Gain of 20q11.21 in Human Pluripotent Stem Cells Impairs TGF-β-Dependent Neuroectodermal Commitment

Gain of 20q11.21 is one of the most common recurrent genomic aberrations in human pluripotent stem cells. Although it is known that overexpression of the antiapoptotic gene Bcl-xL confers a survival advantage to the abnormal cells, their differentiation capacity has not been fully investigated. RNA sequencing of mutant and control hESC lines, and a line transgenically overexpressing Bcl-xL, shows that overexpression of Bcl-xL is sufficient to cause most transcriptional changes induced by the gain of 20q11.21. Moreover, the differentially expressed genes in mutant and Bcl-xL overexpressing lines are enriched for genes involved in TGF-β- and SMAD-mediated signaling, and neuron differentiation. Finally, we show that this altered signaling has a dramatic negative effect on neuroectodermal differentiation, while the cells maintain their ability to differentiate to mesendoderm derivatives. These findings stress the importance of thorough genetic testing of the lines before their use in research or the clinic. •Bcl-xL overexpression drives the transcriptomic profile of 20q11.21 mutant lines•20q11.21 mutant lines downregulate CHCHD2, a known TGF-β pathway modulator•Mutant lines differentially express genes involved in TGF-β and SMAD signaling•Mutant lines show impaired ectoderm commitment due to TGF-β signaling deregulation In this article Spits and colleagues show that Bcl-xL overexpression is the main driver of the distinct transcriptomic profile of human embryonic stem cells with a gain of 20q11.21. The cells have an abnormal TGF-β- and SMAD-mediated signaling, which impairs commitment to neuroectoderm while differentiation to the other lineages remains unaffected.