Integrative analysis of the gastric cancer long non-coding RNA-associated competing endogenous RNA network

Abstract

Gastric cancer (GC) is a common type of cancer, and identification of novel diagnostic biomarkers associated with this disease is important. The present study aimed to identify novel diagnostic biomarkers associated with the prognosis of GC, using an integrated bioinformatics approach. Differentially expressed long non-coding RNAs (lncRNAs) associated with GC were identified using Gene Expression Omnibus datasets (GSE58828, GSE72305 and GSE99416) and The Cancer Genome Atlas database. A competing endogenous RNA network that incorporated five lncRNAs [long intergenic non-protein coding RNA 501 (LINC00501), LINC00365, SOX21 antisense divergent transcript 1 (SOX21-AS1), GK intronic transcript 1 (GK-IT1) and DLEU7 antisense RNA 1 (DLEU7-AS1)], 29 microRNAs and 114 mRNAs was constructed. Gene Ontology and protein-protein interaction network analyses revealed that these lncRNAs may be involved in 'biological regulation', 'metabolic process', 'cell communication', 'developmental process', 'cell proliferation', 'reproduction' and the 'cell cycle'. The results of receiver operating characteristic curve analysis demonstrated that LINC00501 (AUC=0.819), LINC00365 (AUC=0.580), SOX21-AS1 (AUC=0.736), GK-IT1 (AUC=0.823) and DLEU7-AS1 (AUC=0.932) had the potential to become valuable diagnostic biomarkers for GC. Associations with clinicopathological characteristics demonstrated that LINC00501 expression was significantly associated with sex (P=0.015) and tumor grade (P=0.022). Furthermore, LINC00365 expression was significantly associated with lymph node metastasis (P=0.025). Gene set enrichment analysis revealed that LINC00501, LINC00365 and SOX21-AS1 were enriched in signaling pathways associated with GC. Reverse transcription-quantitative PCR analysis demonstrated that LINC00501 expression (P=0.043) was significantly upregulated in GC tissues, whereas the expression levels of LINC00365 (P=0.033) and SOX21-AS1 (P=0.037) were significantly downregulated in GC tissues. Taken together, the results of the present study suggest that LINC00501, LINC00365, SOX21-AS1, GK-IT1 and DLEU7-AS1 may be used as novel diagnostic biomarkers for GC, and may be functionally associated with GC development and progression.

Keywords: Gene Expression Omnibus; The Cancer Genome Atlas; competing endogenous RNA; gastric cancer; long non-coding RNA.

Figure 1.

Differentially expressed gastric cancer-related genes in the Gene Expression Omnibus database. Red dots represent upregulated genes (adjusted P<0.05 and log FC>1), green dots represent downregulated genes (adjusted P<0.05 and log FC<-1); and black dots represent genes that were not identified to be significantly differentially expressed. FC, fold-change; adj.P.Val, adjusted P-value.

Figure 2.

Top 20 gastric cancer-related differentially expressed genes in the Gene Expression Omnibus database. (A) Differentially expressed long non-coding RNAs. (B) Differentially expressed mRNAs. Red represents upregulated genes, while green represents downregulated genes. The number indicates the fold-change in each dataset.

Figure 3.

Competing endogenous RNA network. Red arrows represent long non-coding RNAs, green diamonds represent microRNAs and blue circles represent mRNAs. miR, microRNAs.

Figure 4.

Functional enrichment analysis of differentially expressed genes. Gene Ontology analysis of significantly enriched (A) biological processes, (B) cellular components and (C) molecular functions. (D) Protein-protein interaction network.

Figure 5.

ROC curve analysis of the five long non-coding RNAs. The red line represents the sensitivity curve, while the black line represents the identifying line. ROC, receiver operating characteristic; AUC, area under the curve; LINC00, long intergenic non-protein coding RNA; SOX21-AS1, SOX21 antisense divergent transcript 1; GK-IT1, GK intronic transcript 1; DLEU7-AS1, DLEU7 antisense RNA 1.

Figure 6.

Associations between long non-coding RNAs and clinicopathological characteristics. Association between LINC00501 expression and (A) sex and (B) tumor grade. (C) Association between LINC00365 expression and lymph node metastasis. LINC00, long intergenic non-protein coding RNA.

Figure 7.

GSEA pathways of the long non-coding RNAs. GSEA pathways of (A) LINC00501, (B) LINC00365 and (C) SOX21-AS1. GSEA, gene set enrichment analysis; LINC00, long intergenic non-protein coding RNA; SOX21-AS1, SOX21 antisense divergent transcript 1.

Figure 8.

Reverse transcription-quantitative PCR-based validation of the expression levels of five long non-coding RNAs in gastric cancer tissues. LINC00, long intergenic non-protein coding RNA; DLEU7-AS1, DLEU7 antisense RNA 1; GK-IT1, GK intronic transcript 1; SOX21-AS1, SOX21 antisense divergent transcript 1.