Effects of somatic mutations on cellular differentiation in iPSC models of neurodevelopment

Abstract

The use of induced pluripotent stem cells (iPSC) as models for development and human disease has enabled the study of otherwise inaccessible tissues. A remaining challenge in developing reliable models is our limited understanding of the factors driving irregular in vitro differentiation of iPSCs, particularly the impact of acquired somatic mutations. We leveraged data from a pooled dopaminergic neuron differentiation experiment of 238 iPSC lines profiled with single-cell and whole-exome sequencing to study how somatic mutations affect differentiation outcomes. Differentiation was tracked at three time points corresponding to neural progenitors, early neurons and mature neurons. We found that deleterious somatic mutations in key developmental genes, notably the BCOR gene, are strongly associated with failure in dopaminergic neuron differentiation, with lines carrying such mutations also showing larger proliferation rate in culture. We further identified broad differences in cell type composition between failed and successfully differentiating lines, as well as significant changes in gene expression contributing to the inhibition of neurogenesis, a functional process also targeted by deleterious mutations in failed lines. Our work highlights the need to routinely measure the burden of deleterious mutations in iPSC lines and calls for caution in interpreting differentiation-related phenotypes in disease-modelling experiments.

Expression bias in retinoic acid responsive genes defines variations in neural differentiation of human pluripotent stem cells

“…Recent progress in selecting specific hPSC lines for stem cell therapeutics (70, 71, 97, 98) stresses the continuing value of further defining the genetic and epigenetic control of human cellular variation as hPSCs adopt neural fates. Novel methods that define single-cell genome mosaicism are being combined with lineage tracing (99–104) to provide a new understanding of the importance of cellular selection in neural development (19, 105).…”

Cerebral Organoids as an Experimental Platform for Human Neurogenomics

“…A pervasive cell culture-associated cell stress response has been identified as a potential confounding factor in organoid experiments [ 32 , 33 ]. Some of the potential consequences include genomic instability and the acquisition of somatic mutations in iPS derived models [ 104 ]. To overcome these limitations, algorithmic approaches have been developed to regress gene expression signatures related to cell stress [ 34 ].…”