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
Oncology Letters
Join Editorial Board Propose a Special Issue
Print ISSN: 1792-1074 Online ISSN: 1792-1082
Journal Cover
January-2020 Volume 19 Issue 1

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
January-2020 Volume 19 Issue 1

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

  • Supplementary Files
    • Supplementary_Data.pdf
Article Open Access

Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis

  • Authors:
    • Weiping Chen
    • Song Zhu
    • Yifei Zhang
    • Jinghua Xiao
    • Dongbo Tian
  • View Affiliations / Copyright

    Affiliations: Department of Respiratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China, Department of Radiotherapy, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
    Copyright: © Chen et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1008-1016
    |
    Published online on: December 2, 2019
       https://doi.org/10.3892/ol.2019.11169
  • 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

Lung cancer is a common malignancy worldwide. The aim of the present study was to investigate differentially expressed genes (DEGs) between non‑small‑cell lung cancer (NSCLC) and normal lung tissue, and to reveal the potential molecular mechanism underlying NSCLC. The Gene Expression Omnibus database was used to obtain three gene expression profiles (GSE18842, GSE30219 and GSE33532). DEGs were obtained by GEO2R. Gene Ontology and pathway enrichment analyses were performed for DEGs in the Database for Annotation, Visualization and Integrated Discovery. A protein‑protein interaction (PPI) network of DEGs was constructed and analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins database and Cytoscape software. A survival analysis was performed and protein expression levels of DEGs in human NSCLC were analyzed in order to determine clinical significance. A total of 764 DEGs were identified, consisting of 428 upregulated and 336 downregulated genes in NSCLC tissues compared with normal lung tissues, which were enriched in the ‘cell cycle’, ‘cell adhesion molecules’, ‘p53 signaling pathway’, ‘DNA replication’ and ‘tight junction’. A PPI network of DEGs consisting of 51 nodes and 192 edges was constructed. The top 10 genes were identified as hub genes from the PPI network. High expression of 4 of the 10 hub genes was associated with worse overall survival rate in patients with NSCLC, including CDK1, PLK1, RAD51 and RFC4. In conclusion, the present study aids in improving the current understanding of aberrant gene expression between NSCLC tissues and normal lung tissues underlying tumorgenesis in NSCLC. Identified hub genes can be used as a tumor marker for diagnosis and prognosis or as a drug therapy target in NSCLC.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

View References

1 

Ansari J, Shackelford RE and El-Osta H: Epigenetics in non-small cell lung cancer: From basics to therapeutics. Transl Lung Cancer Res. 5:155–171. 2016. View Article : Google Scholar : PubMed/NCBI

2 

Ramshankar V and Krishnamurthy A: Lung cancer detection by screening-presenting circulating miRNAs as a promising next generation biomarker breakthrough. Asian Pac J Cancer Prev. 14:2167–2172. 2013. View Article : Google Scholar : PubMed/NCBI

3 

Naruke T, Goya T, Tsuchiya R and Suemasu K: Prognosis and survival in resected lung carcinoma based on the new international staging system. J Thorac Cardiovasc Surg. 96:440–447. 1988. View Article : Google Scholar : PubMed/NCBI

4 

Ginsberg RJ and Rubinstein LV: Randomized trial of lobectomy versus limited resection for T1 N0 non-small cell lung cancer. Lung Cancer Study Group. Ann Thorac Surg. 60:615–622; discussion 622–623. 1995. View Article : Google Scholar : PubMed/NCBI

5 

Goldstraw P, Crowley J, Chansky K, Giroux DJ, Groome PA, Rami-Porta R, Postmus PE, Rusch V and Sobin L; International Association for the Study of Lung Cancer International Staging Committee; Participating Institutions, : The IASLC Lung Cancer Staging Project: Proposals for the revision of the TNM stage groupings in the forthcoming (seventh) edition of the TNM Classification of malignant tumours. J Thorac Oncol. 2:706–714. 2007. View Article : Google Scholar : PubMed/NCBI

6 

Lu X, Yang X, Zhang Z and Wang D: Meta-analysis of serum tumor markers in lung cancer. Zhongguo Fei Ai Za Zhi. 13:1136–1140, (In Chinese). PubMed/NCBI

7 

Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC and Lempicki RA: DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol. 4:P32003. View Article : Google Scholar : PubMed/NCBI

