Autism mutations rewire protein interaction networks to drive neurodevelopmental pathology
INTRODUCTION
Autism spectrum disorder (ASD) is characterized by extreme genetic heterogeneity, with more than 250 high-confidence risk (hcASD) genes identified to date. Defined by rare, large-effect coding variants, these genes show functional and developmental convergence in transcriptomic analyses. However, these approaches have provided only limited mechanistic insight and have not identified specific therapeutic targets beyond the genetic variants themselves. Because proteins are the primary functional units of the cell, mapping the physical ASD interactome—and determining how ASD variants rewire it—is essential to move beyond gene lists and broad pathophysiologic themes toward a deeper causal understanding of neurodevelopmental pathology.
RATIONALE
To augment our molecular understanding of ASD, we used affinity purification–mass spectrometry (AP-MS) to map 100 hcASD proteins and 54 patient-derived missense variants, substantially expanding the known ASD protein interaction landscape. By integrating these datasets with AlphaFold structural modeling and functional studies in Xenopus and human forebrain organoids, we investigated whether genetically distinct risk factors converge onto shared biology and if convergent neurodevelopmental phenotypes arise through the selective rewiring of protein-protein interactions (PPIs) by disease-associated variants.
RESULTS
The resulting ASD-PPI network contains more than 1800 interactions, 87% of which were previously unreported. The network, which is enriched in neural progenitor cells (NPCs) of the excitatory lineage, exhibits a highly interconnected architecture, with risk proteins converging onto shared complexes, including DCAF7. Functional interrogation of selected interactions demonstrated that disruption of the previously uncharacterized DCAF7-DYRK1A-KIAA0232 complex impairs progenitor proliferation and reduces forebrain size in vivo. Furthermore, patient-derived missense mutations frequently induced convergent PPI rewiring. Distinct FOXP1 mutations, for example, weakened its physical interaction with FOXP4, leading to gain-of-function redistribution of FOXP4 to ectopic genomic targets. In human forebrain organoids, this biochemical rewiring drove premature differentiation of cortical neurons and altered neural activity. Genetic deletion of FOXP4 in a FOXP1-mutant background rescued these neurodevelopmental defects; although the exact mechanism requires further determination, this suggests that the rewired interaction underlies the mutant phenotype.
CONCLUSION
Together, these findings define a dual-layered model of molecular convergence in ASD: convergence through shared interaction networks in the wild-type state and convergence through recurrent functional consequences of interaction rewiring in the mutant state. More broadly, this work establishes a scalable framework for systematic interrogation of the autism proteome, enables prioritization of druggable protein interfaces, and provides a rational foundation for precision therapeutic strategies aimed at restoring neurodevelopmental trajectories.
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Belinda Wang; Rasika Vartak; Kelsey M Hennick; Yefim Zaltsman; Zun Zar Chi Naing; Benjamin J Polacco; Ali Bashir; Manon Eckhardt; Mehdi Bouhaddou; Jiewei Xu; Nawei Sun; Micaela C Lasser; Yuan Zhou; Justin McKetney; Keelan Z Guiley; Pawel Gniewek; Una Chan; Naufa Amirani; Owen Griffiths; Nishant Chadha; Reshmi Tognatta; Merve Cakir; Martin Gordon; Prachi Khare; Sam Drake; Vanessa Drury; David F Burke; Silvano Gonzalez; Sahar Alkhairy; Reuben Thomas; Stephanie Lam; Montana Morris; Ethel Bader; Mélanie Dos Santos; Anastassia V Komarova; Maxwell Bennett; Craig Ennis; Octavio Castillo; Yvonne Lim; Robert Martin; Meghan Seyler; Tierney Baum; Rebecca Krasnoff; George Wang; Sagnik Middya; Sheng Wang; Presley Pham; Juan Arbelaez; Dexter Pratt; Sofia Bali; Shivali Chag; Julia A Kaye; Nadir Mahmood; Lee Spraggon; Thomas Rolland; Shawn Hervey-Jumper; James S Fraser; Thomas Bourgeron; Steven Finkbeiner; Caroline Demeret; Danielle L Swaney; Sourav Bandyopadhyay; Trey Ideker; Pedro Beltrao; Helen Rankin Willsey; Ruth Hüttenhain; Kirsten Obernier; Tomasz J Nowakowski; Matthew W State; A Jeremy Willsey; Nevan J Krogan
INTRODUCTION
Autism spectrum disorder (ASD) is characterized by extreme genetic heterogeneity, with more than 250 high-confidence risk (hcASD) genes identified to date. Defined by rare, large-effect coding variants, these genes show functional and developmental convergence in transcriptomic analyses. However, these approaches have provided only limited mechanistic insight and have not identified specific therapeutic targets beyond the genetic variants themselves. Because proteins are the primary functional units of the cell, mapping the physical ASD interactome—and determining how ASD variants rewire it—is essential to move beyond gene lists and broad pathophysiologic themes toward a deeper causal understanding of neurodevelopmental pathology.
RATIONALE
To augment our molecular understanding of ASD, we used affinity purification–mass spectrometry (AP-MS) to map 100 hcASD proteins and 54 patient-derived missense variants, substantially expanding the known ASD protein interaction landscape. By integrating these datasets with AlphaFold structural modeling and functional studies in Xenopus and human forebrain organoids, we investigated whether genetically distinct risk factors converge onto shared biology and if convergent neurodevelopmental phenotypes arise through the selective rewiring of protein-protein interactions (PPIs) by disease-associated variants.
RESULTS
The resulting ASD-PPI network contains more than 1800 interactions, 87% of which were previously unreported. The network, which is enriched in neural progenitor cells (NPCs) of the excitatory lineage, exhibits a highly interconnected architecture, with risk proteins converging onto shared complexes, including DCAF7. Functional interrogation of selected interactions demonstrated that disruption of the previously uncharacterized DCAF7-DYRK1A-KIAA0232 complex impairs progenitor proliferation and reduces forebrain size in vivo. Furthermore, patient-derived missense mutations frequently induced convergent PPI rewiring. Distinct FOXP1 mutations, for example, weakened its physical interaction with FOXP4, leading to gain-of-function redistribution of FOXP4 to ectopic genomic targets. In human forebrain organoids, this biochemical rewiring drove premature differentiation of cortical neurons and altered neural activity. Genetic deletion of FOXP4 in a FOXP1-mutant background rescued these neurodevelopmental defects; although the exact mechanism requires further determination, this suggests that the rewired interaction underlies the mutant phenotype.
CONCLUSION
Together, these findings define a dual-layered model of molecular convergence in ASD: convergence through shared interaction networks in the wild-type state and convergence through recurrent functional consequences of interaction rewiring in the mutant state. More broadly, this work establishes a scalable framework for systematic interrogation of the autism proteome, enables prioritization of druggable protein interfaces, and provides a rational foundation for precision therapeutic strategies aimed at restoring neurodevelopmental trajectories.
Web | DOI | PDF | Science | Open Access