Single-Cell RNA Sequencing of Sox17-Expressing Lineages Reveals Distinct Gene Regulatory Networks and Dynamic Developmental Trajectories

Stem Cells. 2023 Jun 15;41(6):643-657. doi: 10.1093/stmcls/sxad030.


During early embryogenesis, the transcription factor SOX17 contributes to hepato-pancreato-biliary system formation and vascular-hematopoietic emergence. To better understand Sox17 function in the developing endoderm and endothelium, we developed a dual-color temporal lineage-tracing strategy in mice combined with single-cell RNA sequencing to analyze 6934 cells from Sox17-expressing lineages at embryonic days 9.0-9.5. Our analyses showed 19 distinct cellular clusters combined from all 3 germ layers. Differential gene expression, trajectory and RNA-velocity analyses of endothelial cells revealed a heterogenous population of uncommitted and specialized endothelial subtypes, including 2 hemogenic populations that arise from different origins. Similarly, analyses of posterior foregut endoderm revealed subsets of hepatic, pancreatic, and biliary progenitors with overlapping developmental potency. Calculated gene-regulatory networks predict gene regulons that are dominated by cell type-specific transcription factors unique to each lineage. Vastly different Sox17 regulons found in endoderm versus endothelial cells support the differential interactions of SOX17 with other regulatory factors thereby enabling lineage-specific regulatory actions.

Keywords: Sox17; endoderm; endothelium; hematopoiesis; hepato-pancreato-biliary system; single-cell RNA sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation
  • Cell Lineage / genetics
  • Embryonic Development* / genetics
  • Endoderm / metabolism
  • Endothelial Cells* / metabolism
  • Gene Expression Regulation, Developmental*
  • Gene Regulatory Networks*
  • HMGB Proteins / genetics
  • HMGB Proteins / metabolism
  • Mice
  • SOXF Transcription Factors* / genetics
  • SOXF Transcription Factors* / metabolism
  • Sequence Analysis, RNA
  • Transcription Factors / metabolism


  • HMGB Proteins
  • Sox17 protein, mouse
  • SOXF Transcription Factors
  • Transcription Factors