New long noncoding RNA biomarkers and ceRNA networks on miR-616-3p in colorectal cancer: Bioinformatics-based study

IF 17.7 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Accounts of Chemical Research Pub Date : 2024-02-01 DOI:10.4103/jrms.jrms_786_22

Mohammad Abdolvand, Zahra Mohammadi Chermahini, Sahar Bahaloo, Mohammad Hassan Emami, Alireza Fahim, H. Rahimi, E. Amjadi, Fatemeh Maghool, Fattah Rohani, Mina Dadkhah, Nooshin Farhadian, Nasimeh Vatandoust, Shirin Abdolvand, Maliheh Roozbahani Darehsari, Mohammad Chehelgerdi, F. Beni, Mahsa Khodadoostan, S. Hemati, Mansoor Salehi

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Abstract

Cancer development is aided by the role of long noncoding RNAs (lncRNAs) that act as competing endogenous RNAs (ceRNAs) absorbing microRNAs (miRNAs). We aimed to discover a novel regulatory axis in colorectal cancer (CRC) and potential biomarkers based on miR-616-3p. The gene expression omnibus database was mined for differentially expressed lncRNAs (DELs) and mRNAs. LncRNAs and mRNAs were predicted using the RegRNA and TargetScan databases. A combination of the ciBioPortal and Ensemble databases was used to locate the mRNAs. Cytoscape 3.7.1-built CeRNA networks. A quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to confirm the expression levels of these RNA molecules. Statistical analyses were implemented by GraphPad Prism 9. qRT-PCR showed (Linc01282, lnc-MYADM-1:1, and Zinc Finger Protein 347 [ZNF347]) were overexpressed whereas, (salt-inducible kinases 1 [SIK1], and miR-616-3p) were down regulated. These results identify unique, unreported lncRNAs as CRC prognostic biomarkers, as well as prospective mRNAs as new treatment targets and predictive biomarkers for CRC. In addition, our study uncovered unexplored ceRNA networks that should be studied further in CRC.

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结直肠癌中 miR-616-3p 的新长非编码 RNA 生物标记物和 ceRNA 网络：基于生物信息学的研究

长非编码 RNA（lncRNA）作为竞争性内源性 RNA（ceRNA）吸收 microRNA（miRNA），有助于癌症的发展。我们的目的是发现结直肠癌（CRC）的新型调控轴和基于 miR-616-3p 的潜在生物标志物。我们在基因表达综合数据库中挖掘了差异表达的 lncRNAs (DELs) 和 mRNAs。使用 RegRNA 和 TargetScan 数据库预测 LncRNA 和 mRNA。结合使用 ciBioPortal 和 Ensemble 数据库来定位 mRNA。Cytoscape 3.7.1 构建了 CeRNA 网络。利用定量实时聚合酶链反应（qRT-PCR）确认这些 RNA 分子的表达水平。qRT-PCR显示（Linc01282、lnc-MYADM-1:1和锌指蛋白347 [ZNF347]）表达过高，而（盐诱导激酶1 [SIK1]和miR-616-3p）表达降低。这些结果确定了独特的、未报道的 lncRNAs 作为 CRC 预后生物标志物，以及作为 CRC 新治疗靶点和预测性生物标志物的前瞻性 mRNAs。此外，我们的研究还发现了在 CRC 中应进一步研究的未被探索的 ceRNA 网络。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.