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Cited by 27Sarcoma Diagnosis and TreatmentBioinformatics and Genomic NetworksBone Tumor Diagnosis and Treatments

Gene expression profiling analysis of osteosarcoma cell lines

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SUN, LU, LI, JIE, YAN, BING·2015·Molecular Medicine Reports
DOI 10.3892/mmr.2015.3958PMC PMC4526047
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Abstract

Osteosarcoma (OS) is the most common type of primary bone malignancy and has a poor prognosis. To investigate the mechanisms of osteosarcoma, the present analyzed the GSE28424 microarray. GSE28424 was downloaded from the Gene Expression Omnibus, and included a collective of 19 OS cell lines and four normal bone cell lines, which were used as controls. Subsequently, the differentially expressed genes (DEGs) were screened using the Limma package in Bioconductor. Gene Ontology (GO) and pathway enrichment analysis of the DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, interactions between the proteins encoded by the DEGs were identified using STRING, and the protein‑protein interaction (PPI) network was visualized using Cytoscape. In addition, modular analysis of the PPI network was performed using the Clique Percolation Method (CPM) in CFinder. A total of 1,170 DEGs were screened, including 530 upreguated and 640 downregulated genes. The enriched functions included organelle fission, immune response and response to wounding. In addition, RPL8 was observed to be involved with the ribosomal pathway in module A of the PPI network of the DEGs. PLCG1, SYK and PLCG2 were also involved in the B‑cell receptor signaling pathway in module B and the Fc‑epsilon RI signaling pathway in module C. In addition, AURKA (degree=39), MAD2L1 (degree=38), CDCA8 (degree=38), BUB1 (degree=37) and MELK (degree=37) exhibited higher degrees of connectivity in module F. The results of the present study suggested that the RPL8, PLCG1, PLCG2, SYK, MAD2L1, AURKA, CDCA8, BUB1 and MELK genes may be involved in OS.

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  • Another study of osteosarcoma cell lines found PLCγ2 to be a differentially regulated gene.

    “siRNA targeting Ezrin, a cytoplasmic peripheral protein involved in metastatic spreading of osteosarcoma and dependent on PIP2, also resulted in PLCγ2 upregulation in human osteosarcoma cell lines (155, 156), while another study of osteosarcoma cell lines found PLCγ2 to be a differentially regulated gene (157).”

    From The role of PLCγ2 in immunological disorders, cancer, and neurodegeneration (2021) · cites this paper as [157]

