USP7 substrates identified by proteomics analysis reveal the specificity of USP7
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA752331 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15349300_1.fastq.gz | Fastqsanger.gz | |||
| SRR15349300_2.fastq.gz | Fastqsanger.gz | |||
| SRR15349301_1.fastq.gz | Fastqsanger.gz | |||
| SRR15349301_2.fastq.gz | Fastqsanger.gz | |||
| SRR15349302_1.fastq.gz | Fastqsanger.gz |
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Project description:Deubiquitylating enzymes (DUBs) remove ubiquitin chains from proteins and regulate protein stability and function. USP7 is one of the most compressively studied DUBs. Since USP7 has several well-known substrates important for cancer progression, such as MDM2, N-MYC and PTEN, USP7 becomes a promising drug target. However, systematic identification of USP7 substrates have not yet been performed. In this study, we carried out proteome profiling with label-free quantification using control and single/double KO cells of USP7 and its closest homolog USP47. Our proteome profiling for the first time reveal the proteome changes caused by USP7 and/or USP47 deletion. Combining protein profiling, transcriptome analysis and tandem-affinity purification of USP7-associated proteins, we compiled a list of 20 high-confidence USP7 substrates, which include known and novel USP7 substrates. We experimentally validated MGA and PHIP as new substrates of USP7. Further, we showed that MGA deletion partially phenocopied proliferation defect observed in cells with USP7 deletion. Additionally, we established that USP7 deletion repress interferon gamma response. Moreover, we showed that the cytotoxicity of USP7 inhibitors were independent of USP7. In conclusion, our study is the first proteome-wide analysis of potential USP7 substrates, which provides a resource for further functional studies.
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Project description: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.
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Project description:Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control stability or activity of substrates. Identification of DUB substrates is challenging because multiple DUBs can act on the same substrate, thwarting genetic approaches. Here, we circumvent redundancy by chemically inhibiting multiple DUBs simultaneously in Xenopus egg extract. We discovered a set of proteins that depends on DUBs for their stability and we confirmed their DUB-dependent regulation with human orthologs, demonstrating evolutionary conservation. We next extended this approach, developing a new method to profile DUB specificity. By adding recombinant DUBs to extract where DUB activity was broadly inhibited, but ubiquitylation and degradation were active at physiological rates, we profiled the ability of DUBs to rescue degradation of these new substrates. We found that USP7 has a unique ability to broadly antagonize their degradation. Together, we identify novel DUB substrates and present an approach to characterize DUB specificity that overcomes challenges posed by DUB redundancy.
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Project description:Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.
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Project description:Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.
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