Proximity labeling uncovers the synaptic proteome under physiological and pathological conditions

Abstract

Synapses are fundamental units of neurotransmission and play a central role in the formation and function of neural circuits. These dynamic structures exhibit morphological and functional plasticity in response to experience and activity, supporting higher brain functions such as learning, memory, and emotion. Their molecular composition includes diverse membrane-associated and cytoskeletal proteins that mediate intercellular signaling, regulate synaptic plasticity, and maintain structural stability. Disruptions in these protein networks, often referred to as synaptopathies, are closely linked to psychiatric and neurological disorders. Such disruptions commonly manifest as region-specific changes in synapse number, morphology, or signaling efficacy. Although a large number of synaptic proteins have been identified through conventional proteomic approaches, our understanding of synaptic specificity and plasticity remains limited. This is primarily due to insufficient spatial resolution, lack of cell-type specificity, and challenges in applying these methods to intact neural circuits in vivo. Recent advances in proximity labeling techniques such as BioID and APEX can spatial proteomics limiting cell compartments and cell-type. BioID also enables proteomic analysis within synaptic compartments under both physiological and pathological conditions in vivo. These technologies allow unbiased, high-resolution profiling of protein networks in specific synapse types, synaptic clefts, and glial-neuronal interfaces, thereby providing new insights into the molecular basis of synaptic diversity and function. In this short review, we summarize recent developments in synaptic proteomics enabled by proximity labeling. We also discuss how these approaches have advanced our understanding of synapse-specific molecular architecture and their potential to inform the mechanisms of synapse-related brain disorders, as well as the development of targeted diagnostic and therapeutic strategies.

Keywords: BioID; cytoskeleton; proteomics; spine formation; synapse; synaptopathy.

FIGURE 1

Synaptic proteomics approaches using proximity labeling to uncover physiological and pathological conditions. (A) A schematic diagram and applications of BioID, APEX, and HRP are shown. The proteins of interest (bait proteins) are fused with BioID (a biotin ligase), APEX (ascorbate peroxidase), or HRP (horseradish peroxidase) and expressed in cells. BioID biotinylates lysine residues of proteins in proximity to the bait protein, whereas APEX and HRP biotinylate tyrosine residues of nearby proteins. In the BioID approach, various types of biotin ligases can be selected. Moreover, BioID technologies can be applied to in vivo studies (iBioID). The biotinylated proteins are identified using mass spectrometry, followed by analyses of molecular localization and function based on the constructed protein networks. (B) Proximity labeling methods (BioID, APEX, and HRP) enable high spatial resolution mapping of proteins localized to specific synapse types, the synaptic cleft, and tripartite synapses. These synaptic proteomics approaches have also been applied to the study of synaptopathies, including autism spectrum disorder, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. These neuropsychiatric disorders are characterized by abnormalities in synapse formation, function, and plasticity.