Meta-analysis of the effects of bovine in vitro embryo production on gene expression

Bovine embryo production, with both in vivo and in vitro production methods being employed, has acquired worldwide importance. In vitro culture systems, however, often fail to fully replicate the in vivo environment, potentially leading to altered gene expression at the blastocyst stage. This alteration in gene expression is reflected by post-transfer consequences such as lower pregnancy rates and higher loss rates compared to the transfer of in vivo-derived embryos or artificial insemination. While transcriptomic analyses such as microarray and RNA sequencing (RNA-seq) have been widely used to investigate these gene expression differences, the large number of genes detected and small sample sizes can limit the power of individual analyses. To address this limitation, our research question was whether a robust set of recurrent genes and pathways could be identified across these individual, underpowered analyses. Therefore, we conducted a meta-analysis of transcriptome data from Day 7-8 in vivo and in vitro produced (IVP) bovine blastocysts by subjecting raw data to a standardised analysis to gain a more robust understanding about gene expression patterns during in vitro embryo development. The IVP embryos exhibited up-regulation of genes involved in lipid metabolism and down-regulation of trophoblast-related genes. Additionally, pathways related to cytoplasmic translation and mRNA processing were consistently enriched in IVP embryos. Most notably, energy metabolism was yet again confirmed as altered in IVP embryos. Energy metabolism in IVP embryos is a suitable parameter for assessing the effects of in vitro fertilisation on development and should be used as a key marker to evaluate assisted reproductive protocols for improving whole animal outcomes.