Lineage dynamics of murine pancreatic development at single-cell resolution

Abstract

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.

Defining multistep cell fate decision pathways during pancreatic development at single‐cell resolution

“…The y ‐axis represents the count of UMI (unique molecular identifiers) associated with each individual barcode. B, CStatistical analyses of mapped reads (B) and detected genes (C) for available 10X Genomics samples. Dt‐SNE analysis identified pancreatic epithelial cells and nonpancreatic lineage cells. The published data are from (GEO: GSE101099; Byrnes et al , ). EExpression pattern of marker genes of various lineages in our data in (D). Ft‐SNE analysis of the 10X Genomics data identified four pancreatic cell groups in E14.5 pancreas. The published data are from (GEO: GSE101099; Byrnes et al , ). GExpression patterns of marker genes in different groups in (F). HHeat maps showing the expression of the group‐enriched genes identified from the 10X Genomics data.…”

“…The published data are from (GEO: GSE101099; Byrnes et al , ). EExpression pattern of marker genes of various lineages in our data in (D). Ft‐SNE analysis of the 10X Genomics data identified four pancreatic cell groups in E14.5 pancreas. The published data are from (GEO: GSE101099; Byrnes et al , ). GExpression patterns of marker genes in different groups in (F). HHeat maps showing the expression of the group‐enriched genes identified from the 10X Genomics data. Each column represents a single cell, and each row represents one gene.…”

“…Each column represents a single cell, and each row represents one gene. The published data are from (GEO: GSE101099; Byrnes et al , ). ISmart‐seq2 data identified four pancreatic cell groups in E14.5 pancreas. JHeat map showing the expression of the group‐enriched genes identified from Smart‐seq2 data. Each column represents a single cell, and each row represents one gene.…”

“…Gene counts are on the left. KVenn diagrams showing the overlapped gene counts of differentially expressed genes in (H) and (J). Lt‐SNE analysis of the 10X Genomics data identified subpopulations in the EP‐early and EP‐late/endocrine populations in (F). The published data are from (GEO: GSE101099; Byrnes et al , ). MHeat map showing the expression of the EP subgroup‐enriched genes from the 10X Genomics data. TFs are listed on the right.…”

Pancreatic development: one cell at a (pseudo)time

“…Over the past several years, single‐cell RNA‐sequencing (scRNA‐seq) has enhanced our understanding of pancreatic lineage trajectories during development, with multiple groups deciphering cell lineage dynamics during pancreas organogenesis. Taken together, these studies have revealed that seemingly equivalent embryonic pancreatic progenitors contain previously underappreciated cellular heterogeneity, including a new intermediate EP population defined by the expression of Fev (Byrnes et al , ) a subset of EP cells expressing Myt1 biased toward β‐cell fate (Liu et al , ), and a progenitor of α cells marked by the expression of SLC38A5 (Stanescu et al , ).…”