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Bioinformatics analysis of a disease-specific lncRNA–miRNA–mRNA regulatory network in recurrent spontaneous abortion (RSA)

  • Gynecologic Endocrinology and Reproductive Medicine
  • Published:
Archives of Gynecology and Obstetrics Aims and scope Submit manuscript

Abstract

Background

This study investigated the molecular mechanisms of long non-coding RNAs (lncRNAs) in RSA using the lncRNA–miRNA–mRNA regulatory network.

Methods

The present study obtained expression datasets of long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), and microRNAs (miRNAs) from blood samples of individuals with unexplained recurrent spontaneous abortion (RSA) and healthy controls. Differentially expressed lncRNAs (DELs), mRNAs (DEMs), and miRNAs (DEmiRs) were identified. A regulatory network comprising lncRNA, miRNA, and mRNA was constructed, and Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to analyze the biological functions of DEM. Also, a protein–protein interaction (PPI) network was made and key genes were identified.

Results

A total of 57 DELs, 212 DEmiRs, and 301 DEMs regarding RSA were identified. Later analysis revealed a lncRNA–miRNA–mRNA network comprising nine lncRNAs, 14 miRNAs, and 65 mRNAs. Then, the ceRNA network genes were subjected to functional enrichment and pathway analysis, which showed their association with various processes, such as cortisol and thyroid hormone synthesis and secretion, human cytomegalovirus infection, and parathyroid hormone synthesis. In addition, ten hub genes (ITGB3, GNAI2, GNAS, SRC, PLEC, CDC42, RHOA, RAC1, CTNND1, and FN1) were identified based on the PPI network results.

Conclusion

In summary, the outcomes of our study provided some data regarding the alteration genes involved in RSA pathogenic mechanism via the lncRNA–miRNA–mRNA network and reveal the possibility of identifying new lncRNAs and miRNAs as promising molecular biomarkers.

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Data availability

The authors declare that all generated and analyzed data are included in the study.

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Authors and Affiliations

  1. Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran

    Somayeh Reiisi

  2. Department of Computer Science, Faculty of Mathematical Sciences, Shahrekord University, Shahrekord, Iran

    Kambiz Ahmadi

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  1. Somayeh Reiisi
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  2. Kambiz Ahmadi
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SR wrote the manuscript and coordinated the study, participated in intellectual discussions of the data, and revised the manuscript. KA performed most of the bioinformatics data analysis.

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Correspondence to Somayeh Reiisi.

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Reiisi, S., Ahmadi, K. Bioinformatics analysis of a disease-specific lncRNA–miRNA–mRNA regulatory network in recurrent spontaneous abortion (RSA). Arch Gynecol Obstet 309, 1609–1620 (2024). https://doi.org/10.1007/s00404-023-07356-3

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