Human Post-Implantation Development in vitro by de novo Embryonic and Extra-Embryonic Lineage Patterning
Pedroza, Gassaloglu et al., 2023
Investigating human development is a significant scientific challenge due to the technical and ethical limitations of working with bona fide embryo samples. In the face of these difficulties, stem cells have been applied to experimentally model inaccessible stages of human development in vitro 1-11 . Here we show that human pluripotent stem cells can be triggered to self-organise into three-dimensional structures that recapitulate the spatiotemporal events of early human post-implantation embryonic development. Importantly, our system reproducibly captures de novo differentiation and co- development of embryonic and extra-embryonic lineages, establishes key signalling hubs with secreted modulators, and undergoes gastrulation-like symmetry breaking. Single-cell transcriptomics confirms differentiation into diverse cell states of the native gastrulating human embryo 12 , including signatures of post-implantation epiblast, amniotic ectoderm, primitive streak, mesoderm, and hypoblast, as well as pre- patterning of non-neural ectoderm and yolk sac. Collectively, our system captures key features of human embryonic development spanning from Carnegie-stage 13 (CS) 4 to CS7, providing a reproducible, tractable, and permutable experimental platform to understand the basic cellular and molecular mechanisms that underlie human development, and a high-throughput platform to dissect developmental disorders and congenital pathologies.
This repository contains the code used to process and generate the single-cell RNA-sequencing data and figures, and the Whole Genome Bissulfite Sequencing figures presented in Pedroza et al., 2023: "Human post-implantation development in vitro by de novo embryonic and extra-embryonic lineage patterning". Analysis methods and logic underlying decisions are described within the analysis summary. The processed data contains our reorganized in vivo reference object, as used for the reference mapping analyses, and the hEE CellTypist scores for each reference cell type.
The hEE scRNA-seq data can be found in the Gene Expression Omnibus (GEO) under accession code GSE208195.