Snabel, R. R. | bioRxiv Science

bioRxiv2024

Single-cell roadmap of cardiac differentiation identifies roles for ZNF711 and retinoic acid in balanced epicardial and cardiomyocyte lineage commitment

Stem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. Here we show how cardiac monolayer, embryoid body, and engineered heart tissue trajectories compare in a single-cell roadmap of atrial and ventricular differentiation conditions. Using a multiomic approach and gene-regulatory network inference, we identified regulators of the epicardial, atrial and ventricular cardiomyocyte lineages. We identified ZNF711 as a regulatory switch and safeguard for cardiomyocyte commitment. We show that ZNF711 ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation by regulation of shared and complementary target genes, showing an interplay between ZNF711 and retinoic acid in cardiac lineage commitment. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/588683v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@e3733forg.highwire.dtl.DTLVardef@a34e61org.highwire.dtl.DTLVardef@16eccdcorg.highwire.dtl.DTLVardef@14bb7a5_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIWe present an atlas of cardiac differentiation under different culture conditions, showing progenitor trajectories and cell states reminiscent of the fetal heart. C_LIO_LIMultiome and chromatin accessibility analysis identified candidate regulators of cardiomyocyte and non-cardiomyocyte lineages. C_LIO_LIDistinct trajectories of lineage commitment and differentiation under different culture conditions shows plasticity of first and second heart field progenitors and different ratios of cardiomyocyte and non-myocyte lineages. C_LIO_LIZNF711 is required for balanced commitment to epicardial and ventricular cardiomyocyte lineages. Retinoic acid rescues a requirement for ZNF711 in cardiomyocyte differentiation, promoting both atrial cardiomyocyte and epicardial differentiation. C_LI

developmental biology↗

bioRxiv2022

ONECUT2 restricts Microfold cell numbers in the small intestine; a multi-omics study

Microfold (M) cells reside in the intestinal epithelium of Peyers patches. Their unique ability to take up and transport antigens from the intestinal lumen to the underlying lymphoid tissue is key in the regulation of the gut-associated immune response. Here, we applied a (single-cell) multi-omics approach to investigate the molecular mechanisms that drive M cell differentiation in mouse small intestinal organoids. We generated a comprehensive profile of chromatin accessibility changes and transcription factor dynamics during in vitro M cell differentiation, allowing us to uncover numerous cell type-specific regulatory elements and associated transcription factors. Single-cell RNA sequencing resulted in the identification of an M cell precursor population. Our new computational tool SCEPIA determined that these precursor cells were characterized by high expression of and motif activity for the transcription factor ONECUT2. Subsequent perturbation experiments revealed that ONECUT2 acts downstream of the RANK/RANKL signalling to support Enterocyte differentiation and restrict M cell lineage specification in vitro and in vivo, thereby regulating mucosal immunity. This study provides a useful blueprint for future investigations of cell fate switches in the intestinal epithelium.

molecular biology↗