The proteomic landscape and temporal dynamics of human and mouse gastruloid development

The embryo establishes a body plan and primes itself for organogenesis during gastrulation. As gastrulation is challenging to study in vivo, stem-cell-derived 'gastruloids' have emerged as powerful surrogates. Although transcriptomics and imaging have been applied extensively to such embryo models, the dynamics of their proteomes remains largely unknown. Here we apply quantitative proteomics to human and mouse gastruloids at four key stages. We leverage these data to map the expression dynamics of protein complexes, and to nominate cooperative proteins. With matched transcriptome data, we investigate global and stage-specific discordance between the transcriptome and proteome and leverage phosphosite dynamics to nominate kinase-substrate relationships. Finally, we apply co-regulation network analysis to identify genes linked to the Commander complex, the perturbation of which leads to morphological defects in gastruloids. Altogether, our work showcases the potential of applying proteomics to embryo models to advance our understanding of mammalian development in ways challenging through transcriptomics alone.