Deepening our understanding of early mammalian embryogenesis

The authors made use of CRISPR-engineered mouse embryonic stem cells and proteomics - an important technology for understanding how organisms develop – to study the formation of gastruloids. Proteins are the building blocks of life and must be present in specific cells at specific times to orchestrate proper development. This study marks the first time protein expression has been investigated in this early stage of mouse development and is now published in Cell Stem Cell today.

Together with the group of Katherina Sonnen (Hubrecht Institute), the team also compared protein expression profiles in gastruloids to those in actual mouse embryos. This investigation unveiled a significant overlap in protein expression between gastruloids and mouse embryos. However, notable differences were also observed, as gastruloids do not (yet) fully recapitulate the complexity and cellular diversity of real embryos.

In collaboration with the lab Boudewijn Burgering and Harmjan Vos (both at UMC Utrecht), they also applied a new technology called single-cell proteomics to investigate protein expression in gastruloids at the level of individual cells. This is technically very challenging because, unlike with DNA or RNA molecules, proteins cannot be amplified prior to analysis. Single-cell proteomics was therefore long thought to be very difficult if not impossible, but recent hardware, software, and sample preparation innovations now enable the analysis of protein expression in individual cells. The analysis revealed that cells of the same type exhibit variations in protein expression in gastruloids.

The researchers further identified proteins that bind to ‘enhancers’ in embryonic stem cells and gastruloids. Enhancers are stretches of DNA in the genome that regulate which proteins are expressed during development. Transcription factors binding to enhancers are like switches to turn on or turn off the expression of genes. Focusing on one of the identified transcription factors, they found that the loss of the ZEB2 protein disrupts early embryonic development in both mouse and human stem cell-based models.

The generated datasets serve as a rich resource for the developmental biology community aiming to increase our understanding of early mammalian embryogenesis. In the future, human and mouse gastruloids, and other stem cell-derived embryo models, can be used to investigate and model various hereditary diseases and in vitro fertilization. Furthermore, the technology that the authors developed to identify proteins binding at enhancers will be very useful to decipher oncogenic transcription factor signalling in cancer cells.