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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
Abstract 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...
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| Published in: | Human reproduction (Oxford) 2022-06, Vol.37 (Supplement_1) |
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| Main Authors: | , , , , , , , , , , , , , , |
| Format: | Article |
| Language: | English |
| Online Access: | Get full text |
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| Summary: | Abstract
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 dir |
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| ISSN: | 0268-1161 1460-2350 |
| DOI: | 10.1093/humrep/deac106.018 |