Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids

Abstract

The pre-conceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of Assisted Reproductive Technologies (ART; ~25%), additives and adjuvants, such as glucocorticoids, are utilized to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study we present a comprehensive single-cell transcriptome, methylome and small RNA atlas in the day 7 human embryo. We demonstrate that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the TE lineage and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sub-lineages, supported by the presence of extravillous trophoblast markers in the polar sub-lineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation (DNA methylation and microRNAs (miRNAs)) likely underlie the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.

The Guinea Pig: A New Model for Human Preimplantation Development

“…Optimal culturing conditions for guinea pig preimplantation embryos remain to be determined. We experimented with media previously reported to be used with the guinea pig 7 , in addition to what is commonly used in different species including M2 and KSOM (mouse) 85 , RDH (rabbit) 66 , mR1ECM (rat) 3 , GTL 86 and Global medium 3 (human) and N2B27 (mouse 34 , human 57 , bovine 67 , ovine 87 , porcine 42 and blastoids 88 ). We found (see Supplementary Table 7) that embryos do not progress in vitro in any of the media tested prior to compaction (1C – non-compacted 16C).…”

“…Human preimplantation embryo transcriptomes were compiled from two single-cell profiling studies 24,49 . These data were reprocessed as reported in 86 . Updated annotations from Meistermann et al 19 were used for the Petropoulos et al datasets 24,27 .…”

Cross-species comparison of mouse and human preimplantation development with an emphasis on lineage specification

“…These groundbreaking models have provided the scientific community with a platform to better understand previously inaccessible aspects of early human development by circumventing some of the ethical constraints and limitations associated with human blastocyst research. Further, the predictive value of blastoids in studies involving drug screening and therapeutic interventions was recently demonstrated by exposing the Kawaga et al model to exogenous glucocorticoid (GC) and comparing it to the human blastocyst (Kagawa et al 2022, Zhao et al 2022). The changes observed in protein expression of genes following GC treatment in the human blastocyst were similarly impacted in blastoids, suggesting that the effects of interventions on gene expression or exposures are modeled well (Zhao et al 2022).…”

“…Further, the predictive value of blastoids in studies involving drug screening and therapeutic interventions was recently demonstrated by exposing the Kawaga et al model to exogenous glucocorticoid (GC) and comparing it to the human blastocyst (Kagawa et al 2022, Zhao et al 2022). The changes observed in protein expression of genes following GC treatment in the human blastocyst were similarly impacted in blastoids, suggesting that the effects of interventions on gene expression or exposures are modeled well (Zhao et al 2022). Amongst the published studies, the production of human blastoids has mainly involved culturing human naïve or reprogrammed pluripotent stem cells with tailored culture media in systems that permit 3D cellular interactions and differentiation.…”

Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development

“…Improved scCOOL-seq (iscCOOL-seq) also dissects complex epigenetic alterations during mouse oocyte growth [92] . The combined approach of the whole-scale transcriptome with DNA methylome, single-cell genome-wide methylome and transcriptome sequencing (scM&T-seq), enables the identification of susceptibility to glucocorticoids in human blastocyst embryos [93] . Single-cell nucleosome occupancy, DNA methylation, and RNA expression sequencing (scNOMeRe-seq) [94] and single-cell chromatin accessibility, RNA barcoding, and DNA methylation sequencing (scChaRM-seq) [95] are tripartite-omics techniques, which are capable of simultaneously acquiring the profiles of the DNA methylome, transcriptome, and chromatin accessibility in single blastomeres in mouse preimplantation embryos (where genetic lineages were remodeled by DNA methylation in 4- and 8-cell embryos) and in single human oocytes, respectively.…”