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  1. [1]Ottaviani G Jaffe N The epidemiology of osteosarcoma Cancer Treat Res 152 3 13 2009 10.1007/978-1-4419-0284-9_1 20213383 · DOI
  2. [2]Ritter J Bielack SS Osteosarcoma Ann Oncol 21 Suppl 7 vii320 vii325 2010 10.1093/annonc/mdq276 20943636 · DOI
  3. [3]Stiller CA Bielack SS Jundt G Steliarova-Foucher E Bone tumours in European children and adolescents, 1978–1997. Report from the automated childhood cancer information system project Eur J Cancer 42 2124 2135 2006 10.1016/j.ejca.2006.05.015 16919776 · DOI
  4. [4]Stiller CA Craft AW Corazziari I EUROCARE Working Group: Survival of children with bone sarcoma in Europe since 1978: results from the EUROCARE study Eur J Cancer 37 760 766 2001 10.1016/S0959-8049(01)00004-1 11311651 · DOI
  5. [5]Yang J Yang D Sun Y Genetic amplification of the vascular endothelial growth factor (VEGF) pathway genes, including VEGFA, in human osteosarcoma Cancer 117 4925 4938 2011 10.1002/cncr.26116 21495021 PMC3465081 · DOI
  6. [6]Quan GM Choong PF Anti-angiogenic therapy for osteosarcoma Cancer Metast Rev 25 707 713 2006 10.1007/s10555-006-9031-1 17160710 · DOI
  7. [7]Dvorak HF Vascular permeability factor/vascular endothelial growth factor: A critical cytokine in tumor angiogenesis and a potential target for diagnosis and therapy J Clin Oncol 20 4368 4380 2002 10.1200/JCO.2002.10.088 12409337 · DOI
  8. [8]Lee Y Tokunaga T Oshika Y Cell-retained isoforms of vascular endothelial growth factor (VEGF) are correlated with poor prognosis in osteosarcoma Eur J Cancer 35 1089 1093 1999 10.1016/S0959-8049(99)00073-8 10533453 · DOI
  9. [9]Takenaka K Yamagishi SI Jinnouchi Y Nakamura K Matsui T Imaizumi T Pigment epithelium-derived factor (PEDF)-induced apoptosis and inhibition of vascular endothelial growth factor (VEGF) expression in MG63 human osteosarcoma cells Life Sci 77 3231 3241 2005 10.1016/j.lfs.2005.05.048 15985268 · DOI
  10. [10]Miller CW Aslo A Tsay C Frequency and structure of p53 rearrangements in human osteosarcoma Cancer Res 50 7950 7954 1990 2253237
  11. [11]Mousses S Mcauley L Bell RS Kandel R Andrulis IL Molecular and immunohistochemical identification of p53 alterations in bone and soft tissue sarcomas Mod Pathol 9 1 6 1996 8821948
  12. [12]Eliseev R Dong Y Sampson E Runx2-mediated activation of the Bax gene increases osteosarcoma cell sensitivity to apoptosis Oncogene 27 3605 3614 2008 10.1038/sj.onc.1211020 18223689 PMC6247425 · DOI
  13. [13]Onda M Matsuda S Higaki S ErbB-2 expression is correlated with poor prognosis for patients with osteosarcoma Cancer 77 71 78 1996 10.1002/(SICI)1097-0142(19960101)77:1<71::AID-CNCR13>3.0.CO;2-5 8630943 · DOI
  14. [14]Namløs HM Meza-Zepeda LA Modulation of the osteosarcoma expression phenotype by microRNAs PloS One 7 e48086 2012 10.1371/journal.pone.0048086 23133552 PMC3485010 · DOI
  15. [15]Irizarry RA Hobbs B Collin F Exploration, normalization and summaries of high density oligonucleotide array probe level data Biostatistics 4 249 264 2003 10.1093/biostatistics/4.2.249 12925520 · DOI · Paper page
  16. [16]Gentleman R Carey VJ Huber W Irizarry RA Dudoit S Bioinformatics and computational biology solutions using R and Bioconductor 746718470 Springer New York NY 2005 10.1007/0-387-29362-0 · DOI
  17. [17]Huang da W Sherman BT Lempicki RA Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat Protoc 4 44 57 2008 10.1038/nprot.2008.211 19131956 · DOI · Paper page
  18. [18]Harris MA Clark J Ireland A The Gene Ontology (GO) database and informatics resource Nucleic Acids Res 32 D258 D261 2004 10.1093/nar/gkh036 14681407 PMC308770 · DOI
  19. [19]Lu M Zhang Q Deng M An analysis of human microRNA and disease associations PloS One 3 e3420 2008 10.1371/journal.pone.0003420 18923704 PMC2559869 · DOI
  20. [20]Franceschini A Szklarczyk D Frankild S STRING v9.1: Protein-protein interaction networks, with increased coverage and integration Nucleic Acids Res 41 D808 D815 2013 10.1093/nar/gks1094 23203871 PMC3531103 · DOI · Paper page
  21. [21]Saito R Smoot ME Ono K A travel guide to Cytoscape plugins Nat Med 9 1069 1076 2012 PMC3649846 23132118
  22. [22]Palla G Derényi I Farkas I Vicsek T Uncovering the overlapping community structure of complex networks in nature and society Nature 435 814 818 2005 10.1038/nature03607 15944704 · DOI · Paper page
  23. [23]Cui XR Hou WR Yang J Hou Y Peng ZS Cloning and sequence analysis of ribosomal protein L8 gene (RPL8) from the (Ailuropoda melanoleuca) 2011 4th International Conference on Biomedical Engineering and Informatics Shanghai, China 1407 1411 2011
  24. [24]Yang J Zhang W New molecular insights into osteosarcoma targeted therapy Curr Opin Oncol 25 398 406 2013 10.1097/CCO.0b013e3283622c1b 23666471 · DOI
