Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation

Abstract

Developmental dyslexia (DD) is a neurodevelopmental condition with complex genetic mechanisms. A number of candidate genes have been identified, some of which are linked to neuronal development and migration and to ciliary functions. However, expression and regulation of these genes in human brain development and neuronal differentiation remain uncharted. Here, we used human long-term self-renewing neuroepithelial stem (lt-NES, here termed NES) cells derived from human induced pluripotent stem cells to study neuronal differentiation in vitro. We characterized gene expression changes during differentiation by using RNA sequencing and validated dynamics for selected genes by qRT-PCR. Interestingly, we found that genes related to cilia were significantly enriched among upregulated genes during differentiation, including genes linked to ciliopathies with neurodevelopmental phenotypes. We confirmed the presence of primary cilia throughout neuronal differentiation. Focusing on dyslexia candidate genes, 33 out of 50 DD candidate genes were detected in NES cells by RNA sequencing, and seven candidate genes were upregulated during differentiation to neurons, including DYX1C1 (DNAAF4), a highly replicated DD candidate gene. Our results suggest a role of ciliary genes in differentiating neuronal cells and show that NES cells provide a relevant human neuronal model to study ciliary and DD candidate genes. Keywords Cilia. Ciliopathies. Reading disorder. Human neuroepithelial stem cells. RNA sequencing Abbreviations BBS Bardet-Biedl syndrome CAGE Cap analysis of gene expression DAVID Database for Annotation, Visualization and Integrated Discovery DCDC2 Doublecortin domain containing 2 DCG Dyslexia candidate gene DCX Doublecortin DD Developmental dyslexia DNAAF Dynein axonemal assembly factor DYX1C1 Dyslexia susceptibility 1 candidate 1 EGF Epidermal growth factor FANTOM Functional annotation of the mammalian genome FDR False discovery rate FGF Fibroblast growth factor Andrea Bieder and Masahito Yoshihara contributed equally to this work.

Differentiation of ciliated human midbrain-derived LUHMES neurons

“…Ciliogenesis was thus found as a prominent aspect during LUHMES neuronal differentiation. Similar ‘ciliary’ observations were made for the differentiation from human neuroepithelial stem (NES) cells and induced pluripotent stem cells (iPSCs) into neurons (Bieder et al, 2020 in press).…”

Genetic and protein interaction studies reveal pathway synergy between the ciliary dyslexia candidate genes DYX1C1 and DCDC2

“…The complex DYX1C1/CPAP/DCDC2 might act in conjunction in migrating neurons, possibly independently of cilium and centrosome. Interestingly, DYX1C1 is highly upregulated in differentiating human neurons (32). Further studies in human stem cell derived neurons might shed more light on the role of these genes in neuronal migration.…”

“…DYX1C1 has been proposed as a cytoplasmic axonemal dynein assembly factor (16, [27][28][29][30]. Recent studies have strengthened a role of DCDC2 and DYX1C1 also in primary cilia and human neurons (31,32).…”

Genetic and Demographic Predictors of Latent Reading Ability in Two Cohorts

“…There is growing awareness that domain general genes have an important role to play in the genetics of reading 77, 78 . Additionally, four out of five of these genes play a role in the neuron migration pathway, which is often hypothesized to be causal to reading disabilities 79, 80 . These findings build on prior work which showed that neuron migration was overrepresented in genetic findings for typical and atypical readers 19, 81 .…”