Effect of vitrification on global gene expression dynamics of bovine elongating embryos

Calf Fitness Associates with Early Embryo and Recipient Metabolomes and with Calf Epigenetic Marks

We used metadata to explore the metabolic interplay between culture medium from in vitro-produced bovine embryos transferred fresh or frozen, recipient blood plasma, and calf fitness, alongside gene expression and methylation in calf lymphocytes. Principal component (PC) analysis (PCA) identified covariates that were depicted in Debiased Sparse Partial Correlation networks and analyzed as enriched pathways. Four PCs explained 13.77, 9.58, 7.73 and 5.84% variability. PC1 clustered only mother weight and two embryonic metabolites. PC2, PC3 and PC4 associated 10, 17, and 5 calf features with 10, 6, and 16 embryonic and 2, 20, and 5 recipient metabolites, respectively. Subsequently, gene methylation and expression, and calf fitness were analyzed by PCA. Three PCs covered 100% variability. PC1 associated acid-base balance, protein metabolism, Cl-, and Ca2+ with IGF2 and IL1R1 expression, and IL4 and IL12B methylation. PC2 linked H19 expression and methylation with growth and biochemical traits. PC3 clustered growth, hydration, and redox balance, with IGF2, IGF2R, IL1R1 and IL3 methylation, and H19, IGF2, IGF2R and IL12B expression. Gene methylation connected with embryo metabolites through networks via K+, Cl-, HCO3- and TCO2. Calf fitness parallels the early metabolic fingerprints of the embryo and recipient, allowing embryo transfer decision-making based on calf health.

Endometrial extracellular vesicles regulate processes related to embryo development and implantation in human blastocysts

STUDY QUESTION

What is the transcriptomic response of human blastocysts following internalization of extracellular vesicles (EVs) secreted by the human endometrium?

SUMMARY ANSWER

EVs secreted by the maternal endometrium induce a transcriptomic response in human embryos that modulates molecular mechanisms related to embryo development and implantation.

WHAT IS KNOWN ALREADY

EVs mediate intercellular communication by transporting various molecules, and endometrial EVs have been postulated to be involved in the molecular regulation of embryo implantation. Our previous studies showed that endometrial EVs carry miRNAs and proteins associated with implantation events that can be taken up by human blastocysts; however, no studies have yet investigated the transcriptomic response of human embryos to this EV uptake, which is crucial to demonstrate the functional significance of this communication system.

STUDY DESIGN, SIZE, DURATION

A prospective descriptive study was performed. Primary human endometrial epithelial cells (pHEECs), derived from endometrial biopsies collected from fertile oocyte donors (n = 20), were cultured in vitro to isolate secreted EVs. Following EV characterization, Day 5 human blastocysts (n = 24) were cultured in the presence or absence of the EVs for 24 h and evaluated by RNA-sequencing.

PARTICIPANTS/MATERIALS, SETTING, METHODS

EVs were isolated from the conditioned culture media using ultracentrifugation, and characterization was performed using western blot, nanoparticle tracking analysis, and transmission electron microscopy. Human blastocysts were devitrified, divided into two groups (n = 12/group), and cultured in vitro for 24 h with or without previously isolated EVs. RNA-sequencing analysis was performed, and DESeq2 was used to identify differentially expressed genes (DEGs) (FDR < 0.05). QIAGEN Ingenuity Pathway Analysis was used to perform the functional enrichment analysis and integration with our recently published data from the pHEECs' EV-miRNA cargo.

MAIN RESULTS AND THE ROLE OF CHANCE

Characterization confirmed the isolation of EVs from pHEECs' conditioned culture media. Among the DEGs in blastocysts co-cultured with EVs, we found 519 were significantly upregulated and 395 were significantly downregulated. These DEGs were significantly enriched in upregulated functions related to embryonic development, cellular invasion and migration, cell cycle, cellular organization and assembly, gene expression, and cell viability; and downregulated functions related to cell death and DNA fragmentation. Further, the intracellular signaling pathways regulated by the internalization of endometrial EVs were previously related to early embryo development and implantation potential, for their role in pluripotency, cellular homeostasis, early embryogenesis, and implantation-related processes. Finally, integrating data from miRNA cargo of EVs, we found that the miRNAs carried by endometrial EVs targeted nearly 80% of the DEGs in human blastocysts.