  25. [25]Salas S Jézéquel P Campion L Deville JL Chibon F Bartoli C Gentet JC Charbonnel C Gouraud W Voutsinos-Porche B Molecular characterization of the response to chemotherapy in conventional osteosarcomas: Predictive value of HSD17B10 and IFITM2 Int J Cancer 125 851 860 2009 10.1002/ijc.24457 19449377 · DOI
  26. [26]Montanaro L Mazzini G Barbieri S Different effects of ribosome biogenesis inhibition on cell proliferation in retinoblastoma protein-and p53-deficient and proficient human osteosarcoma cell lines Cell Prolif 40 532 549 2007 10.1111/j.1365-2184.2007.00448.x 17635520 PMC6495848 · DOI
  27. [27]Fukami K Structure, regulation and function of phospholipase C isozymes J Biochem 131 293 299 2002 10.1093/oxfordjournals.jbchem.a003102 11872156 · DOI
  28. [28]Noh DY Kang H Kim YC Expression of phospholipase C-gamma 1 and its transcriptional regulators in breast cancer tissues Anticancer Res 18 2643 2648 1997 9703922
  29. [29]Mamoune A Kassis J Kharait S Kloeker S Manos E Jones DA Wells A DU145 human prostate carcinoma invasiveness is modulated by urokinase receptor (uPAR) downstream of epidermal growth factor receptor (EGFR) signaling Exp Cell Res 299 91 100 2004 10.1016/j.yexcr.2004.05.008 15302576 · DOI
  30. [30]Kochhar KS Iyer AP Hepatocyte growth factor induces activation of Nck and phospholipase C-γ in lung carcinoma cells Cancer Lett 104 163 169 1996 10.1016/0304-3835(96)04244-9 8665484 · DOI
  31. [31]Kassis J Radinsky R Wells A Motility is rate-limiting for invasion of bladder carcinoma cell lines Int J Biochem Cell Biol 34 762 775 2002 10.1016/S1357-2725(01)00173-X 11950593 · DOI
  32. [32]Zhang B Wu Q Ye XF Liu S Lin XF Chen MC Roles of PLC-gamma2 and PKCalpha in TPA-induced apoptosis of gastric cancer cells World J Gastroenterol 9 2413 2418 2003 14606067 PMC4656512
  33. [33]Dong S Ma L Xu N Research on the reactivation of Syk expression caused by the inhibition of DNA promoter methylation in the lung cancer Neoplasma 58 89 95 2010 10.4149/neo_2011_01_89 21067271 · DOI
  34. [34]Luo P Yang X Ying M Retinoid-suppressed phosphorylation of RARα mediates the differentiation pathway of osteosarcoma cells Oncogene 29 2772 2783 2010 10.1038/onc.2010.50 20190807 · DOI
  35. [35]Agoston AT Argani P De Marzo AM Hicks JL Nelson WG Retinoblastoma pathway dysregulation causes DNA methyltrans-ferase 1 overexpression in cancer via MAD2-mediated inhibition of the anaphase-promoting complex Am J Pathol 170 1585 1593 2007 10.2353/ajpath.2007.060779 17456764 PMC1854953 · DOI
  36. [36]Yu L Guo WC Zhao SH Tang J Chen JL Mitotic arrest defective protein 2 expression abnormality and its clinicopathologic significance in human osteosarcoma Apmis 118 222 229 2010 10.1111/j.1600-0463.2009.02583.x 20132188 · DOI
  37. [37]Yu L Guo W Zhao S Tang J Liu J Knockdown of Mad2 induces osteosarcoma cell apoptosis-involved Rad21 cleavage J Orthop Sci 16 814 820 2011 10.1007/s00776-011-0156-x 21901524 · DOI
  38. [38]Shichiri M Yoshinaga K Hisatomi H Sugihara K Hirata Y Genetic and epigenetic inactivation of mitotic checkpoint genes hBUB1 and hBUBR1 and their relationship to survival Cancer Res 62 13 17 2002 11782350
  39. [39]Bischoff JR Anderson L Zhu Y A homologue of Drosophila aurora kinase is oncogenic and amplified in human colorectal cancers EMBO J 17 3052 3065 1998 10.1093/emboj/17.11.3052 9606188 PMC1170645 · DOI
  40. [40]Branca M Giorgi C Santini D Survivin as a marker of cervical intraepithelial neoplasia and high-risk human papillomavirus and a predictor of virus clearance and prognosis in cervical cancer Am J Clin Pathol 124 113 121 2005 10.1309/L8BWF431WU9AC8FJ 15923164 · DOI
  41. [41]Hayama S Daigo Y Yamabuki T Phosphorylation and activation of cell division cycle associated 8 by aurora kinase B plays a significant role in human lung carcinogenesis Cancer Res 67 4113 4122 2007 10.1158/0008-5472.CAN-06-4705 17483322 · DOI
  42. [42]Pickard MR Green AR Ellis IO Dysregulated expression of Fau and MELK is associated with poor prognosis in breast cancer Breast Cancer Res 11 R60 2009 10.1186/bcr2350 19671159 PMC2750122 · DOI
  43. [43]Lin ML Park JH Nishidate T Nakamura Y Katagiri T Involvement of maternal embryonic leucine zipper kinase (MELK) in mammary carcinogenesis through interaction with Bcl-G, a pro-apoptotic member of the Bcl-2 family Breast Cancer Res 9 R17 2007 10.1186/bcr1650 17280616 PMC1851384 · DOI
  44. [44]Gray D Jubb AM Hogue D Maternal embryonic leucine zipper kinase/murine protein serine-threonine kinase 38 is a promising therapeutic target for multiple cancers Cancer Res 65 9751 9761 2005 10.1158/0008-5472.CAN-04-4531 16266996 · DOI

