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The circRNA–miRNA–mRNA regulatory network in systemic lupus erythematosus

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Abstract

Introduction/objectives

Systemic lupus erythematosus (SLE) was an autoimmune disease with a large variety of clinical manifestations and involving many organs. Its exact etiology was unclear, and studies had shown that T cells may play an important role. In this study, we wished to study the regulatory mechanism of circRNA in the T cells from SLE patients.

Method

GSE84655 was retrieved from the GEO database, and the corresponding probe name was converted into an international standard circRNA name by using the practical extraction and report language. The differentially expressed circRNAs (DECs) were analyzed by using R software. Subsequently, we used multiple bioinformatics methods to obtain the target miRNAs of circRNAs and the downstream mRNAs of miRNAs. Finally, a circRNA–miRNA–mRNA regulatory network was constructed and visualized by using Cytoscape 3.6.1 software.

Results

There were a total of 29 DECs that had been identified, including 2 upregulated circRNAs and 27 downregulated circRNAs. After a lot of in-depth analysis, we finally obtained a circRNA–miRNA–mRNA regulatory network consisting of 8 DECs (hsa_circ_0006770, hsa_circ_0002904, hsa_circ_0034044, hsa_circ_0023685, hsa_circ_0049271, hsa_circ_0074491, hsa_circ_0074559, and hsa_circ_0023461), 4 overlap miRNAs (hsa-miR-326, hsa-miR-569, hsa-miR-638, and hsa-miR-1246), and 13 target mRNAs (EPHB3, USH1G,UBE4A, DCAF7, TBL1XR1, SLC27A4, SMO, NAA30, RSBN1, PLAG1, SOX2, GPATCH11, and DYRK1A).

Conclusions

This study could provide a novel insight into the role of circRNA and the circRNA–miRNA–mRNA regulation network in the SLE. However, it also needed to be verified by subsequent experiments and clinical studies.

Key Points

• There were 29 DECs (2 up and 27 down) between T cells of SLE and health control.

• Hsa-miR-338-3p, hsa-miR-767-3p, and hsa-miR-1827 were the most frequent miRNAs.

• We obtained a circRNA–miRNA–mRNA regulatory network for SLE.

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Data Availability

Not applicable.

Abbreviations

SLE:

Systemic lupus erythematosus

DECs:

Differentially expressed circRNAs

circRNA:

Circular RNA

miRNA:

MicroRNA

HMDD:

Human microRNA Disease Database

PBMC:

Peripheral blood mononuclear cell

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Funding

The work was supported by NSFC (Natural Science Foundation of China) Grant U1605223 to Dr. Guixiu Shi.

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Authors and Affiliations

  1. Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China

    Junhui Zhang, Yuan Liu & Guixiu Shi

  2. Heart Center of Henan Provincial People’s Hospital, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, China

    Junhui Zhang

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  1. Junhui Zhang
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  2. Yuan Liu
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Contributions

Junhui Zhang: analyze the data and write a first draft; Liu Yuan, revised paper; Shi Guixiu, overall guidance and revised paper.

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Correspondence to Yuan Liu or Guixiu Shi.

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Zhang, J., Liu, Y. & Shi, G. The circRNA–miRNA–mRNA regulatory network in systemic lupus erythematosus. Clin Rheumatol 40, 331–339 (2021). https://doi.org/10.1007/s10067-020-05212-2

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