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MetaDE-Based Analysis of circRNA Expression Profiles Involved in Gastric Cancer

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Abstract

Background

Circular RNAs (circRNAs) could play carcinogenic roles in gastric cancer (GC) and have potential to be biomarkers for GC early diagnosis, which needs to be further excavated and supported by more evidence.

Aims

The study aims to identify more authentic circRNA expression profiles that could function as potential biomarkers in GC.

Methods

circRNA expression data in three microarrays were downloaded from Gene Expression Omnibus datasets. A systematic meta-analysis based on an integrated dataset pre-processed from the three microarrays was conducted to identify a panel of differentially expressed circRNAs (DEcircs) by using the metaDE package. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes term enrichment were used to note the corresponding functions of DEcircs. Quantitative real-time polymerase chain reaction was applied to verify the DEcircs expression in cancer tissues and adjacent paracancerous tissues. A GC risk-related circRNAs–miRNAs–mRNAs network was further constructed and analyzed.

Results

MetaDE analysis suggested 64 DEcircs between cancer tissues and adjacent normal tissues. GO and KEGG analysis showed that the parental genes of these DEcircs were mainly associated with histone methylation, Wnt signalosome and histone methylation activity. Hsa_circ_0005927 and hsa_circ_0067934 were verified in GC tissues, and a GC risk-related network was constructed.

Conclusion

MetaDE-based circRNA expression profiles revealed a series of potential biomarkers involved in GC. Two circRNAs, hsa_circ_0005927 and hsa_circ_0067934, could be more authentic biomarkers for GC screening. The GC risk-related network of hsa_circ_0005927/hsa_circ_0067934 and their downstream targets will provide new genetic insights for GC research.

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Availability of data and materials

All data are included in the manuscript.

Abbreviations

GC:

Gastric cancer

qRT-PCR:

Quantitative real-time polymerase chain reaction

GEO:

Gene expression omnibus

FC:

Fold change

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

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Acknowledgments

The authors gratefully acknowledge financial support from the National Nature Science Foundation of China (Ref No. 81772987) and Natural Science Foundation of Liaoning Province in China (Ref No. 20170540987).

Funding

This work is supported partly by grants from the National Nature Science Foundation of China (Ref No. 81772987) and Natural Science Foundation of Liaoning Province in China (Ref No. 20170540987).

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Authors and Affiliations

  1. Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China

    Han-xi Ding, Qian Xu, Ben-gang Wang, Zhi Lv & Yuan Yuan

  2. Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China

    Han-xi Ding, Qian Xu, Ben-gang Wang, Zhi Lv & Yuan Yuan

  3. Hepatobiliary Surgery Department of General Surgery Institute, The First Hospital of China Medical University, Shenyang, China

    Ben-gang Wang

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  1. Han-xi Ding
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Contributions

YY and QX provided direction and guidance throughout the preparation of this manuscript. DH and WB performed data extraction and analysis. DH performed experiments and drafted the manuscript. LZ corrected the grammatical errors in this article. YY reviewed the manuscript and made significance revisions on the drafts. All authors read and approved the final manuscript.

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Correspondence to Yuan Yuan.

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Ding, Hx., Xu, Q., Wang, Bg. et al. MetaDE-Based Analysis of circRNA Expression Profiles Involved in Gastric Cancer. Dig Dis Sci 65, 2884–2895 (2020). https://doi.org/10.1007/s10620-019-06014-6

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