Dose escalation of Wnt stimulation during the exit from pluripotency identifies tranilast as a small molecule regulator of cardiac mesoderm differentiation (ATAC-Seq)

Wnt signalling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single cell RNA-sequencing of cells responding to a dose-escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were then used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified a novel property of the small molecule drug, tranilast. We found that tranilast synergistically activates Wnt signalling to promote cardiac lineage differentiation which we validate in vitro and in vivo. Our study provides an integrated workflow that links experimental datasets, prediction models and small molecule databases to identify novel drug-like compounds that control cell differentiation. Overall design: WTC-11 cells differentiated under different CHIR concentrations +/- tranilast were collected on day 2 of differentiation for Omni-ATAC-seq.We then analysed chromatin accessibility and motif enrichment to understand the mechanisms of tranilast.