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Measuring and modeling how misregulation in gene regulatory networks causes intellectual disability

Final Report Summary - MISREGULATID (Measuring and modeling how misregulation in gene regulatory networks causes intellectual disability)

Introduction and aims: Intellectual disability (ID) refers to significant impairments in intellectual functioning and adaptive behavior. ID affects approximately 2% of the population and has a large impact on the individual and society. Currently, mutations in more than 450 genes have been associated with intellectual disability, but the true number of genes involved is expected to be significantly higher. Many disease-causing mutations for ID have been identified in the ~2% of the genome that specifies the protein sequence of ~25,000 genes. The remaining 98% of the genome contains many gene regulatory elements, which are key determinants of the expression (transcription) level of genes. The transcriptional networks defined by gene regulatory elements guide differentiation, establish cell fate and underlie biological pathways. For many ID patients (~40%) no causative mutation in a gene can be identified. A key unresolved question is whether mutations in gene regulatory elements play an important role in ID.
The overall aim of the research is to understand how and when perturbation of cooperative binding of transcription factors in gene regulatory elements causes aberrant expression of target genes, and to understand how this aberrant gene expression disrupts transcriptional networks and biological pathways underlying ID and co-morbid disorders of the brain.

Results: This project was comprised of a number of subprojects. The results for the subprojects are as follows.
1. We established a previously published protocol to differentiate human induced pluripotent stem cells (hIPSCs) to mature, functional neurons (iNeurons) by overexpression of a single neuronal transcription factor.
2. We characterized these neurons at the epigenetic level using chromatin accessibility profiling (ATAC-Seq), which identifies putative regulatory elements, and gene expression profiling. We have characterized the differences in the chromatin accessibility landscape between iPSCs, characterized the transcriptional networks by transcription factor motif analysis, and related these to changes in gene expression. We have estimated to what extent different classes of regulatory elements contribute to complex neurodevelopmental and psychiatric disorders (proportion of heritability explained and enrichment).
3. We have estimated the contribution of non-coding copy number variation (CNVs), specifically large, rare deletions that only affect regulatory elements, to ID.
4. By analyzing the regulatory networks of skin fibroblasts and iNeurons, we have identified a new set of transcription factors that are able to rapidly induce neuronal morphology and neuronal gene activity when overexpressed in fibroblasts. This provides new insights into the role of these factors in neurodevelopment.

Re-integration: The career integration grant has contributed significantly to my career development at the host institution. I will however no longer pursue an academic career at this institution.