P-240 Human extracellular vesicles (EVs) secreted by aneuploid embryos potentiate development of non-invasive PGT-A RNA biomarkers and stimulate MUC1 up-regulation in primary endometrial stromal cells (ESCs)

Study question

Could EVs secreted by aneuploid embryos a) serve for development of RNA biomarkers for PGT-A and b) elicit a relevant transcriptomic response in decidualised ESCs?

Summary answer

Aneuploid embryo EVs a) contain PPM1J, LINC00561, ANKRD34C and TMED10 in differential abundance from euploid EVs and b) induce up-regulation of MUC1 in decidualised ESCs.

What is known already

Embryo aneuploidy accounts for approximately 50% of all recurrent implantation failures in women >35 years old. PGT-A identifies euploid embryos to increase implantation probability but the technology is controversial as it requires an invasive embryo biopsy with an elusive long-term biosafety. The development of non-invasive methods to screen out aneuploid embryos is paramount. It is also critical to decode the embryo-endometrial dialog underlying implantation failure. We have previously reported that IVF embryos secrete EVs that can be internalised by ESCs, conceptualising that successful implantation to the endometrium is facilitated by EVs, which may additionally serve as biomarkers of ploidy status.

Study design, size, duration

Embryos destined for biopsy on days 5-7 for PGT-A were grown under standard conditions. Spent media (30μl) were collected from euploid (n = 175) and aneuploid embryos (n = 145) at both cleavage (days 1-3) and blastocyst (days 3-5) stage. Media samples from n = 35 cleavage embryos were pooled in order to obtain five euploid and four aneuploidy pools. Blastocyst media were pooled to create one euploid and one aneuploid pool. ESCs were obtained from five women undergoing diagnostic laparoscopy.

Participants/materials, setting, methods

The study was realised at a research hospital. EVs were isolated from euploid and aneuploid Day3 pools with differential ultracentrifugation and EV-RNA sequencing was performed following the SMARTer Stranded Total RNA-Seq approach. ESCs were decidualised (E2:10nM, P4:1uM, cAMP:0.5 mM twice every 48 hours) and treated for 24 hours with 50 ng/ml euploid or aneuploid EVs extracted from blastocyst media. RNA sequencing was performed on ESCs following the Truseq RNAseq protocol.

Main results and the role of chance

Aneuploid cleavage stage embryos (n = 4) secreted EVs that were less abundant in RNA fragments originating from the genes PPM1J (log2fc=-5.13, p = 0.011), LINC00561 (log2fc=-7.87, p = 0.010) and ANKRD34C (log2fc=-7.30, p = 0.017) and more abundant in TMED10 (log2fc=1.63 p = 0.025) compared to EVs (n = 5) from euploid embryos. Decidualisation per se induced downregulation of MUC1 (log2FC=-0.54, p = 0.0028) in ESCs as prerequisite for the establishment of receptive endometrium. The expression of MUC1 transcript in decidualised ESCs was significantly increased following treatment with aneuploid compared to euploid embryo-secreted EVs (log2FC=0.85, p = 0.0201).

Limitations, reasons for caution

The findings of the study may require validation utilising a second cohort of EVs samples.

Wider implications of the findings

This discovery that the RNA cargo of EVs secreted from aneuploid cleavage stage embryos is diverse from that of euploid embryos potentiates the development of non-invasive methodology for PGT-A. The upregulation of MUC1 in decidualised ESCs following aneuploid embryo EV treatment proposes a new mechanism underlying implantation failure.

Trial registration number

NA

P–240 Human extracellular vesicles (EVs) secreted by aneuploid embryos potentiate development of non-invasive PGT-A RNA biomarkers and stimulate MUC1 up-regulation in primary endometrial stromal cells (ESCs)

Study question

Could EVs secreted by aneuploid embryos a) serve for development of RNA biomarkers for PGT-A and b) elicit a relevant transcriptomic response in decidualised ESCs?

Summary answer

Aneuploid embryo EVs a) contain PPM1J, LINC00561, ANKRD34C and TMED10 in differential abundance from euploid EVs and b) induce up-regulation of MUC1 in decidualised ESCs.

