Widespread Remodeling of Synaptic Protein Interaction Networks Following Homeostatic Plasticity in Cortical Neurons Requires Homer1 and Shank3

Summary Neurons maintain constant levels of excitability using homeostatic scaling, which adjusts relative synaptic strength in response to large changes in overall activity. While previous studies have catalogued the transcriptomic and proteomic changes associated with scaling, the resulting alterations in synaptic protein interaction networks (PINs) are less well understood. Here, we monitor a glutamatergic synapse PIN composed of 380 binary interactions among 21 protein members to identify protein complexes altered by synaptic scaling. In cultured cortical neurons, we observe widespread bidirectional PIN alterations with up-versus downscaling. In the barrel cortex, the PIN response to 48 hours of sensory deprivation exhibits characteristics of both upscaling and downscaling, consistent with emerging models of excitatory/inhibitory balance in cortical plasticity. Mice lacking Homer1 or Shank3B do not undergo normal PIN rearrangements, suggesting that these Autism Spectrum Disorder (ASD)-linked proteins serve as structural hubs for synaptic homeostasis. Our approach demonstrates how previously identified RNA and protein-level changes induced during homeostatic scaling translate into functional PIN alterations.