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    The bioinformatic approach reveals the SNP-mediated lncRNA NONHSAT017462.2 and hsa-miR-6887-3P interaction with the potential impact on the ESCC risk

  • Mahsa Shirani,1 Ghazal Jamalifar ,2 Setayesh Zarei,3 Shadi Omidghaemi,4 Mansoureh Azadeh,5,*
    1. Zist Fanavary Novin Institute, Isfahan 14115‑111, Iran
    2. Zist Fanavary Novin Institute, Isfahan 14115‑111, Iran
    3. Zist Fanavary Novin Institute, Isfahan 14115‑111, Iran
    4. Zist Fanavary Novin Institute, Isfahan 14115‑111, Iran
    5. Zist Fanavary Novin Institute, Isfahan 14115‑111, Iran


  • Introduction: Esophageal cancer is the sixth leading cause of death from cancer and one of the most minor studied cancers worldwide. This study's objective was to explore the regulatory network constituted by long noncoding RNA (lncRNA), miRNA, and mRNA (MMP-9) in ESCC.
  • Methods: We evaluated the significance of gene expression in ESCC by analyzing raw data from the Gene Expression Omnibus (GEO) database with GEO2R and also we used DAVID, KEGG pathway, miRWalkv.3, and Venn diagram. Eventually, we illustrate the effective SNP between lncRNA-miRNA with the LncRNASNP2 database.
  • Results: We chose gene expression datasets of GSE161533 from the GEO database to find out a fundamental gene and their interaction network during the progression and metastasis of ESCC. Matrix metalloproteinase-9 (MMP-9) separately extracted to undertake KEGG pathway (cancer signaling pathway)enrichment analysis using DAVID. We used miRWalkv.3 and LncRNASNP2 online databases to search for the targets of gene miRNAs. To summarize, we compared the overlap between two lists of miRNA identifiers by using area-proportional Venn diagrams. Using the LncRNASNP2 database, we found the SNP rs763141577 in hsa-miR-6887-3P target sites on lncRNA NONHSAT017462.2 influence the miRNA–lncRNA interactions, thereby alter their functions. These findings allow us to infer that it is the changes of the related functions and pathways that caused the tumorigenesis of ESCC
  • Conclusion: The study demonstrates that SNP rs763141577(T/C) in lncRNA NONHSAT017462.2SNP provides an alternate binding site for microRNA hsa-miR-6887-3p which affects the overexpression of the MMP-9 gene plays an important role in esophageal cancer metastasis.
  • Keywords: esophageal squamous cell cancer, MMP-9, lncRNASNP2, SNP, lncRNA, hsa-miR-6887-3P0