P-542 Accuracy of Rapid Prenatal Testing by 24-chromosome analysis using Next Generation Sequencing

Study question

What is the accuracy of NGS versus QF-PCR in the Rapid Prenatal Testing?

Summary answer

NGS seems to be a reliable alternative for Rapid Prenatal Testing and expand the aneuploidy screening to all 24 chromosomes.

What is known already

As part of the prenatal care, whenever an invasive testing is needed, rapid prenatal analysis is performed to rule out the most common aneuploidies (i.e., trisomy for chromosomes 13, 18 and 21), using FISH or QF-PCR. Some studies describe the use of the NGS as an alternative to detect genetic alterations in the DNA from amniocytes or chorionic villus sampling (CVS) in Prenatal Genetic Testing.

Study design, size, duration

This research study evaluates the accuracy of NGS analysis for Rapid Prenatal Testing comparing the results with gold standard techniques. A total of 32 amniotic fluid samples clinically analysed by karyotype (n = 3) or QF-PCR (n = 29) were used as reference resulting in: normal male (n = 3); normal female (n = 9); trisomy 13 (n = 3); trisomy 18 (n = 5; one by karyotype); trisomy 21 (n = 10; one by karyotype); partial trisomy 3q26q26/partial monosomy 5p13p15.33 (n = 1; by karyotype); and triploid XXY (n = 1).

Participants/materials, setting, methods

All 32 samples were analysed using an NGS platform validated for PGT-A (Preimplantation Genetic Testing for aneuploidy). Ion ReproSeq™ PGS kit was used for library preparation, Ion Chef™ and Ion S5 System instruments for sequencing and Ion Reporter software for data analysis (Thermo Fisher Scientific, USA), with a proprietary bioinformatics pipeline (v2.0) for the analysis of 24-chromosome aneuploidies and partial duplication/deletions (≥10Mb). NGS results were compared with the reference QF-PCR/Karyotype results for accuracy evaluation.

Main results and the role of chance

When comparing NGS versus QF-PCR/Karyotype results, we observed a 100% concordance for the detection of trisomy 13 (3 out of 3 samples), trisomy 18 (5 out of 5 samples), trisomy 21 (10 out of 10 sample) and partial trisomy 3q/partial monosomy 5p (1 out of 1 sample). We did not identify false positives for any of the chromosomes in which comparison could be done as they were analysed in the reference samples (chromosomes 13, 18, 21, X and Y for QF-PCR reference samples, and all 24 chromosomes for Karyotype reference samples). In one of the samples, the triploid XXY, the NGS profile for the sex chromosomes was compatible either with a normal male result with maternal cell contamination or with a triploid XXY result, and was finally classified as non-informative for NGS.

Limitations, reasons for caution

The NGS cannot identify deletions/duplications <10Mb and mosaicism <30%. The platform used cannot identify some types of polyploidies, therefore, additional analysis (Short Tandem Repeats, karyotype, or SNP-arrays) when normal results are needed. However, improvements in technology that are currently underway will solve this limitation.

Wider implications of the findings

Based on the experience gained since the implantation of the NGS method for the characterization of the chromosomal status of DNA samples, the use of the NGS platform and protocols for the rapid prenatal test samples has as benefit to expand the screening analysis to all 24 chromosomes.

Trial registration number

Not applicable

Heterogeneous nuclear ribonucleoprotein C1 may control miR-30d levels in endometrial exosomes affecting early embryo implantation

STUDY QUESTION

Is there a specific mechanism to load the microRNA (miRNA), hsa-miR-30d, into exosomes to facilitate maternal communication with preimplantation embryos?

SUMMARY ANSWER

The heterogeneous nuclear ribonucleoprotein C1 (hnRNPC1) is involved in the internalization of endometrial miR-30d into exosomes to prepare for its subsequent incorporation into trophectoderm cells.

WHAT IS KNOWN ALREADY

Our group previously described a novel cell-to-cell communication mechanism involving the delivery of endometrial miRNAs from the maternal endometrium to the trophectoderm cells of preimplantation embryos. Specifically, human endometrial miR-30d is taken up by murine blastocysts causing the overexpression of certain genes involved in embryonic adhesion (Itb3, Itga7 and Cdh5) increasing embryo adhesion rates.

