Unbiased In Silico Analysis of Gene Expression Pinpoints Circulating miRNAs Targeting KIAA1324, a New Gene Drastically Downregulated in Ovarian Endometriosis

Carole Abo; Louise Biquard; Laura Girardet; Sandrine Chouzenoux; Pierre-Alexandre Just; Charles Chapron; Daniel Vaiman; Bruno Borghese

doi:10.3390/biomedicines10092065

Unbiased In Silico Analysis of Gene Expression Pinpoints Circulating miRNAs Targeting KIAA1324, a New Gene Drastically Downregulated in Ovarian Endometriosis

Biomedicines. 2022 Aug 24;10(9):2065. doi: 10.3390/biomedicines10092065.

Authors

Carole Abo^{1

2}, Louise Biquard^{1

2}, Laura Girardet^{1

2}, Sandrine Chouzenoux^{1

2}, Pierre-Alexandre Just^{1

2

3}, Charles Chapron^{1

2

4}, Daniel Vaiman^{1

2}, Bruno Borghese^{1

2

4}

Affiliations

¹ U1016 Institut Cochin, Institut National de la Santé et de la Recherche Médicale, UMR8104 Centre National de la Recherche Scientifique, 75016 Paris, France.
² Faculty of Medicine, University of Paris, 75006 Paris, France.
³ Department of Pathological Anatomy and Cytology, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75004 Paris, France.
⁴ Department of Gynecologic Surgery, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75004 Paris, France.

Abstract

Objective: To identify circulating miRNAs associated with ovarian endometriosis (OMA), and to analyze candidate genes targeted by these miRNAs. Methods: Putative regulating miRNAs were identified through an original bioinformatics approach. We first queried the miRWalk 2.0 database to collect putative miRNA targets. Then, we matched it to a transcriptomic dataset of OMA. Moving from gene expression in the tissue to possible alterations in the patient plasma, a selection of these miRNAs was quantified by qRT-PCR in plasma samples from 93 patients with isolated OMA and 95 patients surgically checked as free from endometriosis. Then, we characterized the genes regulated by more than one miRNA and validated them by immunohistochemistry and transfection experiments on endometrial cell primary cultures obtained from endometrial biopsies of 10 women with and without endometriosis with miRNA mimics. Stromal and epithelial cells were isolated and cultured separately and gene expression levels were measured by RT-qPCR. Results: Eight miRNAs were identified by bioinformatics analysis. Two of them were overexpressed in plasma from OMA patients: let-7b-5p and miR-92a-3p (p < 0.005). Three miRNAs, let-7b and miR-92a-3p, and miR-93-5p potentially targeted KIAA1324, an estrogen-responsive gene and one of the most downregulated genes in OMA. Transfection experiments with mimics of these two miRNAs showed a strong decrease in KIAA1324 expression, up to 40%. Immunohistochemistry revealed a moderate-to-intense staining for KIAA1324 in the eutopic endometrium and a faint-to-moderate staining in the ectopic endometrium for half of the samples, which is concordant with the transcriptomic data. Discussion and Conclusion: Our results suggested that KIAA1324 might be involved in endometriosis through the downregulating action of two circulating miRNAs. As these miRNAs were found to be overexpressed, their quantification in plasma could provide a tool for an early diagnosis of endometriosis.

Keywords: KIAA1324 (EIG121); biomarkers; endometriosis; miRNA.

Grants and funding

Fondation pour la Recherche Médicale (FRM), EndoFrance patients’ association, and academic research funding.