University of Sydney researchers have developed a powerful way to test how closely lab-grown biological models resemble real human embryos, finding that while some models perform well, none yet fully capture the complexity of early human development.

The scientists say the research creates one of the most comprehensive reference maps of early human embryo development, which they used to benchmark the biological accuracy of stem-cell-derived embryo models. They systematically evaluated four leading human blastoid-generation methods and found substantial differences in how faithfully they reproduce the cell types and developmental processes seen in natural human embryos.

Pengyi Yang, PhD, associate professor at the University of Sydney and an ARC Future Fellow in the School of Mathematics and Statistics and Unit Head of Computational Systems Biology at the Children’s Medical Research Institute, said the work gives scientists a more objective way to understand the strengths and limitations of embryo models. “Human embryo models have enormous potential for studying the earliest days of an embryo’s development, but there has been no consistent way to assess how accurately these reflect real human development. Our framework allows researchers to compare these models against a detailed biological reference and determine which cell types and developmental processes are faithfully reproduced, and which are not.”

Yang, who also leads the Trans-Regulatory Biology group at the Charles Perkins Centre, is senior and corresponding author of the team’s published paper in Cell Systems, titled “Systematic transcriptomic evaluation of blastoid models of early human development.” In their paper the team stated, “The reference map generated from this study enables the benchmarking of blastoids that may guide the optimization of the protocol for the generation of high-fidelity blastoid models that faithfully recapitulate the natural human blastocyst.”

The study of early human embryogenesis from blastocyst formation to gastrulation has been constrained by what the authors describe as “… technical challenges and ethical concerns associated with human embryo research.” But research on blastoid embryo models, which are derived from stem cells, offers scientists a way to study the biological events that underpin fertility, pregnancy success, and early human development without relying on donated human embryos.

While these research models are not actual human embryos—current models cannot develop into a human embryo—they could help answer questions that have long been difficult to investigate because of technical and ethical constraints. “Recent achievements in generating blastocyst-like structures from stem cells, the blastoids, that are reminiscent of human blastocysts in morphology and cellular composition have opened an avenue to glean knowledge of the biology of early human embryogenesis,” the team continued.

However, just because something looks like an embryo, does that mean it is behaving like one biologically? The University of Sydney team developed a computational framework that helps answer that question. “Establishing a systematic evaluation framework for assessing the fidelity of blastoids in modeling the human blastocyst is critical for enhancing the quality of these stem cell-based embryo models (SCBEMs),” they noted. “… we set out to develop a computational workflow for systematically assessing how closely blastoids generated by current state-of-the-art protocols recapitulate human blastocyst cell states and develop mental features.”

To do this the team combined and harmonized more than 14,000 single-cell transcriptomes—the set of RNA molecules in a cell—from human embryos spanning key stages of their development. This allowed them to create a reference map of how cells normally differentiate and organize themselves during the days immediately before and after implantation.

The investigators then compared that reference against four widely used blastoid-generation protocols developed by international research groups. Rather than assessing whether the models simply resembled embryos under a microscope, the researchers examined their molecular identities, developmental timing, lineage structure, and other biological characteristics.

The results showed that some blastoid models reproduced all three major cell lineages of a natural human blastocyst, or the early embryo, relatively well, while others failed to accurately represent certain cell types or contained large numbers of cells that could not be confidently matched to any known embryonic state. No single model perfectly replicated a natural human blastocyst. “Results of the benchmarking revealed substantial differences between protocols in recapitulating the composition, developmental timing, and coordinated lineage specification of the human blastocyst, highlighting that high-fidelity SCBEMs should reproducibly generate appropriately staged and developmentally coordinated blastocyst cell states,” the authors reported.

Yang said the findings highlight both the promise and current limitations of embryo models. “The encouraging finding is that some models capture important aspects of early embryonic development relatively well, although each model has limitations,” he said. “But our study also shows that current models are not biologically equivalent to real human embryos, and researchers need to be careful about the conclusions they draw from them.”

By providing a standardized benchmark, the researchers hope future models can be improved more rapidly and evaluated more rigorously. “Collectively, our work provides a comprehensive and systematic evaluation of the developmental authenticity of in vitro cultured SCBEMs generated by the state-of-the-art protocols,” they concluded. “Yang added, “If we’re going to use these systems to answer important biological questions, we first need to know what they can reliably tell us. Our work provides a roadmap for improving embryo models and ensuring scientific claims remain grounded in what the models can actually support.”

The researchers have made their reference datasets and benchmarking tools publicly available, enabling scientists worldwide to test new embryo models against the same standards.