A three-dimensional human co-culture system reveals reciprocal embryo-endometrial adaptation at implantation onset

Human embryo implantation begins with dynamic, tightly coordinated interactions between embryonic and endometrial compartments, yet the earliest trophoblast-endometrial interface dynamics remain poorly resolved in vivo. Here, using an endometrial assembloid-based three-dimensional co-culture system with human blastoids and natural blastocysts, we analyse implantation-like progression by time-series single-cell transcriptomics and functional perturbation. Importantly, we identify co-culture-induced trophoblast subsets marked by SDC1⁺MMP7⁺ and enriched for transcriptional features associated with extracellular matrix remodelling and cell migration. These subsets are reproducibly detected across independent implantation-like systems, emerge specifically within a decidualized stromal co-culture context, and are further linked to stromal-derived CSF3 signalling by intercellular communication analysis and targeted perturbation. In parallel, the endometrium displays transcriptional changes associated with enhanced decidualization and a glandular hypersecretory transition. Together, our study provides a tractable framework for dissecting reciprocal embryo-endometrial adaptation at the onset of implantation.