Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Molecular Medicine Reports
Join Editorial Board Propose a Special Issue
Print ISSN: 1791-2997 Online ISSN: 1791-3004
Journal Cover
November-2017 Volume 16 Issue 5

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
November-2017 Volume 16 Issue 5

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article

Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis

  • Authors:
    • Chuangang Peng
    • Qi Yang
    • Bo Wei
    • Baoming Yuan
    • Yong Liu
    • Yuxiang Li
    • Dawer Gu
    • Guochao Yin
    • Bo Wang
    • Dehui Xu
    • Xuebing Zhang
    • Daliang Kong
  • View Affiliations / Copyright

    Affiliations: Orthopaedic Medical Center, The 2nd Hospital of Jilin University, Changchun, Jilin 130041, P.R. China, Department of Gynecology and Obstetrics, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Orthopaedics, Jilin Oilfield General Hospital, Songyuan, Jilin 131200, P.R. China, Department of Orthopaedics, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
  • Pages: 7617-7624
    |
    Published online on: September 18, 2017
       https://doi.org/10.3892/mmr.2017.7506
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

The present study aimed to screen potential genes associated with conventional osteosarcoma (OS) and obtain further information on the pathogenesis of this disease. The microarray dataset GSE14359 was downloaded from the Gene Expression Omnibus. A total of 10 conventional OS samples and two non‑neoplastic primary osteoblast samples in the dataset were selected to identify the differentially expressed genes (DEGs) using the Linear Models for Microarray Data package. The potential functions of the DEGs were predicted using Gene Ontology (GO) and pathway enrichment analyses. Protein‑protein interaction (PPI) data were also obtained using the Search Tool for the Retrieval of Interacting Genes database, and the PPI network was visualized using Cytoscape. Module analysis was then performed using the Molecular Complex Detection module. Additionally, the potential microRNAs (miRNAs) for the upregulated DEGs in the most significant pathway were predicted using the miRDB database, and the regulatory network for the miRNAs‑DEGs was visualized in Cytoscape. In total, 317 upregulated and 670 downregulated DEGs were screened. Certain DEGs, including cyclin‑dependent kinase 1 (CDK1), mitotic arrest deficient 2 like 1 (MAD2L1) and BUB1 mitotic checkpoint serine/threonine‑protein kinase (BUB1), were significantly enriched in the cell cycle phase and oocyte meiosis pathway. DEGs, including replication factor C subunit 2 (RFC2), RFC3, RFC4 and RFC5, were significantly enriched in DNA replication and interacted with each other. RFC4 also interacted with other DEGs, including CDK1, MAD2L1, NDC80 kinetochore complex and BUB1. In addition, RFC4, RFC3 and RFC5 were targeted by miRNA (miR)‑802, miR‑224‑3p and miR‑522‑3p. The DEGs encoding RFC may be important for the development of conventional OS, and their expression may be regulated by a number of miRNAs, including miR‑802, miR‑224‑3p and miR‑522‑3p.
View Figures

Figure 1

Figure 2

Figure 3

View References

1 

Messerschmitt PJ, Garcia RM, Abdul-Karim FW, Greenfield EM and Getty PJ: Osteosarcoma. J Am Acad Orthop Surg. 17:515–527. 2009. View Article : Google Scholar : PubMed/NCBI

2 

Mohseny AB, Tieken C, Van Der Velden PA, Szuhai K, de Andrea C, Hogendoorn PC and Cleton-Jansen AM: Small deletions but not methylation underlie CDKN2A/p16 loss of expression in conventional osteosarcoma. Genes Chromosomes Cancer. 49:1095–1103. 2010. View Article : Google Scholar : PubMed/NCBI

3 

Bae Y, Yang T, Zeng HC, Campeau PM, Chen Y, Bertin T, Dawson BC, Munivez E, Tao J and Lee BH: miRNA-34c regulates Notch signaling during bone development. Hum Mol Genet. 21:2991–3000. 2012. View Article : Google Scholar : PubMed/NCBI

4 

Silva A, Yunes JA, Cardoso BA, Martins LR, Jotta PY, Abecasis M, Nowill AE, Leslie NR, Cardoso AA and Barata JT: PTEN posttranslational inactivation and hyperactivation of the PI3K/Akt pathway sustain primary T cell leukemia viability. J Clin Invest. 118:3762–3774. 2008. View Article : Google Scholar : PubMed/NCBI

5 

Freeman SS, Allen SW, Ganti R, Wu J, Ma J, Su X, Neale G, Dome JS, Daw NC and Khoury JD: Copy number gains in EGFR and copy number losses in PTEN are common events in osteosarcoma tumors. Cancer. 113:1453–1461. 2008. View Article : Google Scholar : PubMed/NCBI

