Quantitative Proteomics Unveils Comprehensive Tissue-Specific VCP Interaction Networks in Mice

Area of Science:

• Biochemistry and Molecular Biology
• Cellular Biology
• Genetics

Background:

• Valosin-containing protein (VCP) is a AAA ATPase hexamer crucial for protein degradation pathways like ERAD.
• VCP dysregulation is linked to multisystem proteinopathy, ALS, and cancer, but its tissue-specific functions are poorly understood.
• Understanding VCP's diverse interactomes is key to elucidating its versatile biological roles.

Purpose of the Study:

• To systematically profile the tissue-specific VCP interactome in vivo.
• To identify novel VCP-binding partners across various mouse tissues.
• To provide mechanistic insights into VCP's functional versatility and potential therapeutic targets.

Main Methods:

• Generation of HA-N-tagged VCP knock-in mice using CRISPR/Cas9.
• Affinity purification coupled with data-independent acquisition (DIA) mass spectrometry.
• Systematic profiling of VCP interactors across eight mouse tissues and validation in HepG2 cells.

Main Results:

• Identification of 923 high-confidence VCP-binding partners.
• Discovery of established interactors (e.g., UBX2B, UFD1) and novel candidates.
• Novel interactors implicated in energy metabolism (TCA cycle, oxidative phosphorylation) and protein quality control (proteasome, ERAD).
• Validation of VCP interactions with hepatic proteins DAXX and PRKAG2.

Conclusions:

• This study presents the first in vivo atlas of the VCP interaction network.
• The findings offer mechanistic insights into tissue-specific VCP functions.
• The identified interactome provides potential therapeutic avenues for VCP-related disorders.