USP50 Data Analysis

HGNC Gene Name
ubiquitin specific peptidase 50
HGNC Gene Symbol
USP50
Identifiers
hgnc:20079 NCBIGene:373509 uniprot:Q70EL3
Orthologs
mgi:1922333 rgd:1564751
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for USP50
Number of Papers
6 retrieved on 2022-05-22

DepMap Analysis

The Dependency Map (DepMap) is a genome-wide pooled CRISPR-Cas9 knockout proliferation screen conducted in more than 700 cancer cell lines spanning many different tumor lineages. Each cell line in the DepMap contains a unique barcode, and each gene knockout is assigned a “dependency score” on a per cell-line basis which quantifies the rate of CRISPR-Cas9 guide drop. It has been found that proteins with similar DepMap scores across cell lines, a phenomenon known as co-dependent genes, have closely related biological functions. This can include activity in the same or parallel pathways or membership in the same protein complex or the same pathway.

We identified the strongest seven co-dependent genes (“Symbol”) for DUBs and ran GO enrichment analysis. We used Biogrid, IntAct, and Pathway Commons PPIDs, and the NURSA protein-protein interaction databases (PPIDs) to determine whether co-dependent genes interact with one another. The “Evidence” column contains the PPIDs in which the interaction appears as well as whether there is support for the association by an INDRA statement. As another approach to identify potential interactors, we looked at proteomics data from the Broad Institute's Cancer Cell Line Encyclopedia (CCLE) for proteins whose expression across ~375 cell lines strongly correlated with the abundance of each DUB; it has previously been observed that proteins in the same complex are frequently significantly co-expressed. The correlations and associated p-values in the CCLE proteomics dataset are provided. And, we determined whether co-dependent genes yield similar transcriptomic signatures in the Broad Institute's Connectivity Map (CMap). A CMap score greater than 90 is considered significantly similar.

DepMap Correlations

Symbol Name DepMap Correlation Evidence CCLE Correlation CCLE Z-score CCLE p-value (adj) CCLE Significant CMAP Score CMAP Type
SEMG1 semenogelin 1 -0.24
EPB42 erythrocyte membrane protein band 4.2 0.227
CTXN2 cortexin 2 0.223
RNF122 ring finger protein 122 0.215
TRIM69 tripartite motif containing 69 0.215
STARD9 StAR related lipid transfer domain containing 9 0.213
RNF39 ring finger protein 39 -0.211

Dependency GO Term Enrichment

Gene set enrichment analysis was done on the genes correlated with USP50using the terms from Gene Ontology and gene sets derived from the Gene Ontology Annotations database via MSigDB.

Using the biological processes and other Gene Ontology terms from well characterized DUBs as a positive control, several gene set enrichment analyses were considered. Threshold-less methods like GSEA had relatively poor results. Over-representation analysis with a threshold of of the top 7 highest absolute value Dependency Map correlations yielded the best results and is reported below.

GO Identifier GO Name GO Type p-value p-value (adj.) q-value

Transcriptomics

The following table shows the significantly differentially expressed genes after knocking out USP50 using CRISPR-Cas9.

Knockout Differential Expression

Symbol Name log2-fold-change p-value p-value (adj.)
RPS24 ribosomal protein S24 6.46e-01 2.14e-10 4.71e-06
HSP90AB1 heat shock protein 90 alpha family class B member 1 8.01e-01 4.77e-07 5.27e-03

Gene Set Enrichment Analysis

There were too few differentially expressed genes to run a meaningful GSEA.

Literature Mining

INDRA was used to automatically assemble known mechanisms related to USP50 from literature and knowledge bases. The first section shows only DUB activity and the second shows all other results.

Deubiquitinase Activity

psp cbn pc bel_lc signor biogrid lincs_drug tas hprd trrust ctd vhn pe drugbank omnipath conib crog dgi | rlimsp isi tees geneways eidos trips medscan sparser reach
USP50 deubiquitinates PYCARD. 7 / 7
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USP50 deubiquitinates the ASC protein.

ubibrowser
The deubiquitinating enzyme, ubiquitin-specific peptidase 50, regulates inflammasome activation by targeting the ASC adaptor protein

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However, the Flag-USP50 (C53S) mutant, did not affect polyubiquitination of the ASC protein, indicating that the Cys residue at position 53 is critical for the catalytic activity of USP50 deubiquitination of the ASC protein.

