Heparan sulfate regulates the fate decisions of human pluripotent stem cells

Heparan sulfate (HS) is an anionic polysaccharide generated by all animal cells. Studies in model organisms have revealed some of its critical developmental roles, though HS role in human pluripotent stem cell (hPSC) self-renewal and differentiation is poorly understood. We, therefore, generated HS-deficient hPSCs by disrupting EXT1 glycosyltransferase. The depletion of heparan sulfate resulted in impaired differentiation of EXT1-/- cells to the mesendoderm lineage. To elucidate the underlying mechanisms behind defective ME differentiation, we further assessed the global transcriptomic profiles of wildtype (WT) and EXT1-/- hPSCs following directed differentiation. The hierarchical gene clustering showed that the upregulated genes were mainly associated with neuronal development, whereas the downregulated genes were associated with extracellular matrix organization and regulation of signal transduction. Consistent with these findings, EXT1-/- hPSCs failed to activate FGF and Nodal pathways during mesendoderm induction. These results underscore the previously unexplored roles of heparan sulfate in the Activin/Nodal pathway. Taken together, our study provides insight into the mechanistic roles of HS in hPSC fate decisions. To investigate how HS regulates cell fate decisions in hPSCs, we generated a cell line that lacks HS. The EXT1 locus was targeted using CRISPR/Cas9. Wildtype H9 cells and EXT1-/- hPCS were subjected to chemically defined conditions that induce mesendoderm differentiation. 28 hours after induction, both cell types were collected for RNA-seq analysis. Comparative gene expression profiling was performed using data obtained from RNA-seq of quadrupliate samples each of H9 and EXT1-/- cells.