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Updated: Aug 23, 2025
Ubiquitin Chain Analysis by Parallel Reaction Monitoring
Published on: June 17, 2020
USP7 substrates identified by proteomics analysis reveal the specificity of USP7
Litong Nie1, Chao Wang1, Xiaoguang Liu1
1Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.
Abstract:
Deubiquitylating enzymes (DUBs) remove ubiquitin chains from proteins and regulate protein stability and function. USP7 is one of the most extensively studied DUBs, since USP7 has several well-known substrates important for cancer progression, such as MDM2, N-MYC, and PTEN. Thus, USP7 is a promising drug target. However, systematic identification of USP7 substrates has not yet been performed. In this study, we carried out proteome profiling with label-free quantification in control and single/double-KO cells of USP7and its closest homolog, USP47 Our proteome profiling for the first time revealed the proteome changes caused by USP7 and/or USP47 depletion. Combining protein profiling, transcriptome analysis, and tandem affinity purification of USP7-associated proteins, we compiled a list of 20 high-confidence USP7 substrates that includes known and novel USP7 substrates. We experimentally validated MGA and PHIP as new substrates of USP7. We further showed that MGA deletion reduced cell proliferation, similar to what was observed in cells with USP7 deletion. In conclusion, our proteome-wide analysis uncovered potential USP7 substrates, providing a resource for further functional studies.
Insights
Researchers identified new targets for the deubiquitylating enzyme USP7, a potential cancer drug target. This study systematically reveals USP7 substrates, aiding future cancer therapy development.
Area of Science:
- Biochemistry
- Molecular Biology
- Cancer Research
Background:
- Deubiquitylating enzymes (DUBs) regulate protein stability and function by removing ubiquitin chains.
- USP7 is a key DUB with known substrates implicated in cancer progression, making it a promising therapeutic target.
- A systematic identification of USP7 substrates has been lacking.
Purpose of the Study:
- To systematically identify USP7 substrates using proteome profiling.
- To investigate the roles of USP7 and its homolog USP47 in protein regulation.
- To discover novel USP7 substrates for further functional studies and therapeutic targeting.
Main Methods:
- Proteome profiling using label-free quantification in USP7 and USP47 knockout cells.
- Transcriptome analysis.
- Tandem affinity purification of USP7-associated proteins.
Main Results:
- The study revealed proteome changes upon USP7 and/or USP47 depletion for the first time.
- A list of 20 high-confidence USP7 substrates, including novel ones, was compiled.
- MGA and PHIP were experimentally validated as new USP7 substrates, with MGA deletion impacting cell proliferation.
Conclusions:
- Proteome-wide analysis provides a valuable resource for understanding USP7 function.
- Identification of novel substrates like MGA and PHIP opens new avenues for cancer research.
- This study advances the potential of USP7 as a drug target by providing a comprehensive substrate list.
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