基于生物信息学和实验验证鉴定胆囊癌侵袭转移相关 miRNA。
Identification of invasion-metastasis associated MiRNAs in gallbladder cancer by bioinformatics and experimental validation.
机构信息
Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University, No. 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.
Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.
出版信息
J Transl Med. 2022 Apr 28;20(1):188. doi: 10.1186/s12967-022-03394-8.
BACKGROUND
Recent studies exploring the roles of invasion-metastasis associated miRNAs in gallbladder cancer (GBC) are limited. In the study, we aimed to identify the invasion-metastasis associated miRNAs in GBC by bioinformatics and experimental validation.
METHODS
MiRNAs of different expression were identified by comparing GBC tumor samples with different survival from Gene Expression Omnibus database. MiRTarBase was used for identifying the potential target genes of miRNAs. Then, we performed Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. And miRNA-gene and protein-protein interaction (PPI) network were constructed for hub genes evaluation. We further explored and compared miR-642a-3p and miR-145-5p expression in both The Cancer Genome Atlas database and our hospital data. Finally, quantitative real-time PCR, wound healing assay, and Transwell assay were conducted to validate the invasion-metastasis associated miRNAs in GBC.
RESULTS
In GSE104165 database, 25 up-regulated and 97 down-regulated miRNAs were detected with significantly different expression in GBC tumor samples. Then, 477 potential target genes were identified from the 2 most up-regulated miRNAs (miR-4430 and miR-642a-3p) and 268 genes from the 2 most down-regulated miRNAs (miR-451a and miR-145-5p). After GO and KEGG analysis, mTOR and PI3K-Akt signaling pathways were found associated with the potential target genes. Based on PPI network, the top 10 highest degree hub nodes were selected for hub genes. Furthermore, the miRNA-hub gene network showed significant miR-642a-3p up-regulation and miR-145-5p down-regulation in both GBC tissues and cell lines. In the experimental validation, miR-145-5p up-regulation and miR-642a-3p down-regulation were confirmed to suppress GBC invasion and metastasis.
CONCLUSIONS
MiR-642a-3p and miR-145-5p were identified as invasion-metastasis associated miRNAs via bioinformatics and experimental validation, and both up-regulation of miR-642a-3p and down-regulation of miR-145-5p would be served as novel treatment options for GBC in the future.
背景
最近的研究探索了侵袭转移相关 miRNA 在胆囊癌（GBC）中的作用，但这些研究仍很有限。本研究通过生物信息学和实验验证来鉴定 GBC 中与侵袭转移相关的 miRNA。
方法
通过比较基因表达综合数据库中不同生存的 GBC 肿瘤样本，鉴定出不同表达的 miRNA。使用 MiRTarBase 来鉴定 miRNA 的潜在靶基因。然后，我们进行了基因本体论（GO）分析和京都基因与基因组百科全书（KEGG）通路富集分析。构建 miRNA-基因和蛋白质-蛋白质相互作用（PPI）网络，以评估关键基因。我们进一步在 The Cancer Genome Atlas 数据库和我院数据中探索和比较 miR-642a-3p 和 miR-145-5p 的表达。最后，进行定量实时 PCR、划痕愈合实验和 Transwell 实验以验证 GBC 中的侵袭转移相关 miRNA。
结果
在 GSE104165 数据库中，检测到 GBC 肿瘤样本中 25 个上调和 97 个下调的 miRNA 表达具有显著差异。然后，从 2 个上调最显著的 miRNA（miR-4430 和 miR-642a-3p）中鉴定出 477 个潜在靶基因，从 2 个下调最显著的 miRNA（miR-451a 和 miR-145-5p）中鉴定出 268 个潜在靶基因。经过 GO 和 KEGG 分析，发现 mTOR 和 PI3K-Akt 信号通路与潜在靶基因相关。基于 PPI 网络，选择了前 10 个最高度的节点作为关键基因。此外，miRNA-关键基因网络显示 miR-642a-3p 在 GBC 组织和细胞系中均呈显著上调，miR-145-5p 呈显著下调。在实验验证中，证实 miR-145-5p 的上调和 miR-642a-3p 的下调可抑制 GBC 的侵袭和转移。
结论
miR-642a-3p 和 miR-145-5p 通过生物信息学和实验验证被鉴定为与侵袭转移相关的 miRNA，上调 miR-642a-3p 和下调 miR-145-5p 都可能成为未来 GBC 的新治疗选择。
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