Mesodermal-niche interactions direct specification and differentiation of pancreatic endocrine cells in human multilineage organoids

Abstract Tissues develop and function within complex microenvironments, where diverse cell types interact through tightly regulated spatial and temporal cues. These interactions shape cell identity, differentiation, and spatial organisation, ultimately establishing functional tissue architecture. Understanding and modelling these processes in humans therefore require multicellular systems that capture the cellular diversity and interactions of developing tissues. Here, we combine spatial transcriptomics of the human foetal pancreas with an induced pluripotent stem cell (iPSC)-based multilineage model that recapitulates key features of human endocrine pancreatic development and incorporates a mesoderm-derived cellular niche. We comprehensively characterise the multilineage organoid transcriptomes across differentiation stages and benchmark their fidelity against single-cell and spatial transcriptomic profiles of human foetal pancreas. We demonstrate that iPSC-derived pancreatic mesenchymal cells promote endocrine commitment by restricting off-target cell fates and enhancing β-cell differentiation. Together, these findings establish a framework for investigating the cellular mechanisms underlying human endocrine development and disease.