Screening and bioinformatics analysis of circular RNA expression profiles in hepatitis B-related hepatocellular carcinoma
Screening and bioinformatics analysis of circular RNA expression profiles in hepatitis B-related hepatocellular carcinoma
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DOI：
10.3233/cbm-170910
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发表时间：
2018-01-01
影响因子：
3.1
通讯作者：
Ding, Hui-Guo
中科院分区：
文献类型：
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作者：
Wang, Shanshan;Cui, Shichang;Ding, Hui-Guo
背景：环状RNA在肝细胞癌（HCC）的发生、发展中起重要作用。然而，在B型肝炎病毒（HBV）相关的肝癌中circRNA的表达谱仍有待研究。对3例患者的3例HCC和3对相邻的非肿瘤（NT）组织进行微阵列分析。使用10对HCC组织通过定量实时逆转录PCR（qRT-PCR）验证从微阵列数据获得的鉴定的上调和下调的circRNA。分离总RNA并用RNase R处理以去除线性RNA，然后与阵列杂交以筛选circRNA。结果：基于芯片数据，我们发现24个circRNA在肝癌组织中表达上调，23个circRNA表达下调（倍数变化>= 2.0，P < 0.05），其中24个表达上调，23个表达下调。其中，通过qRT-PCR验证了6个候选circRNA（hsa_circRNA_102814、100381、103489、101764、100327和103361）。其中，hsa_circRNA 100381、103489上调和101764下调在10个验证HCC组织中被发现具有显著差异。与NT样品相比，HCC中的circRNA簇异常表达。CircRNA_101764是circRNA/microRNA共表达网络中最大的节点，尤其是与hsa-miR-181家族共表达，在细胞网络中起着重要作用。对circRNA/miRNA相互作用的注释表明，circRNA的生物学效应可能通过结合miRNA来实现。GO分析表明，许多靶基因参与了生物学过程、细胞组分和分子功能。KEGG通路分析发现有近30个靶基因富集，其中PI 3 K-Akt信号通路参与的基因数量最多。结论：本研究全面探讨了HBV相关HCC中差异表达的circRNA的表达，结果提示circRNA_101764可能在HCC的发生发展中起重要作用。
BACKGROUND: Circular RNAs (circRNAs) play an important role in pathogenesis and development of hepatocellular carcinoma (HCC). However, circRNA expression profiles in hepatitis B Virus (HBV)-related HCC remain to be studied.METHODS: Total 13 HBV-related HCC patients were enrolled for study. Three HCC and 3 paired adjacent non-tumorous (NT) tissues from 3 patients were performed for microarray. Ten pairs of HCC tissues were used to verify the identified up-regulated and down-regulated circRNAs obtained from the microarray data by quantitative real-time reverse transcription PCR (qRT-PCR). Total RNA was isolated and treated with Rnase R to remove linear RNA, then hybridized to the array to screen for circRNAs. Bioinformatics analyses including clustering, differential expression, annotation of circRNA/microRNA (miRNA) interactions, Go analysis and KEGG pathway analysis, were performed.RESULTS: Based on the microarray data, we found significantly up-regulation of 24 circRNAs and down-regulation of 23 circRNAs in the HCC samples compared to NT samples (fold change >= 2.0 and P < 0.05). Of them, 6 candidate circRNAs (hsa_circRNA_102814, 100381, 103489, 101764, 100327, and 103361) were verified by qRT-PCR. Of them, hsa_circRNA 100381, 103489 up-regulation and 101764 down-regulation were found to be significantly different in the 10 validation HCC tissue. Clusters of circRNAs were aberrantly expressed in HCC compared with NT samples. CircRNA_101764 was the largest nodes in circRNA/microRNA co-expression network, especially co-expression with hsa-miR-181 family, which plays an important role in cell network. Annotation of circRNA/miRNA interactions indicated that the biological effects of circRNA may be achieved by binding of miRNAs. GO analysis revealed that numerous target genes were involved in the biological processes, cellular component and molecular function. There was nearly 30 target genes enrichment on KEGG pathways analysis, PI3K-Akt signaling pathway which the most number of genes involved.CONCLUSION: In this study, we comprehensively explored the expression of differentially expressed circRNAs in HBV-related HCC, and our results indicate that circRNA_101764 may play an important role in the development of HCC.