Single cell transcriptome dynamics from pluripotency to FLK1⁺ mesoderm

Area of Science:

• Developmental Biology
• Stem Cell Biology
• Transcriptomics

Background:

• Hemangiogenic progenitors, crucial for blood and endothelial cells, arise from FLK1-expressing (FLK1+) mesoderm, regulated by the transcription factor ETV2.
• FLK1+ mesoderm also contributes to smooth muscle and cardiomyocytes, but its generation and cell fate allocation processes are not fully understood.
• Existing single-cell RNA sequencing studies offer static snapshots, lacking insights into continuous dynamic developmental processes.

Purpose of the Study:

• To capture and analyze the continuous developmental process of hemangiogenesis from *in vitro*-differentiated mouse embryonic stem (ES) cells.
• To elucidate the developmental trajectory of FLK1+ mesoderm and its allocation to various cell fates.
• To identify key transcription factors and signaling pathways involved in hemangiogenesis and mesoderm differentiation.

Main Methods:

• Performed single-cell RNA sequencing (scRNA-seq) on *in vitro*-differentiated mouse ES cells.
• Analyzed the temporal gene expression dynamics to reconstruct continuous developmental pathways.
• Utilized bioinformatic approaches to identify transcription factor modules and regulatory networks.

Main Results:

• Hemangiogenic progenitors develop through intermediate gastrulation stages, specified by overlapping transcription factor modules in a 'relay'-like manner.
• The transcriptional program of FLK1+ mesoderm is maintained in the smooth muscle lineage, suggesting smooth muscle as the default fate.
• SRC kinase was identified as a contributor to ETV2-mediated activation of the hemangiogenic program.

Conclusions:

• This study provides a continuous transcriptome map of hemangiogenesis from ES cells, offering dynamic insights into mesoderm development.
• The findings suggest a default smooth muscle fate for FLK1+ mesoderm and highlight the role of sequential transcription factor activity.
• The generated map serves as a valuable resource for future research in basic and applied mesoderm development studies.