Multi-omics analysis of uterine fluid extracellular vesicles reveals a resemblance with endometrial tissue across the menstrual cycle: biological and translational insights
Authors: Apostolov Apostol , Mladenović Danilo , Tilk Kadi , Lõhmus Andres , Baev Vesselin , Yahubyan Galina , Sola-Leyva Alberto , Bergamelli Mathilde , Görgens André , Zhao Cheng , EL Andaloussi Samir , Kalinina Aive , Acharya Ganesh , Lanner Fredrik , Saare Merli , Peters Maire , Piomboni Paola , Luddi Alice , Salumets Andres , Aleksejeva Elina 
Published: February 2025

Abstract

STUDY QUESTION
Does the molecular composition of uterine fluid extracellular vesicles (UF-EVs) reflect endometrial tissue changes across the menstrual cycle?

SUMMARY ANSWER
Concordance between endometrial tissue and UF-EVs exists on miRNA and mRNA levels along the menstrual cycle phases and UF-EV surface proteomic signatures suggest EVs originate from several major endometrial cell populations.

WHAT IS KNOWN ALREADY
The clinical value of endometrial receptivity testing is restricted by invasiveness and the use of only one omics level of input. There is promising evidence that UF-EVs can reflect changes in mid-secretory endometrium, highlighting the potential to establish endometrial receptivity testing right before embryo transfer. However, the dynamic changes of UF-EVs molecular cargo have not been directly compared to endometrial tissue on multiple omics levels.

STUDY DESIGN, SIZE, DURATION
This cross-sectional study included fertile women from four menstrual cycle phases: proliferative and early-, mid- and late-secretory phases. In total, 26 paired samples of UF and endometrial tissue were collected. mRNA and miRNA were sequenced, and differential analysis was performed on consecutive phases. UF-EVs were profiled for various protein surface markers associated with different cell types. EVs from epithelial endometrial organoid-conditioned culture media was used as a reference of pure epithelial endometrial EVs.

PARTICIPANTS/MATERIALS, SETTING, METHODS
Paired UF and endometrial tissue samples were collected from 26 fertile, reproductive-age women. EV isolation from UF was validated using electron microscopy and western blotting, and particle numbers were measured by nanoparticle-tracking analysis. The transcriptome and miRNome of UF-EVs and endometrial tissue were sequenced, and differential expression analysis was conducted on consecutive phases of the menstrual cycle. Bead-based EV flow cytometry targeting 37 surface protein markers was used to characterize EVs from UF and endometrial organoids.

MAIN RESULTS AND THE ROLE OF CHANCE
Surface proteome analysis revealed that UF-EVs from the mid-secretory phase had significantly increased expression of natural killer cell marker CD56 (p &lt; 0.005), pan-leukocyte marker CD45 (p &lt; 0.005), pan-T-cell marker CD3 (p &lt; 0.005) and coagulation-related protein CD142 (p &lt; 0.005) compared to those from the proliferative phase, whereas markers associated with endometrial epithelial cells (CD29, CD133 and CD326) did not significantly change across the menstrual cycle. Transcriptomic analysis highlighted differential expression of histone and metallothionein genes that correlated between paired UF-EVs and endometrial tissues in each tested menstrual cycle phase. Principal component analysis of miRNomes of paired UF-EVs and endometrial tissue samples resulted in similar clustering patterns, where mid- and late-secretory samples clustered closely, and proliferative and early-secretory phase samples clustered separately. Half of the differentially expressed miRNAs in each phase in UF-EVs were also differentially expressed in the endometrium. Importantly, nine mid-secretory phase UF-EV DE miRNAs were identified, five of which were common between UF-EVs and endometrial biopsies, including hsa-miR-30d-5p and hsa-miR-200b-3p, both of which were previously implicated in implantation. While, notably, three of the nine miRNAs, hsa-miR-200b-3p, hsa-miR-141-3p and hsa-miR-200a-3p, were predicted to regulate mRNAs in the endometrial tissue and the pre-implantation embryo trophectoderm.

LARGE SCALE DATA
The data is not publicly available due to ongoing studies. Please contact the corresponding author for access to the data.

LIMITATIONS, REASONS FOR CAUTION
The clinical dating of the menstrual cycle phase is based on the first day of menstruation and the time of the LH-peak, which does not exclude the possibility that the expected endometrial phase was not reached. The wider limitation of our study is the lack of standardized procedures for collecting UF samples in gynaecological practice, which could challenge the replication of our findings.

WIDER IMPLICATIONS OF THE FINDINGS
Evidence that UF-EVs reflect endometrial phases of menstrual cycle supports the use of UF-EVs in endometrial receptivity testing. Additionally, further studies of UF-EVs in endometrial pathologies could be beneficial for diagnostics, considering that more invasive tissue biopsies only reflect the biopsy site and not full endometrium.

STUDY FUNDING/COMPETING INTEREST(S)
This study was supported by European Regional Development Fund Enterprise Estonia’s Applied Research Program under the grant agreement number 2014-2020.4.02.21-0398 (EVREM), the Estonian Research Council (grant PRG1076 and PSG1082), the Horizon Europe NESTOR grant (grant no. 101120075) of the European Commission, the Swedish Research Council (grant 2024-02530), the Novo Nordisk Fonden (grant NNF24OC0092384), and the National Recovery and Resilience Plan of the Republic of Bulgaria, project BG-RRP-2.004-0001-C01. A.S.L. received funding from the Becas Fundación Ramón Areces para Estudios Postdoctorales. All the authors declare no conflict of interest.