NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models

Abstract

The 1.6 Mbp deletion on chromosome 3q29 is associated with a range of neurodevelopmental disorders, including schizophrenia, autism, microcephaly, and intellectual disability. Despite its importance towards neurodevelopment, the role of individual genes, genetic interactions, and disrupted biological mechanisms underlying the deletion have not been thoroughly characterized. Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with tissue-specific individual and pairwise knockdown of 14 homologs of genes within the 3q29 region. We identified developmental, cellular, and neuronal phenotypes for multiple homologs of 3q29 genes, potentially due to altered apoptosis and cell cycle mechanisms during development. Using the fly eye, we screened for 314 pairwise knockdowns of homologs of 3q29 genes and identified 44 interactions between pairs of homologs and 34 interactions with other neurodevelopmental genes. Interestingly, NCBP2 homologs in Drosophila (Cbp20) and X. laevis (ncbp2) enhanced the phenotypes of homologs of the other 3q29 genes, leading to significant increases in apoptosis that disrupted cellular organization and brain morphology. These cellular and neuronal defects were rescued with overexpression of the apoptosis inhibitors Diap1 and xiap in both models, suggesting that apoptosis is one of several potential biological mechanisms disrupted by the deletion. NCBP2 was also highly connected to other 3q29 genes in a human brain-specific interaction network, providing support for the relevance of our results towards the human deletion. Overall, our study suggests that NCBP2-mediated genetic interactions within the 3q29 region disrupt apoptosis and cell cycle mechanisms during development.

Convergent and distributed effects of the schizophrenia-associated 3q29 deletion on the human neural transcriptome

“…Notably, a recent report identified the Drosophila homolog of NCBP2 as a mediator of neurodevelopmental defects [9]. While we did not find support for inclusion of NCBP2 among prioritized driver genes, our analysis does not preclude the possibility that NCBP2 exacerbates other 3q29 locus haploinsufficiencies.…”

“…Indeed, the individual genetic drivers within the 3q29Del interval have not been identified. No single gene within the interval has been definitively associated with any of the aforementioned neuropsychiatric sequelae, prompting the hypothesis that haploinsufficiency of more than one of the 21 protein-coding genes located in the 3q29 interval is required [9]. However, most 3q29 genes are poorly annotated with limited functional data in existing gene ontology knowledge bases.…”

“…Both DLG1 and PAK2 are homologous to genes linked to intellectual disability [19,20] and evidence from Drosophila indicates that haploinsufficiency of both genes may be required for synaptic defects rather than each individually [21]. A recent study generated combinatorial knockdowns of select homologs of 3q29 interval genes in Drosophila and Xenopus laevis and proposed that a component of the nuclear cap-binding complex, NCBP2 [22], mediates neurodevelopmental defects in 3q29Del syndrome [9]. However, in the 3q29Del mouse model, NCBP2 is not decreased at the protein level in brain tissue, dampening enthusiasm for this gene as a causal element [23].…”

“…To avoid bias and address the knowledge gap for 3q29 interval genes, we employed a systems biology approach, rooted in graph theory [26][27][28], to generate evidence-based predictions that relate individual 3q29 genes to specific biological functions and disease phenotypes. Accumulating evidence indicates that genes work in conjunction, rather than in isolation, to realize most cellular functions that determine the behavior of complex biological systems [9,21,29]. In this holistic context, functional information about well-characterized genes can be leveraged to infer novel biological functions and disease associations for genes that are poorly characterized [30][31][32].…”

Functional assessment of the “two-hit” model for neurodevelopmental defects inDrosophilaandX. laevis

“…Furthermore, functional assays using X. laevis have uncovered developmental defects, behaviors, and molecular mechanisms for several homologs of genes associated with neurodevelopmental disorders, such as NLGN1 (16), CACNA1C (17), GRIK2 (18), and PTEN (19). Using Drosophila and X. laevis models, we recently found that multiple genes within the variably expressive 16p11.2 and 3q29 deletion regions individually contribute to neurodevelopmental defects (20,21), suggesting that no single gene could be solely causative for the wide range of defects observed with deletion of an entire region. Moreover, we identified complex genetic interactions within conserved biological pathways among homologs of genes affected by these CNVs.…”