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Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration

  • Authors:
    • Zhigang Qu
    • Zhe Quan
    • Qi Zhang
    • Zhenyu Wang
    • Qingxu Song
    • Xinming Zhuang
    • Changfeng Fu
    • Feng Xu
    • Yadong Liu
    • Yuanyi Wang
    • Zheng Wang
    • Yi Liu
  • View Affiliations / Copyright

    Affiliations: Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China, Department of Neurosurgery, Shanghai Fengxian District Central Hospital, Shanghai 201400, P.R. China, Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
    Copyright: © Qu et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1504-1512
    |
    Published online on: June 5, 2018
       https://doi.org/10.3892/mmr.2018.9128
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Abstract

The present study aimed to identify novel intervertebral disc degeneration (IDD)‑associated long noncoding (lnc)RNAs and genes. The lncRNA and mRNA microarray dataset GSE56081 was downloaded from the Gene Expression Omnibus database and included 5 samples from patients with degenerative lumbar nucleus pulposus and 5 normal controls. Differentially expressed lncRNAs or differentially expressed genes (DEGs) were identified and co‑expression network analysis was performed followed by functional analysis for genes in the network. Additionally, a microRNA (miRNA)‑lncRNA‑mRNA competing endogenous RNA (ceRNA) regulatory network was constructed based on DEGs and lncRNAs in the co‑expression network. Furthermore, a literature search was performed to identify specific miRNAs that had been previously associated with IDD and a specific miRNA‑associated ceRNA network was extracted from the co‑expression network. A total of 967 genes and 137 lncRNAs were differentially expressed between IDD samples and controls. A co‑expression network was constructed and contained 39 differentially expressed lncRNAs and 209 DEGs, which were primarily involved in ʻskeletal system developmentʼ, ʻresponse to mechanical stimulusʼ and ʻbone developmentʼ. Furthermore, a ceRNA network was established, including 79 miRNAs, 9 downregulated lncRNAs and 148 DEGs. The identified miRNAs included a previously reported disease‑associated miRNA, hsa‑miR‑140. The present study demonstrated that hsa‑miR‑140 was regulated by three lncRNAs in the hsa‑miR‑140‑associated ceRNA network, including KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1), OIP5 antisense RNA 1 (OIP5‑AS1) and UGDH antisense RNA 1 (UGDH‑AS1). KCNQ1OT1 was co‑expressed with neurochondrin (NCDN) and lon peptidase 2, peroxisomal. In addition, the lncRNAs OIP5‑AS1 and UGDH‑AS1 targeted several overlapping co‑expressed genes, including forkhead box F1 (FOXF1) and polycystin 1, transient receptor potential channel interacting (PKD1). Therefore, KCNQ1OT1 may regulate the expression of NCDN, and OIP5‑AS1 and UGDH‑AS1 may affect the expression of FOXF1 and PKD1 in IDD. Further experiments are required to validate the results of the present study, which may provide valuable insights into the identification of novel biomarkers associated with IDD.
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Copy and paste a formatted citation
Spandidos Publications style
Qu Z, Quan Z, Zhang Q, Wang Z, Song Q, Zhuang X, Fu C, Xu F, Liu Y, Wang Y, Wang Y, et al: Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration. Mol Med Rep 18: 1504-1512, 2018.
APA
Qu, Z., Quan, Z., Zhang, Q., Wang, Z., Song, Q., Zhuang, X. ... Liu, Y. (2018). Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration. Molecular Medicine Reports, 18, 1504-1512. https://doi.org/10.3892/mmr.2018.9128
MLA
Qu, Z., Quan, Z., Zhang, Q., Wang, Z., Song, Q., Zhuang, X., Fu, C., Xu, F., Liu, Y., Wang, Y., Wang, Z., Liu, Y."Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration". Molecular Medicine Reports 18.2 (2018): 1504-1512.
Chicago
Qu, Z., Quan, Z., Zhang, Q., Wang, Z., Song, Q., Zhuang, X., Fu, C., Xu, F., Liu, Y., Wang, Y., Wang, Z., Liu, Y."Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration". Molecular Medicine Reports 18, no. 2 (2018): 1504-1512. https://doi.org/10.3892/mmr.2018.9128
Copy and paste a formatted citation
x
Spandidos Publications style
Qu Z, Quan Z, Zhang Q, Wang Z, Song Q, Zhuang X, Fu C, Xu F, Liu Y, Wang Y, Wang Y, et al: Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration. Mol Med Rep 18: 1504-1512, 2018.
APA
Qu, Z., Quan, Z., Zhang, Q., Wang, Z., Song, Q., Zhuang, X. ... Liu, Y. (2018). Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration. Molecular Medicine Reports, 18, 1504-1512. https://doi.org/10.3892/mmr.2018.9128
MLA
Qu, Z., Quan, Z., Zhang, Q., Wang, Z., Song, Q., Zhuang, X., Fu, C., Xu, F., Liu, Y., Wang, Y., Wang, Z., Liu, Y."Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration". Molecular Medicine Reports 18.2 (2018): 1504-1512.
Chicago
Qu, Z., Quan, Z., Zhang, Q., Wang, Z., Song, Q., Zhuang, X., Fu, C., Xu, F., Liu, Y., Wang, Y., Wang, Z., Liu, Y."Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration". Molecular Medicine Reports 18, no. 2 (2018): 1504-1512. https://doi.org/10.3892/mmr.2018.9128
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