Cited by

Sorted by citations

Authors
SUN, L., LI, J., & YAN, B.
Corresponding author
LI, JIE
ORCID
Venue
Molecular Medicine Reports
Publisher
Spandidos Publications
Published
2015-06-18
Volume
12
Issue
3
Pages
4266-4272
ISSN
  • 1791-2997 (ISSN-L)
  • 1791-3004
DOI
10.3892/mmr.2015.3958
PMC
PMC4526047
OpenAlex
W1826803960
Cited by
27
References
0
Citations by year
2026: 2 · 2024: 1 · 2023: 3 · 2022: 2 · 2021: 4 · 2020: 6 · 2019: 1 · 2018: 1 · 2017: 5 · 2016: 1 · 2015: 1
FWCI
2.11
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Molecular Medicine Reports (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Sarcoma Diagnosis and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Health Sciences › Medicine › Rheumatology › Bone Tumor Diagnosis and Treatments
Keywords
osteosarcoma, osteosarcoma cell lines, differentially expressed genes, protein-protein interaction network, RPL8, ribosomal pathway, B cell receptor signaling, AURKA, Mad2, CDCA8, BUB1, MELK, immune response, cell cycle genes
MeSH terms
Bone Neoplasms, Humans, Osteosarcoma, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Cell Line, Tumor, Transcriptome, Protein Interaction Maps

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