Integrating single-cell imaging and RNA sequencing datasets links differentiation and morphogenetic dynamics of human pancreatic endocrine progenitors

Basic helix-loop-helix genes, particularly proneural genes, are well-described triggers of cell differentiation, yet information on their dynamics is limited, notably in human development. Here, we focus on Neurogenin 3 (NEUROG3), which is crucial for pancreatic endocrine lineage initiation. By monitoring both NEUROG3 gene expression and protein in single cells using a knockin dual reporter in 2D and 3D models of human pancreas development, we show an approximately 2-fold slower expression of human NEUROG3 than that of the mouse. We observe heterogeneous peak levels of NEUROG3 expression and reveal through long-term live imaging that both low and high NEUROG3 peak levels can trigger differentiation into hormone-expressing cells. Based on fluorescence intensity, we statistically integrate single-cell transcriptome with dynamic behaviors of live cells and propose a data-mapping methodology applicable to other contexts. Using this methodology, we identify a role for KLK12 in motility at the onset of NEUROG3 expression.

Automated summary

This study investigates the dynamics of NEUROG3 gene expression in human pancreatic development. The researchers find that human NEUROG3 expression is approximately 2-fold slower than that of mice. They also observe heterogeneous peak levels of NEUROG3 expression and demonstrate that both low and high peak levels can trigger the differentiation of cells into hormone-expressing cells. By integrating single-cell transcriptome data with live cell imaging, they propose a data-mapping methodology applicable to other contexts and identify a role for KLK12 in motility at the onset of NEUROG3 expression.