CTNNB1-dependent molecular pathways are disrupted proportional to gene-dosage in a human embryonic stem cell model of early neuronal differentiation

CTNNB1 encodes beta-catenin, a multifunctional protein which acts as a WNT responsive transcriptional co-activator in the nucleus, and separately as a component of cell-cell adhesion complexes. Heterozygous loss-of-function variants as well as some missense variants of CTNNB1 cause a defined neurodevelopmental disorder. The WNT signalling pathways are not always disrupted by pathogenic missense variants of CTNNB1. To explore the gene-dosage dependent effects of CTNNB1, we performed CRISPR/Cas9-mediated genome editing of the H1 human embryonic stem cell line to engineer either mono- or bi-allelic CTNNB1 null alleles. During directed neuronal differentiation, bi-allelic CTNNB1 knockout lines displayed an overt prematurity of neurogenesis which was subtly mirrored in the mono-allelic loss lines. RNA sequencing revealed impact on both cell-cell adhesion, mediated through cadherins and protocadherins, as well as WNT signalling. These stem cells with loss of CTNNB1 provide human-specific insight into the early role of CTNNB1 in neuronal differentiation.