Foxp-regulated signaling pathways in brain development - Diversity

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RESEARCH AND TRAINING PLAN FOR RACHAEL VOLLMER A. SUMMARY OF THE FUNDED GRANT The parent grant (R01MH126481; funding period 06/01/21-05/31/2026) is titled: “Foxp-regulated signaling pathways in brain development.” Two members of the FOXP family of transcription factors, FOXP1 and FOXP2, have been linked to monogenetic forms of intellectual disability, autism spectrum disorders, and specific speech and language deficits. Variants in FOXP1 or FOXP2 are among the most significant genes associated with autism spectrum disorders. We previously showed that Foxp1 and Foxp2 both have significant contributions to cortical and striatal development. We linked these developmental changes via studies of gene expression, electrophysiology, and behaviors. We further identified non-cell-autonomous changes in gene expression using newly available single-cell RNA-sequencing technology. Based on these data, the central hypothesis driving the work in the parent grant and the proposed supplement is that Foxp1 and Foxp2 are key orchestrators of transcriptional signaling cascades in a cell type-specific manner that are important for neuronal function and are at risk in neurodevelopmental disorders such as autism. We propose to identify these cell type-specific contributions in the developing cortex by using rodent models through two specific aims that will utilize snATAC- seq: 1) Determine the cell type-specific gene regulatory programs orchestrated by Foxp1 in the developing cortex; and 2) Determine the cell type-specific gene regulatory programs orchestrated by Foxp2 in the developing cortex. Together, these aims will delineate the cell type contribution of both Foxp1 and Foxp2 to cortical development. The rodent models and cell-type specific genomic datasets will provide insight into the basic molecular mechanisms governing normal mammalian brain development. These research aims support the mission of the NIMH to understand and develop treatments for mental disorders. Finally, the training plan that we have described in this proposal will provide Ms. Vollmer with a cutting-edge skill set in neurogenomics. Aims 1 and 2 of the parent grant are to identify the cell-type specific developmental transcriptional program regulated by Foxp1 or Foxp2 in the mouse brain using single-nuclei RNA-sequencing (snRNA-seq) at several time points. These experiments will utilize previously generated Foxp1 and Foxp2 cKO mice already generated and published using Emx1.Cre (e.g. Araujo et al., Journal of Neuroscience 2017; Usui et al., Genes & Development 2017; Co et al., Cerebral Cortex 2020). Our lab has also recently applied the approach of single- nuclei ATAC-sequencing to uncover the cell type specific contributions of gene regulation and signaling cascades (e.g. Berto et al., Nature Neuroscience 2021). Coupling this chromatin accessibility approach with gene expression at the cell type level, should provide a new level of resolution for understanding how these transcription factors organize developmental signaling cascades. As described below, Rachael Vollmer will advance the aims of the parent grant by using the same Foxp1 and Foxp2 cKO mice proposed for snRNA-seq; however, she will apply snATAC-seq at the same timepoints to understand chromatin accessibility. This cell- specific approach will allow us to narrow down the direct transcriptional targets of Foxp1 and Foxp2 driving the observed phenotypes in these model systems such as impaired cortical migration and behavioral inflexibility.