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.

CHPF promotes gastric cancer tumorigenesis through the activation of E2F1

“…Therefore, enhancing the effects of chemotherapy by seeking new specific therapeutic targets is important for improving the prognosis of gastric cancer. Recently, a number of studies demonstrated that molecular biology and gene technology advancements such as high-throughput sequencing have offered new opportunities to research the molecular mechanisms underlying gastric cancer, and various novel targets have been discovered [18][19][20][21]. For example, Liu et al noted that a potential tumor promoter, NETO2, was upregulated in gastric cancer tissues and could promote the invasion and metastasis of gastric cancer through TNFRSF12Amediated activation of the PI3K/AKT/NF-κB/Snail axis [22].…”

Genome-wide transcriptome profiling of ex-vivo precision-cut slices from human pancreatic ductal adenocarcinoma

“…Annotated transcripts are used to study differentially expressed genes while non-mapped reads can be analyzed to study fusion genes or viral transcripts. Transcriptome sequencing data can also be used to define novel transcripts leading to discovery of neoantigens [13][14][15] .…”

Comprehensive analysis of prognostic genes in gastric cancer

“…In the present work, comprehensive survival analysis and Cox regression analysis found that upregulation of DPT and LRFN4 correlated with good prognosis in gastric cancer patients. DPT is significantly downregulated in gastric cancer tissues [ 48 ], and it may contribute to oral cancer metastasis [ 49 ]. DPT is also involved in the inhibition of proliferation of keratinocytes, osteosarcoma cells, and papillary thyroid carcinoma cells in mice [ 50 ].…”