Next-generation sequencing reveals hsa_circ_0058092 being a potential oncogene candidate involved in gastric cancer

• Published in: Gene Vol. 726; p. 144176
• Main Authors: Bu, Xuefeng, Zhang, Xuanfeng, Luan, Wenkang, Zhang, Riting, Zhang, Yao, Zhang, Anwei, Yan, Yulan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 05.02.2020
• Subjects: Bioinformatics; Biomarkers, Tumor - genetics; Circular RNA; Computational Biology - methods; Female; Gastric cancer; High-Throughput Nucleotide Sequencing - methods; Hsa_circ_0058092; Humans; Male; MicroRNAs - genetics; Middle Aged; Next generation sequencing; Oncogenes - genetics; RNA, Circular - genetics; RNA, Untranslated - genetics; Sialoglycoproteins - genetics; Stomach Neoplasms - genetics; Transcription Factors - genetics; Transcription, Genetic - genetics; ceRNA; circRNA; RNA-seq; Hsa_circ_0058092; PODXL; RT-PCR; miRNA; Circular RNA; mRNA; Gastric cancer; Next generation sequencing; Bioinformatics
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2019.144176

•We detected the expression profile of circRNA in gastric cancer by RNA-seq technique.•We used bioinformatics techniques to analyze and screen the expression profile features.•We identified hsa_circ_0058092 as a potential oncogene in combination with clinical features for further study. Gastric cancer is a serious problem for human health. As part of noncoding RNA, circular RNA (circRNA) plays a key role in the occurrence and development of malignant tumor. We used next generation sequencing technology to detect circRNA expression profiles in 5 paired human gastric cancer tissues. Then, bioinformatics analysis was carried out to analyze the function of dysregulated circRNAs. Hsa_circ_0058092 was selected as the object of follow-up analysis. After using the Cistrome DB dataset the data was used to predict specific transcription factors of hsa_circ_0058092. The relationship between hsa_circ_0058092 and PODXL was further validated using RT-PCR and immunohistochemical techniques. Survival data were collected using a Kaplan-Meier analysis of hsa_circ_0058092. We identified 319 aberrantly expressed circRNAs, Hsa_circ_0058092 was selected for our studies. Functional analysis of hsa_circ_0058092 revealed that it was related to metabolic processes. The prediction results suggested that hsa_circ_0058092 has a relationship with hsa-miR-4269 which could specifically bind to the PODXL sequence. Transcription factor CEBPB may regulate the transcription process of hsa_circ_0058092. The expression of hsa_circ_0058092 was positively correlated with PODXL expression. Immunohistochemical analysis of PODXL showed that the expression of PODXL protein in cancer tissues is higher than that in adjacent tissues. Kaplan-Meier analysis suggested that hsa_circ_0058092 was associated with survival of gastric cancer patients. All of these results showed that hsa_circ_0058092 was a potential oncogene.