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

Mohammad Abdolvand, Zahra Mohammadi Chermahini, Sahar Bahaloo, Mohammad Hassan Emami, Alireza Fahim, Hojjatolah Rahimi, Elham Amjadi, Fatemeh Maghool, Fattah Rohani, Mina Dadkhah, Nooshin Farhadian, Nasimeh Vatandoust, Shirin Abdolvand, Maliheh Roozbahani, Mohammad Chehelgerdi, Faeze Ahmadi Beni, Mahsa Khodadoost, Simin Hemati, Mansoor Salehi

Abstract


Background: 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.

Materials and Methods: 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.

Results: 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.

Conclusion: 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.


Keywords


Colorectal cancer, linc01282, lnc?MYADM?1:1, microRNAs?616?3p, salt?inducible kinases 1, ZNF347

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