Transcriptome profiling of cancer tissues in Chinese patients with gastric cancer by high-throughput sequencing

Abstract

Gastric cancer (GC) is the fifth most common malignancy and the third leading cause of cancer-associated mortality worldwide. Therefore, there is a requirement to identify sufficiently sensitive biomarkers for GC. Genome-wide screening of transcriptome dysregulation among cancerous and normal tissues may provide insights into the underlying molecular mechanisms of GC initiation and progression. At present, high-throughput sequencing techniques have begun to innovate biomedical studies. The RNA-seq method has become an advanced approach in medical studies; it is capable of the accurate detection of gene expression levels. The present study used RNA-seq to evaluate the transcriptional changes between tumor and matched normal samples, and these changes were confirmed by differentially expressed genes in larger samples using the results of sequencing. In total, the upregulation of 28 mRNAs and downregulation of 22 mRNAs between cancerous and normal tissue samples were identified. Subsequently, five differentially expressed genes were selected to verify in large samples and cadherin-1 (CDH1) was selected to detect protein expression levels. The results revealed that CDH1, cyclooxygenase-2 and matrix metalloproteinase genes had significantly higher expression levels, whereas the expression levels of dermatopontin and transforming growth factor β receptor 2 were decreased in GC samples. In particular, CDH1 demonstrated a 36-fold higher expression level in cancer tissues. The western blotting results also revealed high CDH1 expression levels in the validation cohorts. Furthermore, these genes are highly enriched in certain gene ontology categories, including the digestive system process, secretion and digestion. The present study provided a preliminary survey of the transcriptome of Chinese patients with GC, which may improve the detection of aberrant gene expression in GC and the understanding of the mechanisms of tumorigenesis.

Keywords: RNA-seq; differentially expressed gene; gastric cancer; gene ontology.

Figure 1.

Heat map and cluster analysis of the 50 differentially expressed mRNAs in control and gastric cancer tissue samples. Red represents high relative expression levels; Green represents low relative expression levels.

Figure 2.

(A-E) Validation of differentially expressed mRNA in larger cohorts (GC, n=30; control, n=30). The expression levels of five mRNAs in case and control subjects were determined by RT-qPCR. β-actin was used as a normalization control. All reactions were based on three independent repetitions. RT-qPCR, reverse transcription-quantitative polymerase chain reaction; CDH1, cadherin-1; COX-2, cyclooxygenase 2; MMP-9, matrix metalloproteinase-9; DPT, dermatopontin; TGFBR2, transforming growth factor β receptor II. ***P<0.001 compared with the control group.

Figure 3.

Quantification by western blot analysis of the CDH1 protein expression levels in control and case samples (GC, n=30; control, n=30). CDH1, cadherin-1. ***P<0.001 compared with the control group.