What is known already

Embryo aneuploidy accounts for approximately 50% of all recurrent implantation failures in women >35 years old. PGT-A identifies euploid embryos to increase implantation probability but the technology is controversial as it requires an invasive embryo biopsy with an elusive long-term biosafety. The development of non-invasive methods to screen out aneuploid embryos is paramount. It is also critical to decode the embryo-endometrial dialog underlying implantation failure. We have previously reported that IVF embryos secrete EVs that can be internalised by ESCs, conceptualising that successful implantation to the endometrium is facilitated by EVs, which may additionally serve as biomarkers of ploidy status.

Study design, size, duration

Embryos destined for biopsy on days 5–7 for PGT-A were grown under standard conditions. Spent media (30μl) were collected from euploid (n = 175) and aneuploid embryos (n = 145) at both cleavage (days 1–3) and blastocyst (days 3–5) stage. Media samples from n = 35 cleavage embryos were pooled in order to obtain five euploid and four aneuploidy pools. Blastocyst media were pooled to create one euploid and one aneuploid pool. ESCs were obtained from five women undergoing diagnostic laparoscopy.

Participants/materials, setting, methods

The study was realised at a research hospital. EVs were isolated from euploid and aneuploid Day3 pools with differential ultracentrifugation and EV-RNA sequencing was performed following the SMARTer Stranded Total RNA-Seq approach. ESCs were decidualised (E2:10nM, P4:1uM, cAMP:0.5 mM twice every 48 hours) and treated for 24 hours with 50 ng/ml euploid or aneuploid EVs extracted from blastocyst media. RNA sequencing was performed on ESCs following the Truseq RNAseq protocol.

Main results and the role of chance

Aneuploid cleavage stage embryos (n = 4) secreted EVs that were less abundant in RNA fragments originating from the genes PPM1J (log2fc=–5.13, p = 0.011), LINC00561 (log2fc=–7.87, p = 0.010) and ANKRD34C (log2fc=–7.30, p = 0.017) and more abundant in TMED10 (log2fc=1.63 p = 0.025) compared to EVs (n = 5) from euploid embryos. Decidualisation per se induced downregulation of MUC1 (log2FC=–0.54, p = 0.0028) in ESCs as prerequisite for the establishment of receptive endometrium. The expression of MUC1 transcript in decidualised ESCs was significantly increased following treatment with aneuploid compared to euploid embryo-secreted EVs (log2FC=0.85, p = 0.0201).

Limitations, reasons for caution

The findings of the study may require validation utilising a second cohort of EVs samples.

Wider implications of the findings: This discovery that the RNA cargo of EVs secreted from aneuploid cleavage stage embryos is diverse from that of euploid embryos potentiates the development of non-invasive methodology for PGT-A. The upregulation of MUC1 in decidualised ESCs following aneuploid embryo EV treatment proposes a new mechanism underlying implantation failure.

Trial registration number

NA

Global transcriptomic changes occur in uterine fluid-derived extracellular vesicles during the endometrial window for embryo implantation

STUDY QUESTION

Are uterine fluid-derived extracellular vesicles (UF-EVs) a 'liquid biopsy' reservoir of biomarkers for real-time monitoring of endometrial status?

SUMMARY ANSWER

The transcriptomic cargo of UF-EVs reflects the RNA profile of the endometrial tissue as well as changes between the non-receptive and the receptive phase, possibly supporting its use for a novel endometrial receptivity test.

WHAT IS KNOWN ALREADY

EVs have been previously isolated from uterine fluid, where they likely contribute to the embryo-endometrium crosstalk during implantation. Based on a meta-analysis of studies on endometrial tissue implantation-associated genes and the human exosomes database, 28 of the 57 transcripts considered as receptivity markers refer to proteins present in human exosomes. However, the specific transcriptomic content of receptive phase UF-EVs has yet to be defined.

STUDY DESIGN, SIZE, DURATION

Two experimental series were set up. First, we simultaneously sequenced RNA species derived from paired UF-EVs and endometrial tissue samples collected from physiologically cycling women. Second, we analyzed RNA species of UF-EVs collected during the non-receptive (LH + 2) and receptive (LH + 7) phase of proven fertile women and from the receptive (LH + 7) phase of a population of women undergoing ART and transfer of euploid blastocysts.