STUDY DESIGN, SIZE, DURATION

Transfer of maternal miR-30d to preimplantation embryos was confirmed by co-culture of wild-type (WT) and miR-30d knockout (KO) murine embryos with primary cultures of human endometrial epithelial cells (hEECs) in which mir-30d was labeled with specific Molecular Beacon (MB) or SmartFlare probes. Potential molecules responsible for the miR-30d loading into exosomes were purified by pull-down analysis with a biotinylated form of miR-30d on protein lysates from human endometrial exosomes, identified using mass spectrometry and assessed by flow cytometry, western blotting and co-localization studies. The role of hnRNPC1 in the miR-30d loading and transportation was interrogated by quantification of this miRNA in exosomes isolated from endometrial cells in which hnRNPC1 was transiently silenced using small interference RNA. Finally, the transfer of miR-30d to WT and KO embryos was assessed upon co-culture with sihnRNPC1 transfected cells.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Murine embryos from miR-30d WT and KO mice, (strain MirC26tm1Mtm/Mmjax), were obtained by oviduct flushing of superovulated females. Endometrial Exosomes were purified by ultracentrifugation of supernatants from primary cultures of hEECs or Ishikawa cells. MB and Smartflare miR-30d probes were detected by confocal and/or transmission electron microscopy (TEM). hEECs and exosomes derived from them were subjected to pull-down with a biotinylated form of miR-30d. Captured proteins were identified by mass spectrometry (MS/MS). Western blotting was performed to detect hnRNPC1 and CYR61 in whole lysates, subcellular fractions and secreted vesicles from hEECs. Co-localization studies of the selected proteins with the exosomal marker CD63 were performed. FACS analysis was carried out to determine the presence of hnRNPC1 inside exosomes. Silencing of hnRNPC1 was conducted in the Ishikawa Cell Line with the Smart Pool Accell HNRNPC siRNA at a final concentration of 50 nM. RT-qPCRs were done to determine the messenger levels of miR-30d in cells and exosomes. Co-cultures of WT and KO embryos were established with Ishikawa cells double-transfected with sihnRPNC1 and MB probes.

MAIN RESULTS AND THE ROLE OF CHANCE

MS/MS analysis allowed us to identify hnRNPC1 as a possible protein to influence miR-30d loading into exosomes. Co-localization studies of hnRNPC1 with CD63 and FACS analyses suggested the presence of hnRNPC1 inside exosomes. Silencing of hnRNPC1 in Ishikawa cells resulted in a sharp decrease of the levels of miR-30d in both epithelial-like cells (P = 0.0001) and exosomes (P = 0.0152), suggesting its potential role in miR-30d biogenesis and transfer. Co-culture assays of miR-30d KO embryos with sihnRNPC1 hEECs revealed a decrease in embryo-miR-30d acquisition during the adhesion and invasion stages. In turn, transient silencing of hnRNPC1 results in a significant decrease of blastocyst adhesion compared to mock transfection conditions using Block-it, in both WT [Mean ± SD; 67 ± 10.0% vs. 38 ± 8.5%(P = 0.0006)] and miR-30d KO embryos [Mean ± SD; 50 ± 11.5% vs. 26 ± 8.8% (P = 0.0029) (n = 2); 14 embryos transferred per condition tested].

LARGE-SCALE DATA

MS/MS data are available via ProteomeXchange with identifier PXD008773.

LIMITATIONS, REASONS FOR CAUTION

The Ishikawa Cell Line was used as a model of hEECs in silencing experiments due to the low survival rates of primary hEECs after transfection.

WIDER IMPLICATIONS OF THE FINDINGS

The data show that hnRNPC1 may be involved in the internalization of miR-30d inside exosomes. The decreased rates of embryo adhesion in endometrial epithelial-like cells transiently silenced with sihnRNPC1evidence that hnRNPC1 could be an important player in the maternal-embryo communication established in the early stages of implantation.

STUDY FUNDING AND COMPETING INTEREST(S)

This work was supported by the Miguel Servet Program Type I of Instituto de Salud Carlos III [CP13/00038]; FIS project [PI14/00545] to F.V.; the 'Atracció de Talent' Program from VLC-CAMPUS [UV-INV-PREDOC14-178329 to NB]; a Torres-Quevedo grant (PTQ-13-06133) by the Spanish Ministry of Economy and Competitiveness to IM and MINECO/FEDER Grant [SAF2015-67154-R] to C.S. The authors declare there is no conflict of interest.

Hsa-miR-30d, secreted by the human endometrium, is taken up by the pre-implantation embryo and might modify its transcriptome

During embryo implantation, the blastocyst interacts with and regulates the endometrium, and endometrial fluid secreted by the endometrial epithelium nurtures the embryo. Here, we propose that maternal microRNAs (miRNAs) might act as transcriptomic modifier of the pre-implantation embryo. Microarray profiling revealed that six of 27 specific, maternal miRNAs were differentially expressed in the human endometrial epithelium during the window of implantation--a brief phase of endometrial receptivity to the blastocyst--and were released into the endometrial fluid. Further investigation revealed that hsa-miR-30d, the expression levels of which were most significantly upregulated, was secreted as an exosome-associated molecule. Exosome-associated and free hsa-miR-30d was internalized by mouse embryos via the trophectoderm, resulting in an indirect overexpression of genes encoding for certain molecules involved in the murine embryonic adhesion phenomenon--Itgb3, Itga7 and Cdh5. Indeed, this finding was supported by evidence in vitro: treating murine embryos with miR-30d resulted in a notable increase in embryo adhesion. Our results suggest a model in which maternal endometrial miRNAs act as transcriptomic modifiers of the pre-implantation embryo.