LIMITATIONS, REASONS FOR CAUTION

This is an in vitro study in which conditions of endometrial cell culture could not mimic the intrauterine environment.

WIDER IMPLICATIONS OF THE FINDINGS

This study provides novel insights into the functional relevance of EVs secreted by the human endometrium, and particularly the role of EV-miRNA regulation on global transcriptome behavior of human blastocysts during early embryogenesis and embryo implantation. It provides potential biomarkers that could become useful diagnostic targets for predicting implantation success.

STUDY FUNDING/COMPETING INTEREST(S)

This study was supported by the Spanish Ministry of Education through FPU awarded to M.S.-B. (FPU18/03735), Generalitat Valenciana through VALi+d Programme awarded to M.C.C.-G. (ACIF/2019/139), and Instituto de Salud Carlos III and cofounded by the European Social Fund (ESF) "Investing in your future" through the Miguel Servet Program (CP20/00120 [H.F.]; CP19/00149 [I.C.]). The authors have no conflicts of interest to disclose.

TRIAL REGISTRATION NUMBER

N/A.

Development of a formula for scoring competence of bovine embryos to sustain pregnancy

Embryo transfer in cattle and other species is a key reproductive technology to improve genetic merit. However, pregnancy loss after embryo transfer is still a major barrier to optimal utilization of the technology. Furthermore, the lack of a method to objectively quantify embryonic competence hinders investigations aimed at improving the competence of an embryo. Based on the knowledge that bovine embryos have an inherent molecular signature that determines their ability for pregnancy establishment which can result in distinct gene expression profiles, we have previously integrated transcriptomic data from independent experiments to identify eight genes capable of predicting embryo competence for survival with high accuracy. In this study, we developed a function for the R software containing a mathematical formula based on the model coefficients to yield an embryonic competence index (ECI) according to the expression of those eight critical genes. Application of the function to a gene expression dataset generates a quantitative ECI value for each embryo that can be employed in statistical analyses when performing an experiment. The folder with the R project and required datasets can be found in https://zenodo.org/records/12515587.

Double vitrification of embryos adversely affects clinical outcomes

OBJECTIVE

To evaluate the impact of double embryo vitrification on clinical outcomes.

METHODS

This retrospective cohort study included data from January 2013 to March 2021. The study group included women aged 33.3±5.7 years with double-vitrified embryos (n=381), while the control group included women aged 32.1±6.7 years with embryos vitrified once (n=780), all transferred at the blastocyst stage. The primary endpoint was live birth rate (LBR), and secondary endpoints included percent positive βHCG test, clinical/ongoing pregnancy rates, miscarriage/biochemical pregnancy rates and birthweight.

RESULTS

LBR was significantly lower in double-vitrified embryos (30.2%) than in embryos vitrified once (45.6%, p<.05). Similarly, double-vitrified embryos were associated with significantly lower positive βHCG tests (46% vs. 63.3%, p<.05) and clinical (34.9% vs. 52.2%, p<.05) and ongoing pregnancy (31.3% vs. 47.3%, p<.05) rates compared to embryos vitrified once. However, biochemical pregnancy (double vitrified: 24.1% vs. vitrified once: 17.9%, p>.05) and miscarriage rates (double vitrified: 10.2% vs. vitrified once: 9.4%, p>.05), as well as mean birthweight (double-vitrified embryos: 2950g vs. embryos vitrified once: 2837g, p>.05) did not differ significantly between two groups. On a secondary comparison, amongst double-vitrified embryos, the subgroup that was cultured for more than 24 hours between warming and second vitrification achieved significantly higher positive βHCG tests (49%) and clinical pregnancy (38%) rates, compared to embryos re-vitrified on the same day of warming (31.8% and 20.5%, respectively, p<.05). Nevertheless, LBR did not differ significantly amongst these study-group embryos (embryos that remained in culture for more than 24 hours: 32.2% vs. embryos that were re-vitrified on warming day: 20.5%, p>.05).

CONCLUSIONS

Double vitrification of embryos adversely affects clinical outcomes. However, it represents a valuable option concerning embryo wastage, with acceptable success rates.