8 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI

9 

Kanehisa M and Goto S: KEGG: Kyoto encyclopaedia of genes and genomes. Nucleic Acids Res. 28:27–30. 2000. View Article : Google Scholar : PubMed/NCBI

10 

Sanchez-Palencia A, Gomez-Morales M, Gomez-Capilla JA, Pedraza V, Boyero L, Rosell R and Fárez-Vidal ME: Gene expression profiling reveals novel biomarkers in nonsmall cell lung cancer. Int J Cancer. 129:355–364. 2011. View Article : Google Scholar : PubMed/NCBI

11 

Rousseaux S, Debernardi A, Jacquiau B, Vitte AL, Vesin A, Nagy-Mignotte H, Moro-Sibilot D, Brichon PY, Lantuejoul S, Hainaut P, et al: Ectopic activation of germline and placental genes identifies aggressive metastasis-prone lung cancers. Sci Transl Med. 5:186ra662013. View Article : Google Scholar : PubMed/NCBI

12 

Meister M, Belousov A, Xu EC, Schnabel P, Warth A and Hoffman H: Intra-tumor heterogeneity of gene expression profiles in early stage non-small cell lung cancer. J Bioinf Res Stud. 1:12014.

13 

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al: NCBI GEO: Archive for functional genomics data sets-update. Nucleic Acids Res. 41:D991–D995. 2013. View Article : Google Scholar : PubMed/NCBI

14 

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C and Jensen LJ: STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41:D808–D815. 2013. View Article : Google Scholar : PubMed/NCBI

15 

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B and Ideker T: Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498–2504. 2003. View Article : Google Scholar : PubMed/NCBI

16 

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

17 

Győrffy B, Surowiak P, Budczies J and Lánczky A: Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer. PLoS One. 8:e822412013. View Article : Google Scholar : PubMed/NCBI

18 

Jakopovic M, Thomas A, Balasubramaniam S, Schrump D, Giaccone G and Bates SE: Targeting the epigenome in lung cancer: Expanding approaches to epigenetic therapy. Front Oncol. 3:2612013. View Article : Google Scholar : PubMed/NCBI

19 

Singhal S, Vachani A, Antin-Ozerkis D, Kaiser LR and Albelda SM: Prognostic implications of cell cycle, apoptosis, and angiogenesis biomarkers in non-small cell lung cancer: A review. Clin Cancer Res. 11:3974–3986. 2005. View Article : Google Scholar : PubMed/NCBI

20 

Voortman J, Checińska A and Giaccone AG: The proteasomal and apoptotic phenotype determine bortezomib sensitivity of non-small cell lung cancer cells. Mol Cancer. 6:732007. View Article : Google Scholar : PubMed/NCBI

21 

Yang Y, Ikezoe TT, Saito T, Kobayashi M, Koeffler HP and Taguchi H: Proteasome inhibitor PS-341 induces growth arrest and apoptosis of non-small cell lung cancer cells via the JNK/c-Jun/AP-1 signaling. Cancer Sci. 95:176–180. 2004. View Article : Google Scholar : PubMed/NCBI

22 

Huang CL, Yokomise H and Miyatake A: Clinical significance of the p53 pathway and associated gene therapy in non-small cell lung cancers. Future Oncol. 3:83–93. 2007. View Article : Google Scholar : PubMed/NCBI

23 

Kastan MB and Bartek J: Cell-cycle checkpoints and cancer. Nature. 432:316–323. 2004. View Article : Google Scholar : PubMed/NCBI

24 

Malumbres M and Barbacid M: Mammalian cyclin-dependent kinases. Trends Biochem Sci. 30:630–641. 2005. View Article : Google Scholar : PubMed/NCBI

25 

Wang Q, Su L, Liu N, Zhang L, Xu W and Fang H: Cyclin dependent kinase 1 inhibitors: A review of recent progress. Curr Med Chem. 18:2025–2043. 2011. View Article : Google Scholar : PubMed/NCBI

26 

Sharma PS, Sharma R and Tyagi R: Inhibitors of cyclin dependent kinases: Useful targets for cancer treatment. Curr Cancer Drug Targets. 8:53–75. 2008. View Article : Google Scholar : PubMed/NCBI

27 

Malumbres M, Pevarello P, Barbacid M and Bischoff JR: CDK inhibitors in cancer therapy: What is next? Trends Pharmacol Sci. 29:16–21. 2008. View Article : Google Scholar : PubMed/NCBI

