Integrated proteomic and multi-mic characterizations of the synapse reveal RNA processing factor and ubiquitin ligases associated with neurodevelopment disorders
The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human brain and hiPSC-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The integrated proteomic and multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 492 proteins that have not been documented previously. We further investigate three such proteins that are associated with neurodevelopmental disorders – the CUL3 E3 ubiquitin ligase, the DDX3X and YBX1 nucleic-acid binding factors – by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to systematically and more comprehensively resolve the synaptic architecture. Overall design: Investigation of RNA targets of RNA-binding proteins YBX1 and DDX3X in the human iPSC-derived neurons