A comparative analysis of blastoid models through single-cell transcriptomics

Pluripotent-stem-cell-derived blastocyst-like structures (blastoids) offer insights into early human embryogenesis (5–10 days post-fertilization). The similarity between blastoids and human blastocysts remains uncertain. To investigate, we evaluated single-cell RNA sequencing (scRNAseq) data from seven blastoid models, comparing them to peri-implantation blastocysts. We quantified cell-type composition, transcriptomic overlap, lineage profiles, and developmental propensities for primary (epiblast, primitive endoderm, trophectoderm) and potential lineages (amnion, extravillous cytotrophoblasts, syncytial trophoblasts). Blastoids from extended pluripotent stem cells (EPSCs) are distinct from those from naive pluripotent stem cells (nPSCs), which cluster closer to natural blastocysts. EPSC-blastoids show a higher composition of primitive endoderm cells and ambiguous cells with notable endoderm signatures. Starting cell lines' scRNAseq analysis reveals higher heterogeneity in nPSCs and prevalent amnionic signatures in EPSCs. These findings suggest gene expression heterogeneity in founding cells influences blastoid lineage differentiation, aiding protocol optimization for better human embryogenesis models.