TAggiXL: A Fluorescence-Traceable Cross-Linking Strategy for Unbiased Profiling of Protein Aggregation and Interactome Dynamics

Protein aggregation is a hallmark of numerous degenerative diseases, yet its underlying mechanisms remain poorly understood due to the challenges in identifying the composition and interaction networks of these aggregates. To address this issue, we developed TAggiXL, a novel method that combines fluorescence-traceable aggregate isolation with cross-linking proteomics, significantly enhancing the efficiency and precision of isolating protein aggregates. This method facilitates unbiased profiling of aggregated proteomes and their interactomes in live cells. The TAggiXL approach leverages advanced cross-linking proteomics, density gradient centrifugation, and fluorescence tracking to provide detailed characterization of protein aggregation under various stress conditions including HSP90 and proteasome inhibition. Using TAggiXL, we identified key components and interactions within the aggregates, particularly highlighting E3 ubiquitin ligase TRIM26, which plays a crucial role in aggregate formation and autophagic clearance under stress and pathogenic conditions. Moreover, TAggiXL revealed that HSPA1B functions as a central interaction hub within the aggregated proteome. It preferentially interacts with intrinsically disordered regions (IDRs) of aggregate components and demonstrates dynamic behavior within the aggregate. In summary, TAggiXL offers a powerful tool for dissecting the complex composition and interaction networks of protein aggregates, with a significant potential to advance our understanding of protein aggregation in degenerative diseases. It also holds promise for the development of future therapeutic interventions.