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
August-2015 Volume 12 Issue 2

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
August-2015 Volume 12 Issue 2

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 Open Access

Regulation of gene expression in rats with spinal cord injury based on microarray data

  • Authors:
    • Guoqiang Chen
    • Xiutong Fang
    • Meng Yu
  • View Affiliations / Copyright

    Affiliations: Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China
    Copyright: © Chen et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY_NC 3.0].
  • Pages: 2465-2472
    |
    Published online on: April 23, 2015
       https://doi.org/10.3892/mmr.2015.3670
  • 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 investigate the molecular mechanisms of spinal cord injury (SCI) in rats. First, the differentially expressed genes (DGEs) were screened based on GSE45006 microarray data downloaded from Gene Expression Omnibus using the significant analysis of microarray (SAM) method. Screening was performed for DEGs which were negatively or possibly correlated with time and subsequently subjected to gene ontology (GO) functional annotation. Furthermore, pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes was also performed. In addition, a protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Finally, GeneCodis was used to seek transcription factors and microRNAs that are involved in the regulation of DEGs. A total of 806 DEGs were upregulated and 549 DEGs were downregulated in the rats with SCI. Cholesterol metabolism‑associated genes (e.g. HMGCS1, FDFT1 and IDI1) were negatively correlated with time, while injury genes (e.g. SERPING1, C1S and RAB27A) were positively correlated with time after SCI. PCNA, MCM2, JUN and SNAP25 were the hub proteins of the PPI network. The transcription factors LEF1 and SP1 were observed to be associated with the regulation of two DEGs that were involved in the cholesterol‑associated metabolism as well as injury responses. A number of microRNAs (e.g. miR210, miR‑487b and miR‑16) were observed to target cholesterol metabolism‑associated DGEs. The hub genes PCNA, MCM2, JUN and SNAP25 presumably have critical roles in rats with SCI, and the transcription factors LEF1 and SP1 may be important for the regulation of cholesterol metabolism and injury responses following SCI.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

View References

1 

Taoka Y and Okajima K: Spinal cord injury in the rat. Prog Neurobiol. 56:341–358. 1998. View Article : Google Scholar : PubMed/NCBI

2 

Liu CL, Jin AM and Tong BH: Detection of gene expression pattern in the early stage after spinal cord injury by gene chip. Chin J Traumatol. 6:18–22. 2003.PubMed/NCBI

3 

Song G, Cechvala C, Resnick DK, Dempsey RJ and Rao VL: GeneChip analysis after acute spinal cord injury in rat. J Neurochem. 79:804–815. 2001. View Article : Google Scholar : PubMed/NCBI

4 

Bareyre FM, Haudenschild B and Schwab ME: Long-lasting sprouting and gene expression changes induced by the monoclonal antibody IN-1 in the adult spinal cord. J Neurosci. 22:7097–7110. 2002.PubMed/NCBI

5 

Hayashi M, Ueyama T, Nemoto K, Tamaki T and Senba E: Sequential mRNA expression for immediate early genes, cytokines and neurotrophins in spinal cord injury. J Neurotrauma. 17:203–218. 2000. View Article : Google Scholar : PubMed/NCBI

6 

Di Giovanni S, Knoblach SM, Brandoli C, Aden SA, Hoffman EP and Faden AI: Gene profiling in spinal cord injury shows role of cell cycle in neuronal death. Ann Neurol. 53:454–468. 2003. View Article : Google Scholar : PubMed/NCBI

7 

Carmel JB, Galante A, Soteropoulos P, et al: Gene expression profiling of acute spinal cord injury reveals spreading inflammatory signals and neuron loss. Physiol Genomics. 7:201–213. 2001. View Article : Google Scholar

8 

Pan JZ, Ni L, Sodhi A, Aguanno A, Young W and Hart RP: Cytokine activity contributes to induction of inflammatory cytokine mRNAs in spinal cord following contusion. J Neurosci Res. 68:315–322. 2002. View Article : Google Scholar : PubMed/NCBI

9 

Hayashi M, Ueyama T, Nemoto K, Tamaki T and Senba E: Sequential mRNA expression for immediate early genes, cytokines and neurotrophins in spinal cord injury. J Neurotrauma. 17:203–218. 2000. View Article : Google Scholar : PubMed/NCBI