PARTICIPANTS/MATERIALS, SETTING, METHODS

For paired UF-endometrial tissue sampling, endometrial tissue biopsies were obtained with the use of a Pipelle immediately after UF collection performed by lavage of the endometrial cavity. Overall, n = 87 UF samples were collected and fresh-processed for EV isolation and total RNA extraction, while western blotting was used to confirm the expression of EV protein markers of the isolated vesicles. Physical characterization of UF-EVs was performed by Nanoparticle Tracking Analysis. To define the transcriptomic cargo of UF-EV samples, RNA-seq libraries were successfully prepared from n = 83 UF-EVs samples and analyzed by RNA-seq analysis. Differential gene expression (DGE) analysis was used to compare RNA-seq results between different groups of samples. Functional enrichment analysis was performed by gene set enrichment analysis with g:Profiler. Pre-ranked gene set enrichment analysis (GSEA) with WebGestalt was used to compare RNA-seq results with the gene-set evaluated in a commercially available endometrial receptivity array.

MAIN RESULTS AND THE ROLE OF CHANCE

A highly significant correlation was found between transcriptional profiles of endometrial biopsies and pairwise UF-EV samples (Pearson's r = 0.70 P < 0.0001; Spearman's ρ = 0.65 P < 0.0001). In UF-EVs from fertile controls, 942 gene transcripts were more abundant and 1305 transcripts less abundant in the LH + 7 receptive versus the LH + 2 non-receptive phase. GSEA performed to evaluate concordance in transcriptional profile between the n = 238 genes included in the commercially available endometrial receptivity array and the LH + 7 versus LH + 2 UF-EV comparison demonstrated an extremely significant and consistent enrichment, with a normalized enrichment score (NES)=9.38 (P < 0.001) for transcripts up-regulated in LH + 7 in the commercial array and enriched in LH + 7 UF-EVs, and a NES = -5.40 (P < 0.001) for transcripts down-regulated in LH + 7 in the commercial array and depleted in LH + 7 UF-EVs. When analyzing LH + 7 UF-EVs of patients with successful versus failed implantation after transfer of one euploid blastocyst in the following cycle, we found 97 genes whose transcript levels were increased and 64 genes whose transcript levels were decreased in the group of women who achieved a pregnancy. GSEA performed to evaluate concordance in transcriptional profile between the commercially available endometrial receptivity array genes and the comparison of LH + 7 UF-EVs of women with successful versus failed implantation, demonstrated a significant enrichment with a NES = 2.14 (P = 0.001) for transcripts up-regulated in the commercial array in the receptive phase and enriched in UF-EVs of women who conceived, and a not significant NES = -1.18 (P = 0.3) for transcripts down-regulated in the commercial array and depleted in UF-EVs. In terms of physical features, UF-EVs showed a homogeneity among the different groups analyzed except for a slight but significant difference in EV size, being smaller in women with a successful implantation compared to patients who failed to conceive after euploid blastocyst transfer (mean diameter ± SD 205.5± 22.97 nm vs 221.5 ± 20.57 nm, respectively, P = 0.014).

LARGE SCALE DATA

Transcriptomic data were deposited in NCBI Gene Expression Omnibus (GEO) and can be retrieved using GEO series accession number: GSE158958.

LIMITATIONS, REASONS FOR CAUTION

Separation of RNA species associated with EV membranes might have been incomplete, and membrane-bound RNA species-rather than the internal RNA content of EVs-might have contributed to our RNA-seq results. Also, we cannot definitely distinguish the relative contribution of exosomes, microvesicles and apoptotic bodies to our findings. When considering patients undergoing ART, we did not collect UFs in the same cycle of the euploid embryo transfer but in the one immediately preceding. We considered this approach as the most appropriate in relation to the novel, explorative nature of our study. Based on our results, a validation of UF-EV RNA-seq analyses in the same cycle in which embryo transfer is performed could be hypothesized.

WIDER IMPLICATIONS OF THE FINDINGS

On the largest sample size of human EVs ever analyzed with RNA-seq, this study establishes a gene signature to use for less-invasive endometrial receptivity tests. This report is indeed the first to show that the transcriptome of UF-EVs correlates with the endometrial tissue transcriptome, that RNA signatures in UF-EVs change with endometrial status, and that UF-EVs could serve as a reservoir for potential less-invasive collection of receptivity markers. This article thus represents a step forward in the design of less-invasive approaches for real-time monitoring of endometrial status, necessary for advancing the field of reproductive medicine.

STUDY FUNDING/COMPETING INTEREST(S)

The study was funded by a competitive grant from European Society of Human Reproduction and Embryology (ESHRE Research Grant 2016-1). The authors have no financial or non-financial competing interests to disclose.

TRIAL REGISTRATION NUMBER

NA.