NCBP2-mediated apoptosis contributes to developmental defects of the schizophrenia-associated 3q29 deletion

The chromosome 3q29 deletion confers >40-fold risk for schizophrenia and related neurodevelopmental disorders. Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with knockdown of individual 3q29 homologs in different tissues. We identified developmental and neuronal phenotypes for multiple 3q29 homologs, and specifically observed cellular defects due to altered cell cycle and apoptosis mechanisms. We screened 316 pairwise knockdowns of 3q29 genes in the developing eye, and identified 44 interactions between pairs of 3q29 genes and 34 interactions with other neurodevelopmental genes. In particular, NCBP2 synergistically enhanced the phenotypes of other 3q29 homologs in both Drosophila and X. laevis, leading to significant increases in apoptosis that disrupt cellular organization and brain morphology during development. The NCBP2-driven defects were rescued with overexpression of the apoptosis inhibitor Diap1/XIAP in both models. Our study implicates NCBP2-mediated genetic interactions within apoptosis pathways as a potential mechanism for pathogenicity of the 3q29 deletion.