Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism

Abstract

Less than half of human zygotes survive to birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors generate chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and impacts of mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of few embryonic cells. Single-cell genomic data provide an opportunity to quantify mosaicism on an embryo-wide scale. To this end, we extended an approach to infer aneuploidies based on dosage-associated changes in gene expression by integrating signatures of allelic imbalance. We applied this method to published single-cell RNA sequencing data from 74 human embryos, spanning the morula to blastocyst stages. Our analysis revealed widespread mosaic aneuploidies, with 59 of 74 (80%) embryos harboring at least one putative aneuploid cell (1% FDR). By clustering copy number calls, we reconstructed histories of chromosome segregation, inferring that 55 (74%) embryos possessed mitotic aneuploidies and 23 (31%) embryos possessed meiotic aneuploidies. We found no significant enrichment of aneuploid cells in the trophectoderm compared to the inner cell mass, although we do detect such enrichment in data from later postimplantation stages. Finally, we observed that aneuploid cells up-regulate immune response genes and down-regulate genes involved in proliferation, metabolism, and protein processing, consistent with stress responses documented in other stages and systems. Together, our work provides a high-resolution view of aneuploidy in preimplantation embryos, and supports the conclusion that low-level mosaicism is a common feature of early human development.

Developmental potential of aneuploid human embryos cultured beyond implantation

“…Although we did not detect any significant morphological alterations in trisomy 21 and trisomy 15 embryos, whether there are changes at the mRNA and protein levels remains to be explored. In support of this notion, previous reports have shown marked transcriptional alterations in pre-implantation aneuploid human embryos 42,45,46 . Careful analysis of trisomy 16 embryos revealed a marked hypoproliferation phenotype specific to the trophoblast.…”

“…These results rely on inducing aneuploidy by the drug reversine, which can cause chaotic aneuploidies 26 . Interestingly, it has been reported that while rates of aneuploidy between the trophoblast and ICM are not significantly different at the blastocyst stage, aneuploid cells are enriched in the trophoblast of in vitro cultured postimplantation human embryos 42 . Moreover, mouse epiblast cells at early post-implantation stages upregulate the expression of proapoptotic genes, which leads to a lower apoptotic threshold in embryonic versus extraembryonic cells in response to DNA damage 43,44 .…”

Involvement of uterine natural killer cells in the natural selection of human embryos at implantation

“…45,46 A recent analysis of published single-cell RNA-seq data concluded that 80% of human embryos harbour aneuploid cells. 47 This intrinsic genetic instability of human embryos, which gives rise to a vast array of chromosomal errors, poses a major challenge to the endometrium; how to eliminate embryos of low-fitness without compromising implantation of high-quality embryos?…”

PREIMPLANTATION GENETIC TESTING: Single-cell technologies at the forefront of PGT and embryo research

“…Human embryo single-cell RNA-seq datasets (Xue et al 2013, Yan et al 2013, Petropoulos et al 2016 are a very valuable resource and have been used by others not only to study gene signatures of cell differentiation (Blakeley et al 2015, Stirparo et al 2018, EGA (De Iaco et al 2017), embryo metabolism (Zhao et al 2019a) and expression dynamics of sex chromosomes (Zhou et al 2019a), but also to provide insight on transcriptional regulation during human preimplantation development (Grow et al 2015, Hasegawa et al 2015, Bouckenheimer et al 2016. In addition, the impact of aneuploidy on the transcriptome at single cell level has been investigated for the first time by computationally inferring the DNA copy number genome-wide from publicly available single-cell RNA-seq data (Petropoulos et al 2016, Starostik et al 2020. By doing so, similar signatures of aneuploidy were detected, which were previously described for other cell types, such as downregulation of genes involved in proliferation, metabolism and protein processing in addition to an upregulation of immune response genes (Santaguida & Amon 2015, Chunduri & Storchová 2019.…”