Spatiotemporal dissection of cell specification processes during gastrulation and early organogenesis

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One of the most fundamental and remarkable processes in biology is the transformation of a single fertilized egg into a multi-cellular embryo within a short period of time. In the mouse embryo, the basic body plan is laid out within just 48 hours. A single layer of pluripotent cells transforms into a three-layer structure (gastrulation), that gives rise to the main body axes and first organs (early organogenesis). The molecular mechanisms underlying this process remain largely unclear because gene expression profiles of cells change rapidly in time and additionally vary strongly in space. Moreover, cell fate decisions arise from an interplay of various extra- and intracellular signals such as small signaling molecules, transcription factors, receptors and epigenetic modifications. Recent advances in single-cell genomics enable to measure the transcriptomes of millions of single cells with unprecedented molecular resolution. In a first step, I will combine these technologies with new experimental techniques and computational methods that will permit to create accurate spatiotemporal maps of gene expression of the gastrulating embryo. Each single-cell transcriptional state is supplemented by a time coordinate and position within the embryo and cells of neighboring time points are connected with each other through trajectories. This spatiotemporal gene expression map will subsequently serve as the basis to systematically dissect extrinsic and intrinsic signals involved in cellular differentiation processes in the embryo. To this end, I will additionally use a mouse embryoid body system, that undergoes a gastrulation-like differentiation process in vitro. The key focus will be on developing a comprehensive model of the primitive streak program and on understanding early mesoderm patterning. Genetic perturbation experiments will be used to validate the effect of specific genes in vivo and in vitro. The effect of extracellular signaling molecules will be studied by exposing the embryoid bodies to varying concentration levels at specific time points during their development. DNA methylation level profiling in combination with genetic perturbations of the DNA methylation machinery will help to elucidate possible epigenetic drivers of cellular commitment. My longer-term goal is to develop quantitative models of developmental processes that accommodate massive single-cell experimental data within a mechanistic and interpretable framework.