Neural mechanisms of 3q29 deletion syndrome

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PROJECT SUMMARY: Neurodevelopmental disorders such as autism and schizophrenia are known to have a strong hereditary component but the genes and molecular determinants driving clinical phenotypes are not understood. Recurrent genomic copy number variants (CNVs) have emerged as important, highly-penetrant risk factors for these disorders. 3q29 deletion is one such CNV that results in the loss of one copy of 21 protein-coding genes, is strongly associated with autism, and is estimated to have the highest odds ratio of any genetic variant linked to schizophrenia at >40. Phenotypically, the available evidence suggests that 3q29 deletion may compromise brain development. Clinical case reports have described microcephaly and two independent mouse models of 3q29 deletion have reduced brain weight. Alterations in brain growth are relatively common in idiopathic and CNV-associated neurodevelopmental disorders and it has been hypothesized that dysregulated proliferation and maturation of neural progenitor cells (NPCs) may underlie this phenomenon. Here, we propose to rigorously test the proliferation of NPCs differentiated from 3q29 deletion study participant and isogenic induced pluripotent stem cell (iPSC) lines by ELISA, immunofluorescence, and multiparametric flow cytometry. Furthermore, we will generate both dorsal and ventral forebrain 3D organoids to assess the proliferation and differentiation of both glutamatergic and GABAergic progenitors. In addition, we will narrow the list of potential phenotypic driver genes through transcriptomic studies of human iPSC-derived NPCs and forebrain neurons. No single gene within the 3q29 deletion locus is currently associated with autism or schizophrenia prompting the hypothesis that haploinsufficiency of multiple genes within the interval contribute to risk for neurodevelopmental disorders. Indeed, preliminary weighted co- expression network analysis indicates that the 21 protein-coding 3q29 deletion genes congregate in 7 co- expression modules implying that multiple 3q29 genes participate in overlapping biological pathways. We will conduct RNA-seq on NPCs and FACS-isolated neurons to identify differentially-expressed genes in human 3q29 deletion neural cells. We will then re-introduce candidate 3q29 driver genes to NPCs and neurons and determine which 3q29 genes are responsible for dysregulation of downstream targets. The genetic and emerging phenotypic evidence strongly suggests that the 3q29 deletion is a high-priority target for mechanistic investigation. The Emory 3q29 Project has generated 12 iPSC lines from 3q29 deletion carriers along with age, sex, and race/ethnicity-matched controls. The tools are in place to rigorously investigate cellular and molecular alterations attributable to this high-risk variant. These findings will advance our understanding of this disorder and will be an important step toward understanding the genetic and molecular drivers of neurodevelopmental disorders more broadly.