10 

Yakovlev AG and Faden Al: Sequential expression of c-fos protooncogene, TNF-alpha and dynorphin genes in spinal cord following experimental traumatic injury. Mol Chem Neuropathol. 23:179–190. 1994. View Article : Google Scholar : PubMed/NCBI

11 

Liu NK, Wang XF, Lu QB and Xu XM: Altered microRNA expression following traumatic spinal cord injury. Exp Neurol. 219:424–429. 2009. View Article : Google Scholar : PubMed/NCBI

12 

Kosik KS: The neuronal microRNA system. Nat Rev Neurosci. 7:911–920. 2006. View Article : Google Scholar : PubMed/NCBI

13 

Schaefer A, O’Carroll D, Tan CL, et al: Cerebellar neurodegeneration in the absence of microRNAs. J Exp Med. 204:1553–1558. 2007. View Article : Google Scholar : PubMed/NCBI

14 

Gautier L, Cope L, Bolstad BM and Irizarry RA: affy–analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20:307–315. 2004. View Article : Google Scholar : PubMed/NCBI

15 

Smyth GK: Limma: Linear Models for Microarray Data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor Springer. pp. 397–420. 2005

16 

Zhang X, Li J, Liu A, et al: Expression profile in rice panicle: insights into heat response mechanism at reproductive stage. PLoS One. 7:e496522012. View Article : Google Scholar : PubMed/NCBI

17 

Huang da W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar : PubMed/NCBI

18 

Franceschini A, Szklarczyk D, Frankild S, et al: STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41(Database Issue): D808–D815. 2013. View Article : Google Scholar :

19 

Tabas-Madrid D, Nogales-Cadenas R and Pascual-Montano A: GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Res. 40(Web Server Issue): W478–W483. 2012. View Article : Google Scholar : PubMed/NCBI

20 

Jochum W, Passegué E and Wagner EF: AP-1 in mouse development and tumorigenesis. Oncogene. 20:2401–2412. 2001. View Article : Google Scholar : PubMed/NCBI

21 

Raivich G, Bohatschek M, Da Costa C, et al: The AP-1 transcription factor c-Jun is required for efficient axonal regeneration. Neuron. 43:57–67. 2004. View Article : Google Scholar : PubMed/NCBI

22 

Herdegen T and Leah JD: Inducible and constitutive transcription factors in the mammalian nervous system: control of gene expression by Jun, Fos and Krox and CREB/ATF proteins. Brain Res Brain Res Rev. 28:370–490. 1998. View Article : Google Scholar : PubMed/NCBI

23 

Rizo J and Südhof TC: Snares and Munc18 in synaptic vesicle fusion. Nat Rev Neurosci. 3:641–653. 2002. View Article : Google Scholar : PubMed/NCBI

24 

Wang W, Wang F, Liu J, et al: Snap25 ameliorates sensory deficit in rats with spinal cord transection. Mol Neurobiol. 50:290–304. 2014. View Article : Google Scholar : PubMed/NCBI

25 

Bowman GD, O’Donnell M and Kuriyan J: Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature. 429:724–730. 2004. View Article : Google Scholar : PubMed/NCBI

26 

Leonardi E, Girlando S, Serio G, et al: PCNA and Ki67 expression in breast carcinoma: correlations with clinical and biological variables. J Clin Pathol. 45:416–419. 1992. View Article : Google Scholar : PubMed/NCBI

27 

Zhang G, Gibbs E, Kelman Z, O’Donnell M and Hurwitz J: Studies on the interactions between human replication factor C and human proliferating cell nuclear antigen. Proc Natl Acad Sci USA. 96:1869–1874. 1999. View Article : Google Scholar : PubMed/NCBI

28 

Ding T, Wen H, Wei H, et al: Increased expression of TBP/TFIID after spinal cord injury in adult rats. Cell Mol Neurobiol. 34:669–677. 2014. View Article : Google Scholar : PubMed/NCBI

29 

Eide T, Taskén KA, Carlson C, et al: Protein kinase A-anchoring protein AKAP95 interacts with MCM2, a regulator of DNA replication. J Biol Chem. 278:26750–26756. 2003. View Article : Google Scholar : PubMed/NCBI

30 

Carpentieri F, De Felice M, De Falco M, Rossi M and Pisani FM: Physical and functional interaction between the mini-chromosome maintenance-like DNA helicase and the single-stranded DNA binding protein from the crenarchaeon Sulfolobus solfataricus. J Biol Chem. 277:12118–12127. 2002. View Article : Google Scholar : PubMed/NCBI

