The global gene expression outline of the bovine blastocyst: reflector of environmental conditions and predictor of developmental capacity

Abstract

Background Morphological evaluation of embryos has been used to screen embryos for transfer. However, the repeatability and accuracy of this method remains low. Thus, evaluation of an embryo’s gene expression signature with respect to its developmental capacity could provide new opportunities for embryo selection. Since the gene expression outline of an embryo is considered as an aggregate of its intrinsic characteristics and culture conditions, we have compared transcriptome profiles of in vivo and in vitro derived blastocysts in relation to pregnancy outcome to unravel the discrete effects of developmental competence and environmental conditions on bovine embryo gene expression outlines. To understand whether the gene expression patterns could be associated with blastocyst developmental competency, the global transcriptome profile of in vivo (CVO) and in vitro (CVT) derived competent blastocysts that resulted in pregnancy was investigated relative to that of in vivo (NVO) and in vitro (NVT) derived blastocysts which did not establish initial pregnancy, respectively while to unravel the effects of culture condition on the transcriptome profile of embryos, the transcriptional activity of the CVO group was compared to the CVT group and the NVO group was compared to the NVT ones. Results A total of 700 differentially expressed genes (DEGs) were identified between CVO and NVO blastocysts. These gene transcripts represent constitutive regions, indel variants, 3′-UTR sequence variants and novel transcript regions. The majority (82%) of these DEGs, including gene clusters like ATP synthases, eukaryotic translation initiation factors, ribosomal proteins, mitochondrial ribosomal proteins, NADH dehydrogenase and cytochrome c oxidase subunits were enriched in the CVO group. These DEGs were involved in pathways associated with glycolysis/glycogenesis, citrate acid cycle, pyruvate metabolism and oxidative phosphorylation. Similarly, a total of 218 genes were differentially expressed between CVT and NVT groups. Of these, 89%, including TPT1, PDIA6, HSP90AA1 and CALM, were downregulated in the CVT group and those DEGs were overrepresented in pathways related to protein processing, endoplasmic reticulum, spliceasome, ubiquitone mediated proteolysis and steroid biosynthesis. On the other hand, although both the CVT and CVO blastocyst groups resulted in pregnancy, a total of 937 genes were differential expressed between the two groups. Compared to CVO embryos, the CVT ones exhibited downregulation of gene clusters including ribosomal proteins, mitochondrial ribosomal protein, eukaryotic translation initiation factors, ATP synthases, NADH dehydrogenase and cytochrome c oxidases. Nonetheless, downregulation of these genes could be associated with pre and postnatal abnormalities observed after transfer of in vitro embryos. Conclusion The present study provides a detailed inventory of differentially expressed gene signatures and pathways specifically reflective of the developmental environment and future developmental capacities of bovine embryos suggesting that transcriptome activity observed in blastocysts could be indicative of further pregnancy success but also adaptation to culture environment.

Machine‐learning methods applied to integrated transcriptomic data from bovine blastocysts and elongating conceptuses to identify genes predictive of embryonic competence

“…22 Blastocyst data (Bl) were downloaded from the data set GSE131178 in the Gene Expression Omnibus 16 or obtained after request. 12 These data sets were renamed Bl_Zo and Bl_SW, respectively. Elongating conceptus data were downloaded from the data set GSE75750.…”

The first week following insemination is the period of major pregnancy failure in pasture-grazed dairy cows

“…The developmental fate of the preimplantation embryo was assessed by morphology (embryo stages and quality) to understand when pregnancy failure had or would occur, rather than assigning loss to the day of recovery. The concept of predicting future pregnancy outcomes at d 7 has been previously reported using a candidate-gene approach associated with pregnancy outcomes (El-Sayed et al, 2006;Zolini et al, 2020;Salilew-Wondim et al, 2021).…”

“…This is an important distinction when identifying developmental events associated with reproductive outcomes. This is not a new concept, as predicting future pregnancy outcomes at d 7 has been previously reported using a candidate-gene approach and associating those with pregnancy outcomes (El-Sayed et al, 2006;Zolini et al, 2020;Salilew-Wondim et al, 2021). The difference is that we used a morphologically based evaluation system of the obvious poor-quality embryos rather than predicting pregnancy outcome of excellent and good blastocyst-stage embryos.…”

Metabolic signature of spent culture media shows lipid metabolism as a determinant of pregnancy outcomes

“…Results unravelled more than 700 differentially expressed genes between the two types of embryos. More than 80% of these genes were related to mitochondrial functions and ATP generating mechanisms, demonstrating that competent in vivo embryos are characterized by higher expression of genes involved in mitochondrial metabolism (Salilew-Wondim et al, 2021).…”

“…Unfortunately, these adjustments still cannot be efficiently replicated in vitro. Embryos generated in vitro suffer from non-physiological factors such as the composition of the culture media, inadequate oxygen levels, pH, temperature, humidity and others (Salilew-Wondim et al, 2021). These suboptimal conditions can compromise embryonic competence and result in low blastocyst rates (approximately 40% over the number of fertilized oocytes) (Ealy et al, 2019) and high rates of pregnancy loss after IVP embryo transfer (Pedersen et al, 2017).…”