Safety of embryo cryopreservation: insights from mid-term placental transcriptional changes

BACKGROUND

In recent years, with benefits from the continuous improvement of clinical technology and the advantage of fertility preservation, the application of embryo cryopreservation has been growing rapidly worldwide. However, amidst this growth, concerns about its safety persist. Numerous studies have highlighted the elevated risk of perinatal complications linked to frozen embryo transfer (FET), such as large for gestational age (LGA) and hypertensive disorders during pregnancy. Thus, it is imperative to explore the potential risk of embryo cryopreservation and its related mechanisms.

METHODS

Given the strict ethical constraints on clinical samples, we employed mouse models in this study. Three experimental groups were established: the naturally conceived (NC) group, the fresh embryo transfer (Fresh-ET) group, and the FET group. Blastocyst formation rates and implantation rates were calculated post-embryo cryopreservation. The impact of FET on fetal growth was evaluated upon fetal and placental weight. Placental RNA-seq was conducted, encompassing comprehensive analyses of various comparisons (Fresh-ET vs. NC, FET vs. NC, and FET vs. Fresh-ET).

RESULTS

Reduced rates of blastocyst formation and implantation were observed post-embryo cryopreservation. Fresh-ET resulted in a significant decrease in fetal weight compared to NC group, whereas FET reversed this decline. RNA-seq analysis indicated that the majority of the expression changes in FET were inherited from Fresh-ET, and alterations solely attributed to embryo cryopreservation were moderate. Unexpectedly, certain genes that showed alterations in Fresh-ET tended to be restored in FET. Further analysis suggested that this regression may underlie the improvement of fetal growth restriction in FET. The expression of imprinted genes was disrupted in both FET and Fresh-ET groups.

CONCLUSION

Based on our experimental data on mouse models, the impact of embryo cryopreservation is less pronounced than other in vitro manipulations in Fresh-ET. However, the impairment of the embryonic developmental potential and the gene alterations in placenta still suggested it to be a risky operation.

Molecular and cellular programs underlying the development of bovine pre-implantation embryos

Early embryonic mortality is a major cause of infertility in cattle, yet the underlying molecular causes remain a mystery. Over the past half century, assisted reproductive technologies such as in vitro fertilisation and somatic cell nuclear transfer have been used to improve cattle reproductive efficiency; however, reduced embryo developmental potential is seen compared to their in vivo counterparts. Recent years have seen exciting progress across bovine embryo research, including genomic profiling of embryogenesis, new methods for improving embryo competence, and experimenting on building bovine embryos from stem cell cultures. These advances are beginning to define bovine embryo molecular and cellular programs and could potentially lead to improved embryo health. Here, I highlight the current status of molecular determinants and cellular programs of bovine embryo development and new opportunities to improve the bovine embryo health.

Establishment of bovine trophoblast stem cells

Here, we report that a chemical cocktail (LCDM: leukemia inhibitory factor [LIF], CHIR99021, dimethinedene maleate [DiM], minocycline hydrochloride), previously developed for extended pluripotent stem cells (EPSCs) in mice and humans, enables de novo derivation and long-term culture of bovine trophoblast stem cells (TSCs). Bovine TSCs retain developmental potency to differentiate into mature trophoblast cells and exhibit transcriptomic and epigenetic (chromatin accessibility and DNA methylome) features characteristic of trophectoderm cells from early bovine embryos. The bovine TSCs established in this study will provide a model to study bovine placentation and early pregnancy failure.

Cryotop vitrification of large batches of pig embryos simultaneously provides excellent postwarming survival rates and minimal interference with gene expression

