Enteroendocrine cell

Cellular differentiation

Cell

Transcriptome

Mesenchymal stem cell

Progenitor cell

Pancreas

Biology

Gene

Endocrinology

Gene expression

Progenitor

Cell type

Mesenchyme

Stem cell

Computational biology

Cell biology

Endocrine system

Genetics

Hormone

Cell Metabolism

Current differentiation protocols have not been successful in reproducibly generating fully functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single-cell RNA sequencing with spatial transcriptomics at multiple developmental time points and revealed distinct temporal-spatial gene cascades. Cell trajectory inference identified endocrine progenitor populations and branch-specific genes as the progenitors differentiate toward alpha or beta cells. Spatial differentiation trajectories indicated that Schwann cells are spatially co-located with endocrine progenitors, and cell-cell connectivity analysis predicted that they may interact via L1CAM-EPHB2 signaling. Our integrated approach enabled us to identify heterogeneity and multiple lineage dynamics within the mesenchyme, showing that it contributed to the exocrine acinar cell state. Finally, we have generated an interactive web resource for investigating human pancreas development for the research community.

Single-cell transcriptomic and spatial landscapes of the developing human pancreas