Extensive rewiring of the gene regulatory interactions between in vitro-produced conceptuses and endometrium during attachment

ABSTRACT Pregnancy loss is a significant problem when embryos produced in vitro are transferred to a synchronized uterus. Currently, mechanisms that underlie losses of in vitro-produced embryos during implantation are largely unknown. We investigated this problem using cattle as a model of conceptus attachment by analyzing transcriptome data of paired extraembryonic membrane and endometrial samples collected on gestation days 18 and 25, which spans the attachment window in cattle. We identified that the transfer of an in vitro-produced embryo caused a significant alteration in transcript abundance of hundreds of genes in extraembryonic and endometrial tissues on gestation days 18 and 25, when compared to pregnancies initiated by artificial insemination. Many of the genes with altered transcript abundance are associated with biological processes that are relevant to the establishment of pregnancy. An integrative analysis of transcriptome data from the conceptus and endometrium identified hundreds of putative ligand-receptor pairs. There was a limited variation of ligand-receptor pairs in pregnancies initiated by in vitro-produced embryos on gestation day 18, and no alteration was observed on gestation day 25. In parallel, we identified that in vitro production of embryos caused an extensive alteration in the co-expression of genes expressed in the extraembryonic membranes and the corresponding endometrium on both gestation days. Both the transcriptional dysregulation that exists in the conceptus or endometrium independently, and the rewiring of gene transcription between the conceptus and endometrium are a potential component of the mechanisms that contribute to pregnancy losses caused by in vitro production of embryos. SIGNIFICANCE STATEMENT The successful establishment of pregnancies following the transfer of an in vitro produced embryo is essential for cattle production and assisted human reproduction. Most of the pregnancies initiated by the transfer of an in vitro produced embryo fail, in part because of dysfunctional interaction between the embryo and endometrium during pregnancy establishment. Our study identified that conceptuses produced in vitro and their corresponding endometrium have massive dysregulation in gene activity during the peri-implantation window, which affects crucial biological functions necessary for pregnancy. These gene expression alterations are a major contributor to the high rates of pregnancy loss following the transfer of an in vitro produced embryo. Our findings have implications for improving assisted reproduction in both agriculture and biomedicine.