Yang, X. H. | bioRxiv Science

bioRxiv2019

Adopting tipping-point theory to transcriptome profiles unravels disease regulatory trajectory

Differentiation involves bifurcations between discrete cell states, each defined by a distinct gene expression profile. Single-cell RNA profiling allows the detection of bifurcations. However, while current methods capture these events, they do not identify characteristic gene signals. Here we show that BioTIP - a tipping-point theory-based analysis - can accurately, robustly, and reliably identify critical transition signals (CTSs). A CTS is a small group of genes with high covariance in expression that mark the cells approaching a bifurcation. We validated its accuracy in the cardiogenesis with known a tipping point and demonstrated the identified CTSs contain verified differentiation-driving transcription factors. We then demonstrated the application on a published mouse gastrulation dataset, validated the predicted CTSs using independent in-vivo samples, and inferred the key developing mesoderm regulator Etv2. Taken together, BioTIP is broadly applicable for the characterization of the plasticity, heterogeneity, and rapid switches in developmental processes, particularly in single-cell data analysis. HighlightsO_LIIdentifying significant critical transition signals (CTSs) from expression noise C_LIO_LIA significant CTS contains or is targeted by key transcription factors C_LIO_LIBioTIP identifies CTSs accurately and independent of trajectory topologies C_LIO_LISignificant CTSs reproducibly indicate bifurcations across datasets C_LI

systems biology↗

bioRxiv2018

Hedgehog signaling controls progenitor differentiation timing during heart development

Heterochrony, defined as differences in the timing of developmental processes, impacts organ development, homeostasis, and regeneration. The molecular basis of heterochrony in mammalian tissues is poorly understood. We report that Hedgehog signaling activates a heterochronic pathway that controls differentiation timing in multiple lineages. A differentiation trajectory from second heart field cardiac progenitors to first heart field cardiomyocytes was identified by single-cell transcriptional profiling in mouse embryos. A survey of developmental signaling pathways revealed specific enrichment for Hedgehog signaling targets in cardiac progenitors. Removal of Hh signaling caused loss of progenitor and precocious cardiomyocyte differentiation gene expression in the second heart field in vivo. Introduction of active Hh signaling to mESC-derived progenitors, modelled by transient expression of the Hh-dependent transcription factor GLI1, delayed differentiation in cardiac and neural lineages in vitro. A shared GLI1-dependent network in both cardiac and neural progenitors was enriched with FOX family transcription factors. FOXF1, a GLI1 target, was sufficient to delay onset of the cardiomyocyte differentiation program in progenitors, by epigenetic repression of cardiomyocyte-specific enhancers. Removal of active Hh signaling or Foxf1 expression from second heart field progenitors caused precocious cardiac differentiation in vivo, establishing a mechanism for resultant Congenital Heart Disease. Together, these studies suggest that Hedgehog signaling directly activates a gene regulatory network that functions as a heterochronic switch to control differentiation timing across developmental lineages.

developmental biology↗