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A novel variable exonic region and differential expression of LINC00663 non-coding RNA in various cancer cell lines and normal human tissue samples

Tumor Biology volume 37, pages 8791–8798 (2016)Cite this article

Abstract

Long non-coding RNAs (lncRNAs) are found to play crucial roles in several biological processes and have been associated with many complex human diseases including cancers. Several lines of evidences indicate that lncRNAs deregulated in many cancer tissues. In this particular study, differential expression of long intergenic non-coding RNA 663 (LINC00663) was demonstrated in various cancer cell lines and healthy human tissues by using RT-PCR and qPCR methods. While expression level of LINC00663 was most prominent in thyroid gland and uterus, it is least expressed in skeletal muscle tissues. Moreover, LINC00663 was found to be differentially expressed in various cancer cells. Particularly, its expression was highly diminished in DU-145, PC3, HGC-27, CRL-1469, A549, MCF7, and BCPAP cancer cells. Also, LINC00663 expression was most prominent in A172 glioblastoma cells. Additionally, a novel splice variant of LINC00663 RNA was also detected. The sequence and Basic Local Alignment Search Tool (BLAST) analysis results revealed the presence of a novel exonic region between exons 2 and 3. Subsequently, five potential splice variants showing high level of variation have been identified. Secondary structures of these variants with minimum free energy were also demonstrated. Furthermore, putative microRNA (miRNA) binding sites to these variants have been shown. In conclusion, LINC00663 was shown to be differentially expressed in various human tissues and cancer cell lines. Also, LINC00663 undergoes alternative splicing and the novel exonic region alters its secondary structure and its interactions with potential targeting miRNAs. The role of LINC00663 in cancer formation further needs to be investigated with a wide range of studies.

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Acknowledgments

Kaifee Arman is a recipient of Graduate Scholarship from Turkish Scientific and Technological Research Council (TUBITAK) under the program 2215-Graduate Scholarship Programme for International Students.

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Affiliations

  1. Faculty of Medicine, Department of Medical Biology, University of Gaziantep, Gaziantep, Turkey

    Esra Bozgeyik, Yusuf Ziya Igci, Mevan F. Sami Jacksi, Kaifee Arman, Ebru Temiz & Mehri Igci

  2. Faculty of Medicine, Department of Medical Biology, Zirve University, Gaziantep, Turkey

    Serdar A. Gurses

  3. Department of Medical Biology, Adiyaman University, Adiyaman, Turkey

    Ibrahim Bozgeyik & Onder Yumrutas

  4. Department of Medical Biology, Sanko University, Gaziantep, Turkey

    Elif Pala

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  1. Esra Bozgeyik
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  2. Yusuf Ziya Igci
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  3. Mevan F. Sami Jacksi
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  4. Kaifee Arman
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  6. Ibrahim Bozgeyik
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  9. Ebru Temiz
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  10. Mehri Igci
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Correspondence to Esra Bozgeyik.

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Bozgeyik, E., Igci, Y.Z., Sami Jacksi, M.F. et al. A novel variable exonic region and differential expression of LINC00663 non-coding RNA in various cancer cell lines and normal human tissue samples. Tumor Biol. 37, 8791–8798 (2016). https://doi.org/10.1007/s13277-015-4782-3

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  • DOI: https://doi.org/10.1007/s13277-015-4782-3

Keywords

  • Cancer
  • Non-coding RNA
  • LINC00663
  • lncRNA
  • miRNA