Crompton BD, Stewart C, Taylor-Weiner A, et al. The genomic landscape of pediatric Ewing sarcoma. Cancer Discov. 2014;4(11):1326–1341. PMID: 25186949. doi:10.1158/2159-8290.Cd-13-1037
   PubMed Web of Science ®Google Scholar
• Tirode F, Surdez D, Ma X, et al. Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations. Cancer Discov. 2014;4(11):1342–1353. PMID: 25223734; PMCID: PMCPMC4264969. doi:10.1158/2159-8290.Cd-14-0622
   PubMed Web of Science ®Google Scholar
• Rizk VT, Walko CM, Brohl AS. Precision medicine approaches for the management of Ewing sarcoma: current perspectives. Pharmgenomics Pers Med. 2019;12:9–14. PMID: 30697061; PMCID: PMCPMC6340366. doi:10.2147/pgpm.S170612
   PubMed Web of Science ®Google Scholar
• Wang Y, Cheng J, Xu C, et al. Quantitative methylation analysis reveals gender and age differences in p16INK4a hypermethylation in hepatitis B virus-related hepatocellular carcinoma. Liver Int. 2012;32(3):420–428. PMID: 22192146. doi:10.1111/j.1478-3231.2011.02696.x
   PubMed Web of Science ®Google Scholar
• Choi YL, Park SH, Jang JJ, Park CK. Expression of the G1-S modulators in hepatitis B virus-related hepatocellular carcinoma and dysplastic nodule: association of cyclin D1 and p53 proteins with the progression of hepatocellular carcinoma. J Korean Med Sci. 2001;16(4):424–432. PMID: 11511787; PMCID: PMCPMC3054763. doi:10.3346/jkms.2001.16.4.424
   PubMed Web of Science ®Google Scholar
• Tripathi V, Shen Z, Chakraborty A, et al. Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet. 2013;9(3):e1003368. PMID: 23555285; PMCID: PMCPMC3605280. doi:10.1371/journal.pgen.1003368
   PubMed Web of Science ®Google Scholar
• Asl ER, Amini M, Najafi S, et al. Interplay between MAPK/ERK signaling pathway and MicroRNAs: a crucial mechanism regulating cancer cell metabolism and tumor progression. Life Sci. 2021;278:119499. PMID: 33865878. doi:10.1016/j.lfs.2021.119499
   PubMed Web of Science ®Google Scholar
• Singh V, Ram M, Kumar R, Prasad R, Roy BK, Singh KK. Phosphorylation: implications in cancer. Protein J. 2017;36(1):1–6. PMID: 28108801. doi:10.1007/s10930-017-9696-z
   PubMed Web of Science ®Google Scholar
• Hayama S, Daigo Y, Yamabuki T, et al. Phosphorylation and activation of cell division cycle associated 8 by Aurora kinase B plays a significant role in human lung carcinogenesis. Cancer Res. 2007;67(9):4113–4122. PMID: 17483322. doi:10.1158/0008-5472.Can-06-4705
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhao Z, Bao X, et al. Borealin/Dasra B is overexpressed in colorectal cancers and contributes to proliferation of cancer cells. Med Oncol. 2014;31(11):248. PMID: 25260804. doi:10.1007/s12032-014-0248-5
   PubMed Web of Science ®Google Scholar
• Chang JL, Chen TH, Wang CF, et al. Borealin/Dasra B is a cell cycle-regulated chromosomal passenger protein and its nuclear accumulation is linked to poor prognosis for human gastric cancer. Exp Cell Res. 2006;312(7):962–973. PMID: 16427043. doi:10.1016/j.yexcr.2005.12.015
   PubMed Web of Science ®Google Scholar
• Jeon T, Ko MJ, Seo YR, et al. Silencing CDCA8 suppresses hepatocellular carcinoma growth and stemness via restoration of ATF3 tumor suppressor and inactivation of AKT/β-catenin signaling. Cancers. 2021;13(5):1055. PMID: 33801424; PMCID: PMCPMC7958635. doi:10.3390/cancers13051055
   PubMed Web of Science ®Google Scholar
