O-236 A multi-omics genome-plus-transcriptome single-cell atlas of human pre-implantation development reveals the impact of chromosome instability on cell function within the embryo

Study question

Which are the transcriptional signatures of chromosome instability (CIN) on the human pre-implantation embryo biology at single-cell level?

Summary answer

CIN-perturbed cells show gene expression dosage effects as well as signatures of developmental delay and cell competition within the developing human embryo.

What is known already

According to studies analysing whole human embryos at single-cell resolution, as much as 90% of the Day3-4 and up to 100% of the Day6-12 carry one or more cells with mitotic abnormalities. Intriguingly, embryonic CIN does not necessarily preclude normal offspring, since ∼30% of mosaic blastocysts detected by preimplantation genetic testing for aneuploidy (PGT-A) can result in healthy live births. A model of post-implantation human development revealed cell selection mechanisms that deplete aneuploid cells from the germ layers. However, single-cell multi-omics approaches have not yet been applied to resolve the transcriptional signatures of CIN in human embryos.

Study design, size, duration

Cryopreserved human embryos donated for research were dissociated into single cells between Day1-7 post-fertilization. Cells were processed by scG&T-seq generating 295 genomes and 576 transcriptomes. This data was integrated with published single-cell RNA-seq data, totalling 2105 single-cell transcriptomes from 172 embryos. Inference of cells' DNA copy number (CN) from gene expression was benchmarked using G&T-seq data and used for cells lacking DNA-seq data.

Participants/materials, setting, methods

Effects of aneuploidies on gene expression, regulatory programs, lineage specification and developmental progression rates were studied by integrative analysis on single-cell whole genome copy number and whole transcriptome data.

Main results and the role of chance

On the genomic level, we observed frequent acquired numerical and structural chromosomal aberrations. Deletions were more frequent than duplications and were equally spread across pre-implantation stages and cell lineages. Although 88% of the embryos contained aneuploid cells, 63% still contained euploid cells. On the transcriptome level, we disclosed 248 active transcription factors (TFs), including key regulators of cell identity, that constitute 10 major gene regulatory modules driving pre-implantation development. By integrating single-cell DNA-plus-RNA information, we unveil that changes in genes’ CN directly result in transcriptional changes in the same direction, and we disclose aberrant gene regulation. Moreover, we observed cell competition instigating well before ICM/TE cell lineages specification. Common transcriptomic signatures within CIN-perturbed cells were identified. Interestingly, in TE, cell competition signatures co-existed with up-regulation of pro-proliferative and implantation-related genes.

Limitations, reasons for caution

Our study is based on single-cell whole genome expression data from disaggregated IVF pre-implantation embryos.

Wider implications of the findings

Our analyses suggest that while unfit CIN-perturbed cells might be eliminated by cell competition mechanisms, these might be tolerated and potentially beneficial in TE. Thus, encouraging the transfer of mosaic embryos after PGT-A. Besides, we provide a unique comprehensive data resource for future work.

Trial registration number

not applicable

Efficiencies and mechanisms of nuclear reprogramming

The differentiated state of somatic cells is highly stable, but it can be experimentally reversed. The resulting cells can then be redirected into many different pathways. Nuclear reprogramming has been achieved by nuclear transfer to eggs, cell fusion, and overexpression of transcription factors. The mechanisms of nuclear reprogramming are not understood, but some insight into them is provided by comparing the efficiencies of different reprogramming strategies. Here, we compare these efficiencies by describing the frequency and rapidity with which reprogramming is induced and by the proportion of cells and level of expression in which reprogramming is achieved. We comment on the mechanisms that lead to successful somatic-cell reprogramming and on those that resist in helping to maintain the differentiated state of somatic cells.

Mammalian nuclear transplantation to Germinal Vesicle stage Xenopus oocytes - a method for quantitative transcriptional reprogramming

Full-grown Xenopus oocytes in first meiotic prophase contain an immensely enlarged nucleus, the Germinal Vesicle (GV), that can be injected with several hundred somatic cell nuclei. When the nuclei of mammalian somatic cells or cultured cell lines are injected into a GV, a wide range of genes that are not transcribed in the donor cells, including pluripotency genes, start to be transcriptionally activated, and synthesize primary transcripts continuously for several days. Because of the large size and abundance of Xenopus laevis oocytes, this experimental system offers an opportunity to understand the mechanisms by which somatic cell nuclei can be reprogrammed to transcribe genes characteristic of oocytes and early embryos. The use of mammalian nuclei ensures that there is no background of endogenous maternal transcripts of the kind that are induced. The induced gene transcription takes place in the absence of cell division or DNA synthesis and does not require protein synthesis.

Here we summarize new as well as established results that characterize this experimental system. In particular, we describe optimal conditions for transplanting somatic nuclei to oocytes and for the efficient activation of transcription by transplanted nuclei. We make a quantitative determination of transcript numbers for pluripotency and housekeeping genes, comparing cultured somatic cell nuclei with those of embryonic stem cells. Surprisingly we find that the transcriptional activation of somatic nuclei differs substantially from one donor cell-type to another and in respect of different pluripotency genes. We also determine the efficiency of an injected mRNA translation into protein.