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

Abstract

Less than half of human zygotes survive to live birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors lead to chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and fitness consequences of chromosomal mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of a 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 chromosome 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 disaggregated human embryos, spanning the morula to blastocyst stages. Our analysis revealed widespread mosaic aneuploidies across preimplantation development, with 59 of 74 (80%) embryos harboring at least one aneuploid cell (1% FDR). By clustering copy number calls, we reconstructed histories of chromosome mis-segregation, distinguishing meiotic and early mitotic errors from those occurring after lineage differentiation. We observed no significant enrichment of aneuploid cells in the trophectoderm compared to the inner cell mass, though we do detect such an enrichment in published data from later post-implantation stages. Finally, we observed that aneuploid cells exhibit upregulation of immune response genes, as well as downregulation of genes involved in proliferation, metabolism, and protein processing, consistent with stress responses previously 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.

Do human embryos have the ability of self-correction?

“…Low-level mosaicism is a common feature of early human development. A recently published study on single-cell genomic data revealed widespread mosaic aneuploidies, with 80% embryos harboring at least one putative aneuploid cell, with no significant enrichment of aneuploid cells in the TE compared to the ICM [31]. These observations conclusively demonstrate that mosaicism in blastocyst-stage embryos is basically a normal physiological phenomenon that can be found in almost all embryos [14,31].…”

Mechanisms of human embryo development: from cell fate to tissue shape and back

“…few cells and cellular fragmentation indicative of cell death) ( Minasi et al, 2016 ; Fragouli et al, 2013 ). Moreover, despite forming morphologically normal blastocysts, aneuploid embryos display transcriptional and epigenetic alternations that may compromise their subsequent development ( McCallie et al, 2016 ; Licciardi et al, 2018 ; Starostik et al, 2020 ). Autosomal monosomies typically lead to biochemical losses, whereas autosomal trisomies are associated with silent miscarriage (presence of extra-embryonic membranes but lack of embryonic structures) and first-trimester miscarriage ( Ljunger et al, 2005 ; Martinez et al, 2010 ; Ferro et al, 2003 ; Stephenson et al, 2002 ).…”

“…Autosomal monosomies typically lead to biochemical losses, whereas autosomal trisomies are associated with silent miscarriage (presence of extra-embryonic membranes but lack of embryonic structures) and first-trimester miscarriage ( Ljunger et al, 2005 ; Martinez et al, 2010 ; Ferro et al, 2003 ; Stephenson et al, 2002 ). In addition, alterations in the number of chromosomes can be a consequence of mitotic alterations during the first three cleavage divisions, which lead to the formation of mosaic human embryos ( Popovic et al, 2019 ; Starostik et al, 2020 ; Mantikou et al, 2012 ). Given the inaccessibility of human embryos at these stages, several fundamental questions remain to be addressed.…”

Parental genomes segregate into different blastomeres during multipolar zygotic divisions leading to mixoploid and chimeric blastocysts

“…With the recent adoption of single-cell GW haplotyping methods in PGT, the existence of androgenetic, gynogenetic and triploid profiles in human blastomere and trophectoderm biopsies has been uncovered (49,(93)(94)(95)(96). Moreover, mixoploidy and/or chimerism was recently inferred from single-cell transcriptome data in human blastocysts (97). Here, we directly show GW aberrations, identified in biopsied cleavage-stage embryos, to persist throughout the preimplantation period forming mixoploid and/ or chimeric human blastocysts.…”