• Li Y, Benezra R. Identification of a human mitotic checkpoint gene: hsMAD2. Science. 1996;274(5285):246–248. PMID: 8824189. doi:10.1126/science.274.5285.246
   PubMed Web of Science ®Google Scholar
• Bidus MA, Risinger JI, Chandramouli GV, et al. Prediction of lymph node metastasis in patients with endometrioid endometrial cancer using expression microarray. Clin Cancer Res. 2006;12(1):83–88. PMID: 16397028. doi:10.1158/1078-0432.Ccr-05-0835
   PubMed Web of Science ®Google Scholar
• Wang Y, Wang F, He J, et al. miR-30a-3p targets MAD2L1 and regulates proliferation of gastric cancer cells. Onco Targets Ther. 2019;12:11313–11324. PMID: 31908496; PMCID: PMCPMC6927793. doi:10.2147/ott.S222854
   PubMed Web of Science ®Google Scholar
• Li Y, Bai W, Zhang J. MiR-200c-5p suppresses proliferation and metastasis of human hepatocellular carcinoma (HCC) via suppressing MAD2L1. Biomed Pharmacother. 2017;92:1038–1044. PMID: 28609841. doi:10.1016/j.biopha.2017.05.092
   PubMed Web of Science ®Google Scholar
• Kitsera N, Dorosh O, Makukh H. Woman with Turner syndrome and her child with acute leukemia (a case report). Exp Oncol. 2020;42(4):333–336. PMID: 33355873. doi:10.32471/exp-oncology.2312-8852.vol-42-no-4.15275
   PubMedGoogle Scholar
• Zheng P, Li L. FANCI cooperates with IMPDH2 to promote lung adenocarcinoma tumor growth via a MEK/ERK/MMPs pathway. Onco Targets Ther. 2020;13:451–463. PMID: 32021289; PMCID: PMCPMC6970268. doi:10.2147/ott.S230333
   PubMed Web of Science ®Google Scholar
• Sondalle SB, Longerich S, Ogawa LM, Sung P, Baserga SJ. Fanconi anemia protein FANCI functions in ribosome biogenesis. Proc Natl Acad Sci USA. 2019;116(7):2561–2570. PMID: 30692263; PMCID: PMCPMC6377447. doi:10.1073/pnas.1811557116
   PubMed Web of Science ®Google Scholar
• Chan SH, Lim WK, Ishak NDB, et al. Germline mutations in cancer predisposition genes are frequent in sporadic sarcomas. Sci Rep. 2017;7(1):10660. PMID: 28878254; PMCID: PMCPMC5587568. doi:10.1038/s41598-017-10333-x
   PubMed Web of Science ®Google Scholar
• Joo W, Xu G, Persky NS, et al. Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway. Science. 2011;333(6040):312–316. PMID: 21764741; PMCID: PMCPMC3310437. doi:10.1126/science.1205805
   PubMed Web of Science ®Google Scholar
• Nookala RK, Hussain S, Pellegrini L. Insights into Fanconi Anaemia from the structure of human FANCE. Nucleic Acids Res. 2007;35(5):1638–1648. PMID: 17308347; PMCID: PMCPMC1865054. doi:10.1093/nar/gkm033
   PubMed Web of Science ®Google Scholar
• Wang Z, Katsaros D, Shen Y, et al. Biological and clinical significance of MAD2L1 and BUB1, genes frequently appearing in expression signatures for breast cancer prognosis. PLoS One. 2015;10(8):e0136246. PMID: 26287798; PMCID: PMCPMC4546117. doi:10.1371/journal.pone.0136246
   PubMed Web of Science ®Google Scholar
• Roberto GM, Engel EE, Scrideli CA, Tone LG, Brassesco MS. Downregulation of miR-10B* is correlated with altered expression of mitotic kinases in osteosarcoma. Pathol Res Pract. 2018;214(2):213–216. PMID: 29254787. doi:10.1016/j.prp.2017.11.020
   PubMed Web of Science ®Google Scholar
• Li Z, Yang HY, Dai XY, et al. CircMETTL3, upregulated in a m6A-dependent manner, promotes breast cancer progression. Int J Biol Sci. 2021;17(5):1178–1190. PMID: 33867838; PMCID: PMCPMC8040468. doi:10.7150/ijbs.57783
   PubMed Web of Science ®Google Scholar