31 

Bauman WA, Spungen AM, Zhong YG, Rothstein JL, Petry C and Gordon SK: Depressed serum high density lipoprotein cholesterol levels in veterans with spinal cord injury. Paraplegia. 30:697–703. 1992. View Article : Google Scholar : PubMed/NCBI

32 

Myers J, Lee M and Kiratli J: Cardiovascular disease in spinal cord injury: an overview of prevalence, risk, evaluation and management. Am J Phys Med Rehabil. 86:142–152. 2007. View Article : Google Scholar : PubMed/NCBI

33 

Fernández-Hernando C, Suárez Y, Rayner KJ and Moore KJ: MicroRNAs in lipid metabolism. Curr Opin Lipidol. 22:86–92. 2011. View Article : Google Scholar :

34 

Rotllan N and Fernández-Hernando C: MicroRNA regulation of cholesterol metabolism. Cholesterol. 2012:82012. View Article : Google Scholar

35 

Benoit C, Ould-Hamouda H, Crepin D, Gertler A, Amar L and Taouis M: Early leptin blockade predisposes fat-fed rats to overweight and modifies hypothalamic microRNAs. J Endocrinol. 218:35–47. 2013. View Article : Google Scholar : PubMed/NCBI

36 

Hoppe KL and Francone OL: Binding and functional effects of transcription factors Sp1 and Sp3 on the proximal human lecithin: cholesterol acyltransferase promoter. J Lipid Res. 39:969–977. 1998.PubMed/NCBI

37 

Uveges TE, Shan Y, Kramer BE, Wight DC and Parysek LM: Intron 1 is required for cell type-specific, but not injury-responsive, peripherin gene expression. J Neurosci. 22:7959–7967. 2002.PubMed/NCBI

38 

Tetsu O and McCormick F: β-catenin regulates expression of cyclin D1 in colon carcinoma cells. Nature. 398:422–426. 1999. View Article : Google Scholar : PubMed/NCBI

39 

Fehrenschild D, Galli U, Breiden B, et al: TCF/Lef1-mediated control of lipid metabolism regulates skin barrier function. J Invest Dermatol. 132:337–345. 2012. View Article : Google Scholar

40 

Xu D, Zhao W, Pan G, et al: Expression of Nemo-like kinase after spinal cord injury in rats. J Mol Neurosci. 52:410–418. 2014. View Article : Google Scholar : PubMed/NCBI

41 

Fancy SP, Harrington EP, Baranzini SE, et al: Parallel states of pathological Wnt signaling in neonatal brain injury and colon cancer. Nat Neurosci. 17:506–512. 2014. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Chen G, Fang X and Yu M: Regulation of gene expression in rats with spinal cord injury based on microarray data. Mol Med Rep 12: 2465-2472, 2015.
APA
Chen, G., Fang, X., & Yu, M. (2015). Regulation of gene expression in rats with spinal cord injury based on microarray data. Molecular Medicine Reports, 12, 2465-2472. https://doi.org/10.3892/mmr.2015.3670
MLA
Chen, G., Fang, X., Yu, M."Regulation of gene expression in rats with spinal cord injury based on microarray data". Molecular Medicine Reports 12.2 (2015): 2465-2472.
Chicago
Chen, G., Fang, X., Yu, M."Regulation of gene expression in rats with spinal cord injury based on microarray data". Molecular Medicine Reports 12, no. 2 (2015): 2465-2472. https://doi.org/10.3892/mmr.2015.3670
Copy and paste a formatted citation
x
Spandidos Publications style
Chen G, Fang X and Yu M: Regulation of gene expression in rats with spinal cord injury based on microarray data. Mol Med Rep 12: 2465-2472, 2015.
APA
Chen, G., Fang, X., & Yu, M. (2015). Regulation of gene expression in rats with spinal cord injury based on microarray data. Molecular Medicine Reports, 12, 2465-2472. https://doi.org/10.3892/mmr.2015.3670
MLA
Chen, G., Fang, X., Yu, M."Regulation of gene expression in rats with spinal cord injury based on microarray data". Molecular Medicine Reports 12.2 (2015): 2465-2472.
Chicago
Chen, G., Fang, X., Yu, M."Regulation of gene expression in rats with spinal cord injury based on microarray data". Molecular Medicine Reports 12, no. 2 (2015): 2465-2472. https://doi.org/10.3892/mmr.2015.3670
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