Totipotent cells hold enormous potential for regenerative medicine. Thus, the development of cellular models recapitulating totipotent-like features is of paramount importance. Cells resembling the totipotent cells of early embryos arise spontaneously in mouse embryonic stem (ES) cell cultures. Such ‘2-cell-like-cells’ (2CLCs) recapitulate 2-cell-stage features and display expanded cell potential. Here, we used 2CLCs to perform a small-molecule screen to identify new pathways regulating the 2-cell-stage program. We identified retinoids as robust inducers of 2CLCs and the retinoic acid (RA)-signaling pathway as a key component of the regulatory circuitry of totipotent cells in embryos. Using single-cell RNA-seq, we reveal the transcriptional dynamics of 2CLC reprogramming and show that ES cells undergo distinct cellular trajectories in response to RA. Importantly, endogenous RA activity in early embryos is essential for zygotic genome activation and developmental progression. Overall, our data shed light on the gene regulatory networks controlling cellular plasticity and the totipotency program.
Cell competition is emerging as a quality control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mice, 35% of epiblast cells are eliminated prior to gastrulation. Here we show that cells with mitochondrial defects are eliminated by cell competition during early mouse development. Using single cell transcriptional profiling of eliminated mouse epiblast cells we identify hallmarks of cell competition and mitochondrial defects. We go on to demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function triggers cell competition. In the mouse embryo, cell competition eliminates cells with sequence changes in mt-Rnr1 and mt-Rnr2, and that even non-pathological changes in mitochondrial DNA sequence can induce cell competition. Our results suggest that cell competition is a purifying selection that optimises mitochondrial performance prior to gastrulation.
Cell competition is emerging as a quality control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. Here we have performed single cell transcriptional profiling of early mouse embryos and find that the cells eliminated show the hallmarks of cell competition, are mis-patterned and have mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function is sufficient to trigger competition. Importantly, we show that in the embryo loser epiblast cells display mitochondrial DNA mutations and that even small changes in mitochondrial DNA sequence can influence the competitive ability of the cell.Our results therefore suggest that cell competition is a purifying selection that optimises metabolic output prior to gastrulation. Running title: Cell competition and mitochondrial selectionDuring the early stages of mammalian development, the cellular and molecular landscape is 2 profoundly remodelled. As embryonic cells approach gastrulation, when the precursors of all 3 embryonic tissues are specified, they need to rewire the transcriptional, epigenetic, metabolic and 4 signalling networks that govern cell identity (Kojima et al., 2014). These changes are accompanied 5 by a marked acceleration in the proliferation rate (Snow, 1977) and need to be orchestrated with 6 the different morphogenetic processes that re-shape the embryo (reviewed in (Stower and 7 Srinivas, 2018). The scale of this remodelling creates the potential for the emergence of abnormal 8 cells that need to be removed to prevent them from contributing to the soma or germline during 9 development. This requirement implies that there must be stringent cell fitness quality control 10 mechanisms acting around the time of gastrulation. One such control has been postulated to be 11 cell competition, a fitness sensing mechanism eliminating cells that, although viable, are less fit 12 than their neighbours (reviewed in (Bowling et al., 2019; Diaz-Diaz and Torres, 2019; Madan et 13 al., 2018). During cell competition, the cells that are eliminated are generically termed losers, while 14 the fitter cells that survive are referred to as winners. 15Cell competition has been primarily studied in Drosophila, where it was first described in the cell RNA sequencing (scRNA-seq). To ensure we can capture the eliminated cells, as we have 70 done before (Bowling et al., 2018), we isolated embryos at E5.5 and cultured them for 16 hours in 71 the presence of a caspase inhibitors (CI) or vehicle (DMSO) ( Figure 1A and Figure S1A). 72Unsupervised clustering of the scRNA-seq data revealed five clusters: two corresponding to extra-73 embryonic tissues (visceral endoderm and extra-embryonic ectoderm) and three that expressed 74 epiblast marker genes (Figure 1B-C and Figure S1B-D). Interestingly, cells from CI...
A powerful feature of single-cell RNA-sequencing data analysis is the possibility to identify novel rare cell types. However, rare cell types are often missed by standard clustering approaches. We have developed CIARA (Cluster Independent Algorithm for the identification of markers of RAre cell types), a computational tool available in R and Python that outperforms existing methods for rare cell type detection. With CIARA, we found a small group of precursor cells among mouse embryonic stem cells and previously uncharacterized rare populations of cells in a human gastrula.
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