Postdoctoral Researcher Lund University Lund, Skane Lan, Sweden
Abstract: Perturbations in early brain development can lead to neurodevelopmental disorders (NDDs), often with unidentified genetic causes. Their research has been hindered by limited access to human brain tissue and incomplete recapitulation of patient phenotypes in animal models. In this project, we use state-of-the-art iPSC-derived models coupled to cutting-edge gene editing and sequencing techniques to study mutations in TRIM28. TRIM28 is an epigenetic co-repressor protein that silences transposable elements (TEs), repetitive mobile genetic sequences, to protect genome integrity. Perturbations of this pathway in mice result in aberrant neurodevelopment and an inflammatory response in the adult brain. However, to date, a link between TRIM28 and brain disease in humans has not been shown. Our aim is to prove that mutations affecting TRIM28 can cause neurodevelopmental phenotypes and to understand how TRIM28 impaired function and transposable element dysregulation impair neurodevelopment and lead to disease. In this study, we describe two patients with a neurodevelopmental phenotype that carry de novo heterozygous missense mutations in TRIM28. We generated CRISPR-edited induced iPSC lines carrying the two mutations and differentiated them to unguided neural organoids. Combining bulk and single-nuclei RNA-seq and CUT&RUN histone mark profiling, we found that TRIM28 variants lead to loss of H3K9me3 over TEs resulting in transcriptional activation of the elements and nearby protein-coding genes. We saw that these effects are mirrored when silencing TRIM28 using a CRISPRi approach, which suggests a loss-of-function effect of the patients’ mutations. These results show that dysregulation of the TRIM28-mediated epigenetic mechanism and downstream aberrant TE and gene expression can be related to neurodevelopmental phenotypes. Our findings highlight the critical importance of regulating TEs during human brain development and will ultimately lead to the description of a novel monogenic neurodevelopmental disorder caused by mutations in TRIM28.