• Kazi A, Chen L, Xiang S, et al. Global phosphoproteomics reveal CDK suppression as a vulnerability to KRAS addiction in pancreatic cancer. Clin Cancer Res. 2021;27(14):4012–4024. PMID: 33879459. doi:10.1158/1078-0432.Ccr-20-4781
   PubMed Web of Science ®Google Scholar
• Takashima S, Saito H, Takahashi N, et al. Strong expression of cyclin B2 mRNA correlates with a poor prognosis in patients with non-small cell lung cancer. Tumour Biol. 2014;35(5):4257–4265. PMID: 24375198. doi:10.1007/s13277-013-1556-7
   PubMedGoogle Scholar
• Lei CY, Wang W, Zhu YT, Fang WY, Tan WL. The decrease of cyclin B2 expression inhibits invasion and metastasis of bladder cancer. Urol Oncol. 2016;34(5):237.e1–10. PMID: 26706119. doi:10.1016/j.urolonc.2015.11.011
   PubMed Web of Science ®Google Scholar
• Oser MG, Fonseca R, Chakraborty AA, et al. Cells lacking the RB1 tumor suppressor gene are hyperdependent on Aurora B kinase for survival. Cancer Discov. 2019;9(2):230–247. PMID: 30373918; PMCID: PMCPMC6368871. doi:10.1158/2159-8290.Cd-18-0389
   PubMed Web of Science ®Google Scholar
• Zhang X, Wei C, Liang H, Han L. Polo-like kinase 4ʹs critical role in cancer development and strategies for Plk4-targeted therapy. Front Oncol. 2021;11:587554. PMID: 33777739; PMCID: PMCPMC7994899. doi:10.3389/fonc.2021.587554
   PubMed Web of Science ®Google Scholar
• Dai Y, Liu L, Zeng T, et al. Characterization of the oncogenic function of centromere protein F in hepatocellular carcinoma. Biochem Biophys Res Commun. 2013;436(4):711–718. PMID: 23791740. doi:10.1016/j.bbrc.2013.06.021
   PubMed Web of Science ®Google Scholar
• Yang X, Miao BS, Wei CY, et al. Lymphoid-specific helicase promotes the growth and invasion of hepatocellular carcinoma by transcriptional regulation of centromere protein F expression. Cancer Sci. 2019;110(7):2133–2144. PMID: 31066149; PMCID: PMCPMC6609811. doi:10.1111/cas.14037
   PubMed Web of Science ®Google Scholar
• Sun J, Huang J, Lan J, et al. Overexpression of CENPF correlates with poor prognosis and tumor bone metastasis in breast cancer. Cancer Cell Int. 2019;19:264. PMID: 31632198; PMCID: PMCPMC6788011. doi:10.1186/s12935-019-0986-8
   PubMed Web of Science ®Google Scholar
• Varis A, Salmela AL, Kallio MJ. Cenp-F (mitosin) is more than a mitotic marker. Chromosoma. 2006;115(4):288–295. PMID: 16565862. doi:10.1007/s00412-005-0046-0
   PubMed Web of Science ®Google Scholar
• Xiao B, Verma SC, Cai Q, et al. Bub1 and CENP-F can contribute to Kaposi’s sarcoma-associated herpesvirus genome persistence by targeting LANA to kinetochores. J Virol. 2010;84(19):9718–9732. PMID: 20660191; PMCID: PMCPMC2937805. doi:10.1128/jvi.00713-10
   PubMed Web of Science ®Google Scholar
• Lu H, Shi C, Wang S, et al. Identification of NCAPH as a biomarker for prognosis of breast cancer. Mol Biol Rep. 2020;47(10):7831–7842. PMID: 33009967. doi:10.1007/s11033-020-05859-9
   PubMed Web of Science ®Google Scholar
• Xiong Q, Fan S, Duan L, et al. NCAPH is negatively associated with Mcl‑1 in non‑small cell lung cancer. Mol Med Rep. 2020;22(4):2916–2924. PMID: 32945371; PMCID: PMCPMC7453632. doi:10.3892/mmr.2020.11359
   PubMed Web of Science ®Google Scholar
• Yin L, Jiang LP, Shen QS, et al. NCAPH plays important roles in human colon cancer. Cell Death Dis. 2017;8(3):e2680. PMID: 28300828; PMCID: PMCPMC5386579. doi:10.1038/cddis.2017.88
   PubMed Web of Science ®Google Scholar