6 

Zhao G, Cai C, Yang T, Qiu X, Liao B, Li W, Ji Z, Zhao J, Zhao H, Guo M, et al: MicroRNA-221 induces cell survival and cisplatin resistance through PI3K/Akt pathway in human osteosarcoma. PLoS One. 8:e539062013. View Article : Google Scholar : PubMed/NCBI

7 

Namløs HM, Meza-Zepeda LA, Barøy T, Østensen IH, Kresse SH, Kuijjer ML, Serra M, Bürger H, Cleton-Jansen AM and Myklebost O: Modulation of the osteosarcoma expression phenotype by microRNAs. PLoS One. 7:e480862012. View Article : Google Scholar : PubMed/NCBI

8 

Fritsche-Guenther R, Noske A, Ungethüm U, Kuban RJ, Schlag PM, Tunn PU, Karle J, Krenn V, Dietel M and Sers C: De novo expression of EphA2 in osteosarcoma modulates activation of the mitogenic signalling pathway. Histopathology. 57:836–850. 2010. View Article : Google Scholar : PubMed/NCBI

9 

Fritsche-Guenther R, Gruetzkau A, Noske A, Melcher I, Schaser KD, Schlag PM, Kasper HU, Krenn V and Sers C: Therapeutic potential of CAMPATH-1H in skeletal tumours. Histopathology. 57:851–861. 2010. View Article : Google Scholar : PubMed/NCBI

10 

Luo Y, Deng Z and Chen J: Pivotal regulatory network and genes in osteosarcoma. Arch Med Sci. 9:569–575. 2013. View Article : Google Scholar : PubMed/NCBI

11 

Yang Z, Chen Y, Fu Y, Yang Y, Zhang Y, Chen Y and Li D: Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data. BMC Med Genet. 15:802014. View Article : Google Scholar : PubMed/NCBI

12 

Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F and Spencer F: A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association. 99:909–917. 2004. View Article : Google Scholar

13 

Seo J and Hoffman EP: Probe set algorithms: Is there a rational best bet? BMC bioinformatics. 7:3952006. View Article : Google Scholar : PubMed/NCBI

14 

Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 3:Article32004. View Article : Google Scholar : PubMed/NCBI

15 

Benjamini Y and Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological). 57:289–300. 1995.

16 

Olson CF: Parallel algorithms for hierarchical clustering. Parallel Computing. 21:1313–1325. 1995. View Article : Google Scholar

17 

Kolde R: pheatmap: Pretty Heatmaps. R package. version 0.7. 7. 2012.

18 

Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC and Lempicki RA: The DAVID gene functional classification tool: A novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R1832007. View Article : Google Scholar : PubMed/NCBI

19 

Von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P and Snel B: STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31:258–261. 2003. View Article : Google Scholar : PubMed/NCBI

20 

Kohl M, Wiese S and Warscheid B: Cytoscape: Software for visualization and analysis of biological networks. Methods Mol Biol. 696:291–303. 2011. View Article : Google Scholar : PubMed/NCBI

21 

Bader GD and Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics. 4:22003. View Article : Google Scholar : PubMed/NCBI

22 

Wang X: miRDB: A microRNA target prediction and functional annotation database with a wiki interface. RNA. 14:1012–1017. 2008. View Article : Google Scholar : PubMed/NCBI

23 

Reynolds N, Fantes PA and MacNeill SA: A key role for replication factor C in DNA replication checkpoint function in fission yeast. Nucleic Acids Res. 27:462–469. 1999. View Article : Google Scholar : PubMed/NCBI

24 

Redondo-Muñoz J, Rodríguez MJ, Silió V, Pérez-García V, Valpuesta JM and Carrera AC: Phosphoinositide 3-kinase beta controls replication factor C assembly and function. Nucleic Acids Res. 41:855–868. 2013. View Article : Google Scholar : PubMed/NCBI

25 

Loeb LA, Springgate CF and Battula N: Errors in DNA replication as a basis of malignant changes. Cancer Res. 34:2311–2321. 1974.PubMed/NCBI

26 

Tsaniras S Champeris, Kanellakis N, Symeonidou IE, Nikolopoulou P, Lygerou Z and Taraviras S: Licensing of DNA replication, cancer, pluripotency and differentiation: An interlinked world? Semin Cell Dev Biol. 30:174–180. 2014. View Article : Google Scholar : PubMed/NCBI

27 

PosthumaDeBoer J, van Royen B and Helder M: Mechanisms of therapy resistance in osteosarcoma: A review. Oncol Discov. 1:82013. View Article : Google Scholar

28 

Kim MJ, Lee JY and Lee SJ: Transient suppression of nuclear Cdc2 activity in response to ionizing radiation. Oncol Rep. 19:1323–1329. 2008.PubMed/NCBI

