Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation

Abstract

Thousands of transcriptome data sets are available, but approaches for their use in dynamic cell response modelling are few, especially for processes affected simultaneously by two orthogonal influencing variables. We approached this problem for neuroepithelial development of human pluripotent stem cells (differentiation variable), in the presence or absence of valproic acid (signaling variable). Using few basic assumptions (sequential differentiation states of cells; discrete on/off states for individual genes in these states), and time-resolved transcriptome data, a comprehensive model of spontaneous and perturbed gene expression dynamics was developed. The model made reliable predictions (average correlation of 0.85 between predicted and subsequently tested expression values). Even regulations predicted to be non-monotonic were successfully validated by PCR in new sets of experiments. Transient patterns of gene regulation were identified from model predictions. They pointed towards activation of Wnt signaling as a candidate pathway leading to a redirection of differentiation away from neuroepithelial cells towards neural crest. Intervention experiments, using a Wnt/beta-catenin antagonist, led to a phenotypic rescue of this disturbed differentiation. Thus, our broadly applicable model allows the analysis of transcriptome changes in complex time/perturbation matrices.

Optimization of the TeraTox Assay for Preclinical Teratogenicity Assessment

“…TeraTox informs predictions not only based on statistical data patterns but builds upon biological mechanisms and thus may reflect disturbed functionalities, similar to those leading to teratogenicity in vivo . These features put TeraTox conceptually in a group of other assays that use phenotypic changes or disturbed functionalities as readouts ( Dreser et al, 2020 ; Hoelting et al, 2016 ; Meisig et al, 2020 ; Pallocca et al, 2016 ). The model consolidates our previous intention to “focus on germ layers” and corroborates recent work exploring gastruloid models that profiles morphological changes of germ-layers for teratogenicity prediction ( Jaklin et al, 2020 ; Moris et al, 2020 ).…”

Valproic acid promotes the in vitro differentiation of human pluripotent stem cells into spermatogonial stem cell-like cells

“…The increased SSCLC induction efficiency was not only reflected by the higher percentage of PLZF + cells, but also the increased expression of various SSC-related genes. However, whether the increased SSCLC induction efficiency was directly related to altered epigenetic modifications still needs further studies to confirm, because VPA could stimulate signaling pathways or transcript factors to enhance target gene expression rather than directly modulating gene expression through epigenetic regulation [41][42][43][44]. Studies have reported that VPA upregulated Wnt signaling pathway genes during neural differentiation and neurogenesis [41,44], and this effect might be the result of VPA induced beta-catenin and phospho-GSK3 or altered demethylation of Wnt-activators [41,44,45].…”

Optimization of the TeraTox assay for preclinical teratogenicity assessment

“…Therefore, TeraTox informs predictions not only based on statistical data patterns: it builds upon biological mechanisms and thus may reflect disturbed functionalities, similar to those leading to teratogenicity in vivo. This feature puts the TeraTox conceptually in a group of other assays that use phenotypic changes or disturbed functionalities as readouts (17,(93)(94)(95).…”