Self-organized trunk-like-structures with somites and a neural tube

The post-implantation embryo is subject to extensive growth, morphogenetic changes and lineage decisions that take place in utero and are therefore difficult to deconstruct in vivo. A robust in vitro culture system that mimics post-implantation mouse development would pave the path towards understanding the dynamics of these processes and how they are coupled. Small aggregates of mouse embryonic stem cells (mESCs) can undergo gastrulation-like events and elongation in vitro, resulting in aggregates with gene expression domains that reflect the post-occipital embryo (gastruloids1–3). However, these ordered patterns of gene expression do not correlate with embryo-like morphogenesis. Here we show that mechano-chemical manipulation of the aggregates results in Trunk-Like-Structures (TLS) with a high level of organization of the embryonic tissue layers, including the formation of a neural tube and somites. Comparative single-cell RNA-Seq (scRNA-Seq) of TLS and embryos demonstrated the molecular complexity of TLS, confirmed embryo-like gene-regulatory programs, and unveiled the presence of primordial germ cell like cells (PGCLCs). Finally, Tbx6-/- TLS formed ectopic neural tubes, recapitulating the in vivo phenotype. These results suggest that TLS are a powerful platform to study the morphogenetic changes and lineage decisions during post-implantation development in space and time. Single-cell RNAseq data were collected from TLSMG at 96h (6 pooled structures), 108h (5 pooled structures) and 120h (3 pooled structures) after aggregation. Libraries were sequenced with 10X Genomics single cell RNA sequencing system. Bulk RNAseq data were collected from 96h (10 pooled structures), Gastruloids (6 pooled structures), TLSMG (6 pooled structures), TLSMGC (6 pooled structures) and TLSMGCL (6 pooled structures) samples. Libraries and sequencing have been performed following the KAPA stranded RNA-Seq Kit instructions and reccomandation. NanoString profiling data were collected from mESC (20k cells), post-occipital E8.5 mouse embryo (3x pooled), post-occipital E9.5 mouse embryo (3x pooled) and 9 individual TLSMG.