29 

Fu W, Ma L, Chu B, Wang X, Bui MM, Gemmer J, Altiok S and Pledger WJ: The cyclin-dependent kinase inhibitor SCH 727965 (dinacliclib) induces the apoptosis of osteosarcoma cells. Mol Cancer Ther. 10:1018–1027. 2011. View Article : Google Scholar : PubMed/NCBI

30 

Doak SH, Jenkins GJ, Parry EM, Griffiths AP, Baxter JN and Parry JM: Differential expression of the MAD2, BUB1 and HSP27 genes in Barrett's oesophagus-their association with aneuploidy and neoplastic progression. Mutat Res. 547:133–144. 2004. View Article : Google Scholar : PubMed/NCBI

31 

Giantin M, Granato A, Baratto C, Marconato L, Vascellari M, Morello EM, Vercelli A, Mutinelli F and Dacasto M: Global gene expression analysis of canine cutaneous mast cell tumor: Could molecular profiling be useful for subtype classification and prognostication? PLoS One. 9:e954812014. View Article : Google Scholar : PubMed/NCBI

32 

Yu L, Guo WC, Zhao SH, Tang J and Chen JL: Mitotic arrest defective protein 2 expression abnormality and its clinicopathologic significance in human osteosarcoma. Apmis. 118:222–229. 2010. View Article : Google Scholar : PubMed/NCBI

33 

Trougakos IP, Chondrogianni N, Amarantos I, Blake J, Schwager C, Wirkner U, Ansorge W and Gonos ES: Genome-wide transcriptome profile of the human osteosarcoma Sa OS and U-2 OS cell lines. Cancer Genet Cytogenet. 196:109–118. 2010. View Article : Google Scholar : PubMed/NCBI

34 

Kuijjer ML, Peterse EF, van den Akker BE, Briaire-de Bruijn IH, Serra M, Meza-Zepeda LA, Myklebost O, Hassan AB, Hogendoorn PC and Cleton-Jansen AM: IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma. BMC Cancer. 13:2452013. View Article : Google Scholar : PubMed/NCBI

35 

Cao ZQ, Shen Z and Huang WY: MicroRNA-802 promotes osteosarcoma cell proliferation by targeting p27. Asian Pac J Cancer Prev. 14:7081–7084. 2013. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Peng C, Yang Q, Wei B, Yuan B, Liu Y, Li Y, Gu D, Yin G, Wang B, Xu D, Xu D, et al: Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis. Mol Med Rep 16: 7617-7624, 2017.
APA
Peng, C., Yang, Q., Wei, B., Yuan, B., Liu, Y., Li, Y. ... Kong, D. (2017). Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis. Molecular Medicine Reports, 16, 7617-7624. https://doi.org/10.3892/mmr.2017.7506
MLA
Peng, C., Yang, Q., Wei, B., Yuan, B., Liu, Y., Li, Y., Gu, D., Yin, G., Wang, B., Xu, D., Zhang, X., Kong, D."Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis". Molecular Medicine Reports 16.5 (2017): 7617-7624.
Chicago
Peng, C., Yang, Q., Wei, B., Yuan, B., Liu, Y., Li, Y., Gu, D., Yin, G., Wang, B., Xu, D., Zhang, X., Kong, D."Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis". Molecular Medicine Reports 16, no. 5 (2017): 7617-7624. https://doi.org/10.3892/mmr.2017.7506
Copy and paste a formatted citation
x
Spandidos Publications style
Peng C, Yang Q, Wei B, Yuan B, Liu Y, Li Y, Gu D, Yin G, Wang B, Xu D, Xu D, et al: Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis. Mol Med Rep 16: 7617-7624, 2017.
APA
Peng, C., Yang, Q., Wei, B., Yuan, B., Liu, Y., Li, Y. ... Kong, D. (2017). Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis. Molecular Medicine Reports, 16, 7617-7624. https://doi.org/10.3892/mmr.2017.7506
MLA
Peng, C., Yang, Q., Wei, B., Yuan, B., Liu, Y., Li, Y., Gu, D., Yin, G., Wang, B., Xu, D., Zhang, X., Kong, D."Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis". Molecular Medicine Reports 16.5 (2017): 7617-7624.
Chicago
Peng, C., Yang, Q., Wei, B., Yuan, B., Liu, Y., Li, Y., Gu, D., Yin, G., Wang, B., Xu, D., Zhang, X., Kong, D."Investigation of crucial genes and microRNAs in conventional osteosarcoma using gene expression profiling analysis". Molecular Medicine Reports 16, no. 5 (2017): 7617-7624. https://doi.org/10.3892/mmr.2017.7506
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team