In Silico Analysis of Biomarker Potentials of miRNA-Mediated ceRNAs in Gastric Neoplasms

Year 2019, Volume: 5 Issue: 2, 106 - 119, 28.08.2019

Diler Us Altay , Sercan Ergün

https://doi.org/10.19127/mbsjohs.570444

Abstract

Objectives: The objective of this study is to define novel biomarkers for gastric neoplasm (GN) via in silico analysis that takes GN-specific miRNAs, finds their combinatorial target genes (potential ceRNAs), selects ones containing  T-UCR among them and potentiates their relevance with GN. Based on this study we can plan new in vitro and in vivo studies.

Methods: Four miRNAs of which clinical relevances with GN were
proved experimentally were exported via mirTarbase. Using the ComiR database,
1008 genes targeted by these 4 miRNAs simultaneously were identified. Genes
containing T-UCR and showing potential ceRNA activity were extracted. Among
GN-associated ceRNAs including T-UCR, we identified genes with significant
expression differences between GN and normal stomach tissue using the GEPIA
database. The statistical evaluation of the association of NFAT5 and CLK3 genes with
GN was performed by Spearman correlation test in GEPIA database.

Results:
GN-associated ceRNAs cross-matching with genes including T-UCR in their exonic
regions were NFAT5 and CLK3. We identified genes with significant expression differences between
GN and normal stomach tissues among GN-associated ceRNAs including T-UCR.
According to this analysis, only NFAT5 gene
was significantly higher expressed in GN than in normal stomach tissue while
the other didn’t show any significant differential expression pattern. NFAT5 and CLK3 genes were found to be significantly correlated with GN
(p<0.001; R=0.22)

Conclusion:
All in all, this is the study associating NFAT5
gene with GN for the first time and giving it ongogenic potential for GN.
Still, larger and more comprehensive studies are needed on this issue.

Keywords

Gastric neoplasms, miRNA, ceRNA, T-UCR, In silico analysis

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