Here, we provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. We elucidate conserved transcriptional programs along with those that are human specific. Importantly, we validate our RNA-sequencing findings at the protein level, which further reveals differences in human and mouse embryo gene expression. For example, we identify several genes exclusively expressed in the human pluripotent epiblast, including the transcription factor KLF17. Key components of the TGF-β signalling pathway, including NODAL, GDF3, TGFBR1/ALK5, LEFTY1, SMAD2, SMAD4 and TDGF1, are also enriched in the human epiblast. Intriguingly, inhibition of TGF-β signalling abrogates NANOG expression in human epiblast cells, consistent with a requirement for this pathway in pluripotency. Although the key trophectoderm factors Id2, Elf5 and Eomes are exclusively localized to this lineage in the mouse, the human orthologues are either absent or expressed in alternative lineages. Importantly, we also identify genes with conserved expression dynamics, including Foxa2/FOXA2, which we show is restricted to the primitive endoderm in both human and mouse embryos. Comparison of the human epiblast to existing embryonic stem cells (hESCs) reveals conservation of pluripotency but also additional pathways more enriched in hESCs. Our analysis highlights significant differences in human preimplantation development compared with mouse and provides a molecular blueprint to understand human embryogenesis and its relationship to stem cells.

SummaryDespite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR–Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using these refined methods, we efficiently and specifically targeted the gene encoding OCT4 (POU5F1) in diploid human zygotes and found that blastocyst development was compromised. Transcriptomics analysis revealed that, in POU5F1-null cells, gene expression was downregulated not only for extra-embryonic trophectoderm genes, such as CDX2, but also for regulators of the pluripotent epiblast, including NANOG. By contrast, Pou5f1-null mouse embryos maintained the expression of orthologous genes, and blastocyst development was established, but maintenance was compromised. We conclude that CRISPR–Cas9-mediated genome editing is a powerful method for investigating gene function in the context of human development.

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Mouse embryos segregate three different lineages during preimplantation development: trophoblast, epiblast and hypoblast. These differentiation processes are associated with restricted expression of key transcription factors (Cdx2, Oct4, Nanog and Gata6). The mechanisms of segregation have been extensively studied in the mouse, but are not as well characterised in other species. In the human embryo, hypoblast differentiation has not previously been characterised. Here we demonstrate co-exclusive immunolocalisation of Nanog and Gata4 in human blastocysts, implying segregation of epiblast and hypoblast, as in rodent embryos. However, the formation of hypoblast in the human is apparently not dependent upon FGF signalling, in contrast to rodent embryos. Nonetheless, the persistence of Nanog-positive cells in embryos following treatment with FGF inhibitors is suggestive of a transient naïve pluripotent population in the human blastocyst, which may be similar to rodent epiblast and ES cells but is not sustained during conventional human ES cell derivation protocols.

Aneuploidy in human eggs is the leading cause of pregnancy loss and several genetic disorders such as Down's syndrome. Most aneuploidy results from chromosome segregation errors during the meiotic divisions of an oocyte, the egg's progenitor cell. The basis for particularly error-prone chromosome segregation in human oocytes is not known. Here we analyzed meiosis in over 100 live human oocytes and identified an error-prone chromosome-mediated spindle assembly mechanism as major contributor to chromosome segregation defects. Human oocytes assembled a meiotic spindle independently of either centrosomes or other microtubule organizing centers. Instead, spindle assembly was mediated by chromosomes and the small GTPase Ran in a process requiring ~16 hours. This unusually long spindle assembly period was marked by intrinsic spindle instability and abnormal kinetochore-microtubule attachments, which favor chromosome segregation errors and provide a possible explanation for high rates of aneuploidy in human eggs.Meiosis in human oocytes is more prone to chromosome segregation errors than mitosis (1, 2), meiosis during spermatogenesis (3, 4) and female meiosis in other organisms (3,5). Despite its importance for fertility and human development, meiosis in human eggs has hardly been studied. Human oocytes are only available in small numbers, warranting singlecell assays capable of extracting maximal information. While high resolution-live cell microscopy is an ideal method, oocyte development in the ovary poses challenges to direct imaging. We therefore established an experimental system (6) for ex vivo high resolution fluorescence microscopy of human oocytes freshly harvested from women undergoing gonadotropin-stimulated in vitro fertilization cycles. To establish the major stages of meiosis in this system, we simultaneously monitored microtubules and chromosomes for ~24-48 hours ( Fig. 1 and movie S1). Similar to the situation in situ (7), human oocytes matured into fertilizable eggs over this time course as judged by the formation of a polar body. The morphologically identifiable stages (Fig. 1A) Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts breakdown (NEBD, set to 0 hours) provided a time-resolved framework for human oocyte meiosis (Fig. 1B). This reference timeline post NEBD is used throughout this paper.Before NEBD, chromosomes were highly condensed and clustered around the nucleolus. Instead of rapidly nucleating microtubules upon NEBD, human oocytes first formed a chromosome aggregate that was largely devoid of microtubules (Fig. 1A, movie S1 and fig. S1, A and B). Microtubules were first observed at ~5 hours, when they started to form a small aster within the chromosome aggregate. As the microtubule aster grew, the chromosomes became individualized and oriented on the surface of the aster with their kinetochores facing inwards. The microtubule aster then extended into an early bipolar spindle that carried the chromosomes on its surface (Fig. 1A, movie S1 and fig. S1, C to E)...

