Wnt inhibition confers hESCs a unique transcriptional state compatible with differentiation, but not with derivation

Human embryonic stem cells (hESCs) hold great value for future clinical applications. However, standard culture conditions maintain hESCs in a primed state, which bears heterogeneity and a tendency for spontaneous differentiation. To counter these drawbacks, hESCs have been converted to a naive state, but this has in turn restricted the efficiency of existing directed differentiation protocols. We show that adaptation of hESCs to Wnt-inhibiting condition (Wnt-i) conferred a unique transcriptional signature with high levels of pluripotency markers and reduced levels of differentiation markers. Moreover, neuronal and cardiac differentiation of Wnt-i hESCs progressed similarly to primed hESCs, unlike their naïve counterparts. Remarkably, in contrast to mouse, Wnt-i conditions failed to support direct derivation of hESCs, suggesting that active Wnt signaling is required for the transition from inner cell mass to hESCs. Wnt-i hESCs retained advantages of both primed and naive counterparts and may therefore be a better starting point for differentiation towards clinically desired cell types. Biological triplicates of UGent11-2 and UGent11-60 hESC lines cultured in primed, Wnt-i and naive conditions were sequenced.