28 

Yim H: Current clinical trials with polo-like kinase 1 inhibitors in solid tumors. Anticancer Drugs. 24:999–1006. 2013. View Article : Google Scholar : PubMed/NCBI

29 

Baumann P and West SC: Role of the human RAD51 protein in homologous recombination and double-stranded-break repair. Trends Biochem Sci. 23:247–251. 1998. View Article : Google Scholar : PubMed/NCBI

30 

Venkitaraman AR: Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell. 108:171–182. 2002. View Article : Google Scholar : PubMed/NCBI

31 

Raderschall E, Stout K, Freier S, Suckow V, Schweiger S and Haaf T: Elevated levels of Rad51 recombination protein in tumor cells. Cancer Res. 62:219–225. 2002.PubMed/NCBI

32 

Davies AA, Masson JY, McIlwraith MJ, Stasiak AZ, Stasiak A, Venkitaraman AR and West SC: Role of BRCA2 in control of the RAD51 recombination and DNA repair protein. Mol Cell. 7:273–282. 2001. View Article : Google Scholar : PubMed/NCBI

33 

Johnson A, Yao NY, Bowman GD, Kuriyan J and O'Donnell M: The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading. J Biol Chem. 281:35531–35543. 2006. View Article : Google Scholar : PubMed/NCBI

34 

Kim HS and Brill SJ: Rfc4 interacts with Rpa1 and is required for both DNA replication and DNA damage checkpoints in Saccharomyces cerevisiae. Mol Cell Biol. 21:3725–3737. 2001. View Article : Google Scholar : PubMed/NCBI

35 

Xiang J, Fang L, Luo Y, Yang Z, Liao Y, Cui J, Huang M, Yang Z, Huang Y, Fan X, et al: Levels of human replication factor C4, a clamp loader, correlate with tumor progression and predict the prognosis for colorectal cancer. J Transl Med. 12:3202014. View Article : Google Scholar : PubMed/NCBI

36 

Lin J, Marquardt G, Mullapudi N, Wang T, Han W, Shi M, Keller S, Zhu C, Locker J and Spivack SD: Lung cancer transcriptomes refined with laser capture microdissection. Am J Pathol. 184:2868–2884. 2014. View Article : Google Scholar : PubMed/NCBI

37 

Hallou A, Jennings J and Kabla AJ: Tumour heterogeneity promotes collective invasion and cancer metastatic dissemination. R Soc Open Sci. 4:1610072017. View Article : Google Scholar : PubMed/NCBI

38 

Fend F and Raffeld M: Laser capture microdissection in pathology. J Clin Pathol. 53:666–672. 2000. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Chen W, Zhu S, Zhang Y, Xiao J and Tian D: Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis. Oncol Lett 19: 1008-1016, 2020.
APA
Chen, W., Zhu, S., Zhang, Y., Xiao, J., & Tian, D. (2020). Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis. Oncology Letters, 19, 1008-1016. https://doi.org/10.3892/ol.2019.11169
MLA
Chen, W., Zhu, S., Zhang, Y., Xiao, J., Tian, D."Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis". Oncology Letters 19.1 (2020): 1008-1016.
Chicago
Chen, W., Zhu, S., Zhang, Y., Xiao, J., Tian, D."Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis". Oncology Letters 19, no. 1 (2020): 1008-1016. https://doi.org/10.3892/ol.2019.11169
Copy and paste a formatted citation
x
Spandidos Publications style
Chen W, Zhu S, Zhang Y, Xiao J and Tian D: Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis. Oncol Lett 19: 1008-1016, 2020.
APA
Chen, W., Zhu, S., Zhang, Y., Xiao, J., & Tian, D. (2020). Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis. Oncology Letters, 19, 1008-1016. https://doi.org/10.3892/ol.2019.11169
MLA
Chen, W., Zhu, S., Zhang, Y., Xiao, J., Tian, D."Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis". Oncology Letters 19.1 (2020): 1008-1016.
Chicago
Chen, W., Zhu, S., Zhang, Y., Xiao, J., Tian, D."Identification of key candidate tumor biomarkers in non‑small‑cell lung cancer by in silico analysis". Oncology Letters 19, no. 1 (2020): 1008-1016. https://doi.org/10.3892/ol.2019.11169
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