The most commonly used technique to vitrify pig embryos is the super open pulled straw (SOPS), where a maximum of 6 embryos can be vitrified simultaneously per device without compromising the minimum volume necessary for optimal preservation. Since optimal embryo transfer (ET) demands a transfer of 20-40 embryos per recipient, the customary use of SOPS complicates embryo warming and ET in field conditions. Such complications could be avoided when using the Cryotop® (OC) system, which has been proven to be an effective option for vitrifying at least 20 porcine embryos simultaneously. This study aimed to investigate the changes in the transcriptome of blastocysts caused by vitrification using both systems. In vivo-derived blastocysts were OC- (n = 60; 20 embryos/device) and SOPS- (n = 60; 4-6 embryos/device) vitrified and cultured for 24 h after warming. Nonvitrified blastocysts (n = 60) cultured for 24 h postcollection acted as controls. At the end of culture, 48 viable embryos from each group (6 pools of 8 embryos) were selected for microarray (GeneChip® Porcine Genome Array, P/N 900624, Affymetrix) analysis of differentially expressed genes (DEGs). The survival rate of embryos vitrified with the OC and SOPS systems (>97%) was similar to that of the control embryos (100%). Microarray analysis of each vitrification system compared to the control group showed 245 DEGs (89 downregulated and 156 upregulated) for the OC system and 210 (44 downregulated and 166 upregulated) for the SOPS system. Two pathways were enriched for the DEGs specifically altered in each vitrification system compared to the control (glycolysis/gluconeogenesis and carbon metabolism pathways for the OC system and amino sugar and nucleotide sugar metabolism and lysosome pathways in the SOPS group). The OC group showed 31 downregulated and 24 upregulated genes and two enriched pathways (mineral absorption and amino sugar and nucleotide sugar metabolism pathways) when compared to the SOPS group. In summary, vitrification with the OC system altered fewer genes related to apoptosis and activated genes related to cell proliferation. We conclude that vitrification with either the OC or SOPS system has a moderate to low effect on the transcriptome of in vivo-derived porcine blastocysts. Further investigation is needed to elucidate how the differences in the transcriptome of embryos vitrified with these systems affect their subsequent developmental ability after ET.

Effect of bovine oocyte vitrification with EGTA and post-warming recovery with resveratrol on meiotic spindle, mitochondrial function, reactive oxygen species, and developmental competence

The present study aimed to determine the effects of the addition of EGTA to vitrification solutions and a post-warming recovery period supplemented with 1 μM resveratrol on meiotic spindle integrity, mitochondrial activity, ATP content, reactive oxygen species (ROS) levels, and developmental potential of partially denuded, vitrified-warmed bovine oocytes. Results of microtubule distribution and chromosomal arrangement indicated that resveratrol supplementation, irrespective to EGTA addition, reduced the incidence of abnormal meiotic spindles to similar levels of the control group. Mitochondrial membrane potential was similar in all groups, but ATP content was negatively affected by the vitrification-warming procedure and failed to recover after 4 h of post-warming culture. Resveratrol caused the reduction of ROS to lower levels of the control group, and showed the lowest ROS levels when combined with EGTA treatment. Oocytes in all vitrification groups presented lower developmental potential when compared to fresh oocytes. However, oocytes that underwent vitrification supplemented with EGTA and post-warming culture along with resveratrol showed higher developmental competence compared with vitrified-warmed oocytes not supplemented with resveratrol. The results of our study indicate that submitting vitrified-warmed, partially denuded bovine oocytes to a post-warming recovery period supplemented with 1 μM resveratrol improves vitrification outcomes. However, the benefits of EGTA on vitrification and warming of bovine oocytes need to be further investigated.

Fitness of calves born from in vitro-produced fresh and cryopreserved embryos

In cattle, vitrified/warmed (V/W) and frozen/thawed (F/T), in vitro-produced (IVP) embryos, differ in their physiology and survival from fresh embryos. In this study, we analyzed the effects of embryo cryopreservation techniques on the offspring. IVP embryos cultured with albumin and with or without 0.1% serum until Day 6, and thereafter in single culture without protein, were transferred to recipients on Day 7 as F/T, V/W, or fresh, resulting in N = 24, 14, and 13 calves, respectively. Calves were clinically examined at birth, and blood was analyzed before and after colostrum intake (Day 0), and subsequently on Day 15 and Day 30. On Day 0, calves from V/W and F/T embryos showed increased creatinine and capillary refill time (CRT) and reduced heartbeats. Calves from F/T embryos showed lower PCO₂, hemoglobin, and packed cell volume than calves from V/W embryos while V/W embryos led to calves with increased Na⁺ levels. Colostrum effects did not differ between calves from fresh and cryopreserved embryos, indicating similar adaptive ability among calves. However, PCO₂ did not decrease in calves from V/W embryos after colostrum intake. Serum in culture led to calves with affected (P < 0.05) temperature, CRT, HCO 3 - , base excess (BE), TCO₂, creatinine, urea, and anion gap. On Day 15, the effects of embryo cryopreservation disappeared among calves. In contrast, Day 30 values were influenced by diarrhea appearance, mainly in calves from V/W embryos (i.e., lower values of TCO₂, HCO 3 - , and BE; and increased glucose, anion gap, and lactate), although with no more clinical compromise than calves from fresh and F/T embryos. Diarrhea affected PCO₂ and Na⁺ in all groups. Embryo cryopreservation, and/or culture, yield metabolically different calves, including effects on protein and acid-base metabolism.

Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

Background

Currently, there is a high demand for efficient pig embryo cryopreservation procedures in the porcine industry as well as for genetic diversity preservation and research purposes. To date, vitrification (VIT) is the most efficient method for pig embryo cryopreservation. Despite a high number of embryos survives in vitro after vitrification/warming procedures, the in vivo embryo survival rates after embryo transfer are variable among laboratories. So far, most studies have focused on cryoprotective agents and devices, while the VIT effects on porcine embryonic gene expression remained unclear. The few studies performed were based on vitrified/warmed embryos that were cultured in vitro (IVC) to allow them to re–expand. Thus, the specific alterations of VIT, IVC, and the cumulative effect of both remained unknown. To unveil the VIT-specific embryonic alterations, gene expression in VIT versus (vs.) IVC embryos was analyzed. Additionally, changes derived from both VIT and IVC vs. control embryos (CO) were analyzed to confirm the VIT embryonic alterations. Three groups of in vivo embryos at the blastocyst stage were analyzed by RNA–sequencing: (1) VIT embryos (vitrified/warmed and cultured in vitro), (2) IVC embryos and (3) CO embryos.

Results

RNA–sequencing revealed three clearly different mRNA profiles for VIT, IVC and CO embryos. Comparative analysis of mRNA profiles between VIT and IVC identified 321, differentially expressed genes (DEG) (FDR < 0.006). In VIT vs. CO and IVC vs. CO, 1901 and 1519 DEG were found, respectively, with an overlap of 1045 genes. VIT-specific functional alterations were associated to response to osmotic stress, response to hormones, and developmental growth. While alterations in response to hypoxia and mitophagy were related to the sum of VIT and IVC effects.

Conclusions

Our findings revealed new insights into the VIT procedure-specific alterations of embryonic gene expression by first comparing differences in VIT vs. IVC embryos and second by an integrative transcriptome analysis including in vivo control embryos. The identified VIT alterations might reflect the transcriptional signature of the embryo cryodamage but also the embryo healing process overcoming the VIT impacts. Selected validated genes were pointed as potential biomarkers that may help to improve vitrification.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00672-1.

Long-Term Storage Does Not Affect the Expression Profiles of mRNA and Long Non-Coding RNA in Vitrified-Warmed Human Embryos

Although vitrification has been widely applied in assisted reproductive technology, it is unknown whether storage time has any impact on the mRNA and lncRNA expression profiles in human embryos. Eleven women (aged 23-35 years) who had undergone in vitro fertilization treatment were recruited for this study. The transcriptomes of 3 fresh eight-cell embryos and 8 surviving vitrified-warmed eight-cell embryos (4 embryos were cryostored for 3 years, and the others were cryostored for 8 years) were analyzed through single-cell RNA-Seq. No differentially expressed mRNAs or lncRNAs were identified between the 3-years group and 8-years group. A total of 128 mRNAs and 365 lncRNAs were differentially expressed in the 8 vitrified-warmed embryos compared with the fresh embryos. The vitrification-warming impact was moderate, and it was mainly related to the pathways of metabolism, stress response, apoptosis, cell cycle, cell adhesion, and signaling for TFG-β and Hippo. The analysis of target mRNAs suggested that lncRNAs might contribute to the regulation of mRNAs after vitrification-warming. Our findings indicated that long-term storage after vitrification does not affect the mRNA and lncRNA expression profiles in human embryos, however, the procedure of vitrification-warming would lead to minor alteration of transcriptome.