Construction of a focal adhesion signaling pathway-related ceRNA network in pelvic organ prolapse by transcriptome analysis

Xia Yu¹, Li He², Ying Chen², Wenyi Lin³, Hong Liu⁴, Xiu Yang⁴, Ying Ye⁴, Xuemei Zheng², Zhenglin Yang⁵, Yonghong Lin²

Affiliations

¹ Department of Clinical Laboratory, Chengdu Women's and Children's Central Hospital, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
² Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
³ Department of Medical Pathology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
⁴ Department of Surgical, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
⁵ Sichuan Provincial Key Laboratory for Human Disease Gene Study and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.

PMID: 36176289
PMCID: PMC9513229
DOI: 10.3389/fgene.2022.996310

Construction of a focal adhesion signaling pathway-related ceRNA network in pelvic organ prolapse by transcriptome analysis

Xia Yu et al. Front Genet. 2022.

. 2022 Sep 13:13:996310.

doi: 10.3389/fgene.2022.996310. eCollection 2022.

Authors

Xia Yu¹, Li He², Ying Chen², Wenyi Lin³, Hong Liu⁴, Xiu Yang⁴, Ying Ye⁴, Xuemei Zheng², Zhenglin Yang⁵, Yonghong Lin²

Affiliations

¹ Department of Clinical Laboratory, Chengdu Women's and Children's Central Hospital, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
² Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
³ Department of Medical Pathology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
⁴ Department of Surgical, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
⁵ Sichuan Provincial Key Laboratory for Human Disease Gene Study and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.

PMID: 36176289
PMCID: PMC9513229
DOI: 10.3389/fgene.2022.996310

Abstract

Objective: Pelvic organ prolapse (POP) affects a large proportion of adult women, but the pathogenesis of POP remains unclear. The increase in global population aging will impose a substantial medical burden. Herein, we aimed to explore the related RNAs regulating the occurrence of POP and provide potential therapeutic targets. Method: Tissue biopsies were collected from the anterior vaginal wall of six women with POP and six matched subjects without POP. The profiles of mRNAs, circRNAs, lncRNAs, and miRNAs were obtained by whole transcriptome RNA sequencing. Result: The findings revealed that 71 circRNAs, 76 known lncRNAs, 84 miRNAs, and 931 mRNAs were significantly altered (p < 0.05 and |log2FC| > 1). GO and KEGG enrichment analyses indicated that the differentially expressed genes (DEGs) were mainly enriched in the focal adhesion signaling pathway. FLT, ITGA9, VEGFD, PPP1R12B, and ROCK2 were identified as focal adhesion signaling pathway-related hub genes by protein-protein interaction network analysis. Based on the relationships between the DEGs and miRNA, lncRNA and circRNA targets, we constructed a focal adhesion signaling pathway-related ceRNA network. The ceRNA network includes hsa_circ_0002190/hsa_circ_0046843/lnc-CARMN -miR-23a-3p - ROCK2 and hsa_circ_0001326/hsa_circ_0007733/lnc-AC107959/lnc-TPM1-AS - miR-205-5p - ROCK2/PPP1R12B/VEGFD. Moreover, abnormalities in the cytoskeleton in fibroblasts from individuals with POP were observed. Conclusion: In this study, a focal adhesion signaling pathway-related ceRNA network was constructed, and this network may serve as a target for finding suitable drugs for the treatment of POP.

Keywords: PPI; competing endogenous RNA; focal adhesion signaling pathway; pelvic organ prolapse; whole transcriptome RNA sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

**FIGURE 1**
Research strategy employed in the present study.

**FIGURE 2**
Procedure for preparing and analyzing an RNA library. **(A)** Process of preparing and analyzing circRNA, lncRNA, and mRNA libraries. **(B)** Process of preparing and analyzing miRNA libraries. CPC, coding potential calculator; CNCI, coding-noncoding index.

**FIGURE 3**
Whole transcriptome RNA sequencing results comparing the POP and control groups. **(A–D)** Venn diagrams depicting the profiles of circRNAs, lncRNAs, miRNAs, and mRNAs. **(E)** RNA expression ratio in a chromosome (number of RNAs in a related chromosome divided by the total number of RNAs). **(F)** Differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs between the POP and control groups. **(G)** qRT‒PCR validation of the RNA sequencing results using 3 DECs, 3 DELs, 3 DEMs, and 3 DEGs chosen at random. The log2-fold change from the q-RT‒PCR analysis is plotted on the X-axis, and the log2-fold change from the RNA sequencing analysis is plotted on the Y-axis. POP, pelvic organ prolapse; DECs, differentially expressed circRNAs; DELs, differentially expressed lncRNAs; DEMs, differentially expressed miRNAs; DEGs, differentially expressed genes.

**FIGURE 4**
circRNA, lncRNA, miRNA, and mRNA expression profiles. **(A–D)** Heatmaps of DECs, DELs, DEMs, and DEGs in the anterior vaginal wall in the POP and control groups. **(E–H)** Volcano plots of DECs, DELs, DEMs, and DEGs in the anterior vaginal wall in the POP and control groups. POP, pelvic organ prolapse; circRNA, circular RNA; lncRNAs, long noncoding RNAs; miRNA, microRNA; DECs, differentially expressed circRNAs; DELs, differentially expressed lncRNAs; DEMs, differentially expressed miRNAs; DEGs, differentially expressed genes.

**FIGURE 5**
Functional enrichment analysis of DEGs using GO and KEGG and the PPI network. **(A)** Analysis of DEGs using GO and KEGG. **(B)** Top ten KEGG pathways. **(C)** Top ten KEGG pathways related to DEGs. (D) PPI network of focal adhesion pathway hub genes in the KEGG pathway.

**FIGURE 6**
ceRNA network of differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs. The navy-blue circular nodes represent circRNAs, the light blue circular nodes represent lncRNAs, the square nodes represent miRNAs, and the triangular nodes represent mRNAs.

**FIGURE 7**
Cytoskeleton of fibroblasts from the POP and control groups. (400×).

See this image and copyright information in PMC

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Construction of a focal adhesion signaling pathway-related ceRNA network in pelvic organ prolapse by transcriptome analysis

Affiliations

Construction of a focal adhesion signaling pathway-related ceRNA network in pelvic organ prolapse by transcriptome analysis

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

Research Materials

Miscellaneous