Exploring and validating the marmoset as a primate model for chromosomal instability in early development.

Aneuploidy in embryos poses a major barrier to successful human reproduction, contributing to nearly 50% of early miscarriages. Despite its high prevalence in human embryos, the molecular mechanisms regulating aneuploid cell fate during development remain poorly understood. This knowledge gap persists due to ethical constraints in human embryo research and the limitations of existing animal models. In this study, we identified the New World primate marmoset (Callithrix jacchus) as a suitable model for investigating aneuploidy. By calling copy number variants from single-cell RNA sequencing data of marmoset embryonic cells, we identified heterogeneous aneuploidy, indicating chromosomal instability (CIN) in marmoset preimplantation embryos. Furthermore, marmoset aneuploidy displayed lineage-specific behaviour during gastruloid differentiation, similar to humans, suggesting a conserved regulatory mechanism in lineage specification. To develop a more pluripotent cell line to study early specification, we established an efficient approach for generating naïve-like marmoset pluripotent stem cells (cjPSCs). These cells resemble preimplantation epiblast-like cells and exhibit inherent CIN. Transcriptome analysis identified potential pathways contributing to aneuploidy during early embryogenesis, including the downregulation of cell cycle checkpoint signaling and the upregulation of autophagy pathways. Additionally, we found no significant effect of spontaneously occurring aneuploidy in cjPSCs on blastoid formation, suggesting that the consequences of aneuploidy become evident only after gastrulation, with preimplantation lineages exhibiting a higher tolerance for genomic instability. Unexpectedly, aneuploidy enhanced cavity formation during blastoid development, suggesting a potential role in facilitating efficient trophectoderm differentiation. Our findings validate the marmoset as a valuable model for studying CIN during early primate development and provide insight into the mechanisms underlying the prevalence of aneuploidy in primates. Naïve-like cjPSCs recapitulate key phenotypic traits of early embryonic cells, providing a robust system for studying post-implantation aneuploid cell fates in vivo and serving as a foundation for future research in this field.