Development of highly multiplexed and ultra-sensitive spatial (multi-)omics assays to disclose and understand the biology of cellular heterogeneity in pre- and post-implantation embryogenesis at the single-cell level

Following fertilization, instigation of cellular heterogeneity amongst genetically identical cells is an important process of cell lineage specification and proper development of the embryo. However, these earliest phases of life remain poorly understood as methods for single-cell sequencing have low molecular sensitivity, suffer technical noise, and loose spatial cellular and molecular information obstructing fundamental insight in cell-cell communication and molecular polarity within cells. Furthermore, the first cell cycles in human embryos are commonly subject to genome instability, which can exacerbate cellular heterogeneity and have profound effects on further development, although the precise cause(s) and consequences within the cells of the developing embryo remain largely elusive. To get fundamental insights in the biology of cellular heterogeneity, there is a need for near-absolute RNA sensitivity methods that in parallel can provide DNA and/or protein readouts of the same cell at spatial resolution. This project will help establish a state-of the-art in situ hybridization-based spatial transcriptomics platform for embryogenesis research equipped with microfluidics systems and super-resolution imaging solutions. In addition it will expand our assays to enable the characterization of the entire molecular hierarchy (DNA, RNA, protein) to achieve the most comprehensive and sensitive cellular profiling over the course of embryo development to date at spatial resolution