全转录组分析揭示结直肠癌中 hsa_circ_0001955/hsa_circ_0000977 介导的 miRNA-mRNA 调控子网络。
Whole-transcriptome analysis reveals a potential hsa_circ_0001955/hsa_circ_0000977-mediated miRNA-mRNA regulatory sub-network in colorectal cancer.
机构信息
Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China.
Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.
出版信息
Aging (Albany NY). 2020 Mar 28;12(6):5259-5279. doi: 10.18632/aging.102945.
BACKGROUND
Circular RNAs (circRNAs), a novel class of non-coding RNAs, have been found to act as microRNA (miRNA) sponges and thus play key roles in biological processes and pathogenesis. However, studies regarding circRNAs in colorectal cancer (CRC) remain inadequate.
RESULTS
By differential expression analysis, 10 candidate circRNAs (6 upregulated and 4 downregulated circRNAs) were chosen. 9 of 10 circRNAs were available on CSCD and their structure showed the binding potential of miRNA. Intersection analysis revealed that miR-145-5p, miR-3127-5p, miR-761, miR-4766-3p, miR-135a-5p, miR-135b-5p, miR-374a-3p and miR-330-3p were 8 miRNAs with the most potential in binding circRNAs. Further expression validation and correlation analysis demonstrated hsa_circ_0001955/miR-145-5p and hsa_circ_0000977/miR-135b-5p axes as key pathways in CRC. Subsequently, target gene prediction, differential expression analysis, intersection analysis and correlation analysis showed that CDK6, MMP12 and RAB3IP were the three potential downstream targets of hsa_circ_0001955/miR-145-5p axis and FOXO1, MBNL1, MEF2C, RECK, PPM1E, TTLL7 and PCP4L1 were the seven potential downstream targets of hsa_circ_0000977/miR-135b-5p axis in CRC. Finally, we also confirmed that expression of hsa_circ_0001955 or hsa_circ_0000977 was significantly positively correlated with their individual targets in CRC.
CONCLUSIONS
In the present work, we constructed a potential hsa_circ_0001955/hsa_circ_0000977-mediated circRNA-miRNA-mRNA regulatory network in CRC by a series of analysis and experimental validation.
METHODS
Whole-transcriptome microarrays from CRC and matched normal samples were obtained from GEO. The structure of circRNA was identified by CSCD. starBase and miRNet were successively used to predict miRNA of circRNA and target gene of miRNA. Expression correlation between RNA-RNA interactions was assessed using GEO and TCGA data. Finally, a potential circRNA-miRNA-mRNA network was established based on competing endogenous RNA (ceRNA) hypothesis.
背景
环状 RNA（circRNA）作为一类新的非编码 RNA，已被发现可作为 microRNA（miRNA）的海绵，从而在生物学过程和发病机制中发挥关键作用。然而，关于结直肠癌（CRC）中的 circRNA 的研究仍然不足。
结果
通过差异表达分析，选择了 10 个候选 circRNA（6 个上调和 4 个下调 circRNA）。10 个 circRNA 中有 9 个可在 CSCD 上获得，其结构显示出与 miRNA 的结合潜力。交集分析显示，miR-145-5p、miR-3127-5p、miR-761、miR-4766-3p、miR-135a-5p、miR-135b-5p、miR-374a-3p 和 miR-330-3p 是与 circRNA 结合最具潜力的 8 个 miRNA。进一步的表达验证和相关性分析表明，hsa_circ_0001955/miR-145-5p 和 hsa_circ_0000977/miR-135b-5p 轴是 CRC 中的关键途径。随后，靶基因预测、差异表达分析、交集分析和相关性分析表明，CDK6、MMP12 和 RAB3IP 是 hsa_circ_0001955/miR-145-5p 轴的三个潜在下游靶标，而 FOXO1、MBNL1、MEF2C、RECK、PPM1E、TTLL7 和 PCP4L1 是 hsa_circ_0000977/miR-135b-5p 轴在 CRC 中的七个潜在下游靶标。最后，我们还证实 hsa_circ_0001955 或 hsa_circ_0000977 的表达与 CRC 中各自的靶标呈显著正相关。
结论
在本研究中，我们通过一系列分析和实验验证，构建了一个潜在的 hsa_circ_0001955/hsa_circ_0000977 介导的 CRC 环状 RNA-miRNA-mRNA 调控网络。
方法
从 GEO 中获得 CRC 和匹配正常样本的全转录组微阵列。circRNA 的结构通过 CSCD 确定。starBase 和 miRNet 被依次用于预测 circRNA 的 miRNA 和 miRNA 的靶基因。使用 GEO 和 TCGA 数据评估 RNA-RNA 相互作用之间的表达相关性。最后，基于竞争性内源 RNA（ceRNA）假说建立了一个潜在的 circRNA-miRNA-mRNA 网络。
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