Gastruloid optimization

Abstract

The young field of gastruloids brings promise to modeling and understanding early embryonic development. However, being a complex model, gastruloids are prone to variability at different levels. In this perspective, we define the different levels of gastruloid variability, and parameters over which it can be measured. We discuss potential sources for variability, and then propose methods to better control and reduce it. We provide an example from definitive endoderm progression in gastruloids, where we harness gastruloid-to-gastruloid variation in early parameters to identify key driving factors for endoderm morphology. We then devise interventions that steer morphological outcome. A better control over the developmental progression of gastruloids will enhance their utility in both basic research and biomedical applications.

Keywords: gastruloid; optimization; variability.

Figure 1.. Different levels of gastruloid variability.

A given combination of cell line/growth protocol/aggregation format defines an experimental system. Within each system, every experimental repetition involves its own variables (e.g. cell 2D confluency before aggregation, handling differences, state/temperature of medium), that may result in experiment-to-experiment variability. Within each experimental repetition, gastruloid-to-gastruloid differences may manifest in overall morphology (size, aspect-ratio), proportion of different lineages (e.g. mesoderm/endoderm), and patterns and relative locations of different lineages. Variability in developmental tempo may explain some, but not all differences. Green — Brachyury (ME); Red — Sox17 (DE).

Figure 2.. Endoderm morphotype optimization as a test case.

A machine learning approach based on measurable parameters for morphotype variability reduction, using two types of intervention.