Current understanding of cell specification in early mammalian preimplantation development is mainly based on mouse studies. The first lineage differentiation event occurs at the morula stage with outer cells initiating a trophectoderm (TE) program to become the earliest placental progenitors. At subsequent developmental stages, the inner cell mass (ICM) arises from inner cells and is comprised of precursor cells of the embryo proper and yolk sac 1 . Notably, recent gene expression analyses suggest that the mechanisms regulating early lineage specification in the mouse may differ in other mammals, including human 2-5 and cow 6,7 . Here, we examined evolutionary conservation of cell dynamics and a molecular cascade initiating TE segregation in mouse, cow and human embryos using a comparative embryology approach. We discovered that the expression pattern of key TE lineage-associated factors shows a high degree of conservation among all three species. Specifically, at the morula stage outer cells acquire an apico-basal cell polarity, with expression of aPKC and PARD6B at the surface-free domain, nuclear expression of the Hippo signaling pathway effectors, YAP1 and WWTR1, and restricted expression of the transcription factor GATA3, suggesting initiation of a TE program. Furthermore, we demonstrate that inhibition of aPKC, by small-molecule pharmacological modulation and TRIM-Away protein depletion, impairs TE initiation at the morula stage. Altogether, our comparative embryology analysis provides novel insights into early lineage specification in human preimplantation embryos and suggests a similar mechanism initiating a TE program in mouse, cow and human embryos. Main textOur current understanding of cell specification during mammalian preimplantation development mainly relies on mouse studies. At the 8-cell stage, the mouse embryo undergoes a drastic

Chromosome errors, or aneuploidy, affect an exceptionally high number of human conceptions, causing pregnancy loss and congenital disorders. Here, we have followed chromosome segregation in human oocytes from females aged 9 to 43 years and report that aneuploidy follows a U-curve. Specific segregation error types show different age dependencies, providing a quantitative explanation for the U-curve. Whole-chromosome nondisjunction events are preferentially associated with increased aneuploidy in young girls, whereas centromeric and more extensive cohesion loss limit fertility as women age. Our findings suggest that chromosomal errors originating in oocytes determine the curve of natural fertility in humans.

Chromosome segregation errors occurring during the meiotic divisions of a human oocyte are the leading cause of pregnancy loss and several genetic disorders. When chromosomes fail to split into perfect halves during meiosis, the embryo cannot survive or will have a genetic defect, such as Down syndrome. Despite the importance of meiosis in human eggs for fertility and human development, the basis for error-prone chromosome segregation is not known.The authors developed an experimental system for ex vivo high-resolution fluorescence microscopy that allowed them to examine human oocytes freshly harvested from women undergoing gonadotropin-stimulated, in vitro fertilization cycles. Through examination of meiosis in more than 100 live human oocytes, an error-prone, chromosome-mediated, spindle assembly mechanism was identified as a major contributor to chromosome segregation defects. Human oocyte spindle assembly was mediated primarily by chromosomes and the small guanosine triphosphatase Ran independent of centrosomes or other microtubule organizing centers in a process requiring about 16 hours. This unusually slow process is in sharp contrast to mitotic spindles and meiotic spindles in mouse oocytes and other species, which rarely become unstable upon establishment of a bipolar spindle, thus rendering meiosis more efficient and less prone to segregation errors.Spindles assembled during meiosis in human oocytes display a high proportion of abnormal kinetochore-microtubule attachments and are intrinsically unstable. Progression into anaphase with abnormal attachments put human oocytes at risk of chromosome segregation errors, providing 1 mechanism for the high rates of aneuploidy.