Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. Here, we profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time using a combination of single-cell RNA sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing. We identify previously underappreciated cellular heterogeneity of the developing mesenchyme and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. Within the epithelium, we find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating toward a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population toward the alpha or beta cell lineages. This work establishes a roadmap of pancreatic development and demonstrates the broad utility of this approach for understanding lineage dynamics in developing organs.

The Drosophila ovary is a widely used model for germ cell and somatic tissue biology. Here we use single-cell RNA-sequencing (scRNA-seq) to build a comprehensive cell atlas of the adult Drosophila ovary that contains transcriptional profiles for every major cell type in the ovary, including the germline stem cells and their niche cells, follicle stem cells, and previously undescribed subpopulations of escort cells. In addition, we identify Gal4 lines with specific expression patterns and perform lineage tracing of subpopulations of escort cells and follicle cells. We discover that a distinct subpopulation of escort cells is able to convert to follicle stem cells in response to starvation or upon genetic manipulation, including knockdown of escargot, or overactivation of mTor or Toll signalling.

Tissue function depends on the relative proportions of multiple cell types. In the airway, basal stem cells differentiate into both multiciliated and secretory cells, which together protect the lungs from inhaled pathogens and particulates. To define how airway stem cells differentiate, we mapped differentiation trajectories using single-cell mRNA sequencing (scRNA-seq) and identified a transitional intermediate cell state in between basal stem cells and differentiated cells. These intermediate cells induce different gene expression programs that precede differentiation into either multiciliated or secretory cells. For example, we found that within the intermediate cell population, multiciliated cell precursors express Mycl, encoding a MYC-family transcription factor, and secretory cell precursors express Hey1, encoding a transcriptional repressor. We also found that Notch signaling acts on intermediate cells to repress Mycl and induce Hey1. We further show MYCL expression is sufficient to drive multiciliated cell fate, whereas HEY1 expression is sufficient to repress multiciliated cell fate. Using CUT&RUN, we made the surprising observation that MYCL and HEY1 bind to many of the same regulatory elements near genes encoding early regulators of multiciliated cell differentiation. We conclude that intermediate cells receiving Notch signals induce HEY1 to repress the multiciliated cell fate and become secretory cells, while intermediate cells not receiving Notch signals induce MYCL to promote the multiciliated cell fate. These experiments reveal that during airway stem cell differentiation Notch signaling balances the production of two different cell types by regulating the functions of two opposing transcription factors, MYCL and HEY1.