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To further confirm our finding that USP50 deubiquitinates the ASC protein, we performed in vitro deubiquitination assays.

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Ubiquitination of Flag-ASC proteins was significantly decreased in the presence of Flag-USP50 protein, indicating that USP50 directly deubiquitinates the polyubiquitination of the ASC protein.

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Wild-type USP50 and the Flag-USP50 (H322A) mutant significantly deubiquitinated the ASC protein.

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In conclusion, we here demonstrate a novel regulatory mechanism regarding the ASC protein which is deubiquitinated by USP50 and provide experimental evidence emphasizing the importance of a regulatory mechanism mediated by ubiquitination and deubiquitination in inflammasome activation.
USP50 deubiquitinates PYCARD on lysine. 1 / 1
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Lee et al.66 showed that the deubiquitinating enzyme, USP50, binds to and deubiquitinates lysine 63‐linked polyubiquitin chains of ASC and that this is required for NLRP3 inflammasome activation, since USP50‐deficient cells show impaired inflammasome activation.
USP50 deubiquitinates PYCARD at position 63. 1 / 1
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Lee et al.66 showed that the deubiquitinating enzyme, USP50, binds to and deubiquitinates lysine 63‐linked polyubiquitin chains of ASC and that this is required for NLRP3 inflammasome activation, since USP50‐deficient cells show impaired inflammasome activation.
USP50-H322A deubiquitinates PYCARD. 1 / 1
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Wild-type USP50 and the Flag-USP50 (H322A) mutant significantly deubiquitinated the ASC protein.
USP50 deubiquitinates WEE1. 1 / 1
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ubibrowser
USP50 regulates HSP90-dependent Wee1 stability preventing mitotic entry, acting as another G2/M checkpoint

Other Statements

psp cbn pc bel_lc signor biogrid lincs_drug tas hprd trrust ctd vhn pe drugbank omnipath conib crog dgi | rlimsp isi tees geneways eidos trips medscan sparser reach
USP50 affects XRCC6
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USP50 inhibits XRCC6.
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USP50 inhibits XRCC6. 4 / 4
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Interestingly, USP50 associates with the Ku70 protein and reduces the half-life of Ku70 protein.

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Thus, we hypothesize that USP50 mediated Ku70 degradation might be through targeting a ubiquitin E3 ligase that ubiquitinates and degrades Ku70.

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USP50 reduces Ku70 protein stability without affecting its mRNA levels.

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These data suggest that USP50 reduces Ku70 protein stability.
USP50 activates XRCC6.
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USP50 activates XRCC6. 1 / 1
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Additional studies are necessary to elucidate the molecular mechanisms of USP50 mediated destabilization of Ku70 protein.
USP50 affects WEE1
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USP50 activates WEE1.
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USP50 activates WEE1. 3 / 3
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We propose that USP50 may act through a HSP90 dependent mechanism to counteract CDC25B mitotic inducing activity and prevent Wee1 degradation, thereby repressing entry into mitosis following activation of the DNA damage checkpoint.

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In response to DNA damage, USP50 accumulates in the nucleus and may act through an HSP90 dependent mechanism to counteract CDC25B mitotic inducing activity and prevent Wee1 degradation, thereby repressing entry into mitosis following activation of the DNA damage checkpoint [XREF_BIBR].

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USP50 (ubiquitin specific protease 50), a deubiqitinating enzyme (DUB), prevents Wee1 degradation, thereby repressing entry into mitosis following activation of the G2/M DNA damage checkpoint.
USP50 inhibits WEE1.
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USP50 inhibits WEE1. 1 / 1
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We also demonstrate USP50 depletion causes a loss in accumulation of the HSP90 client Wee1, which is an essential component of the G2/M cell cycle arrest.
USP50 affects PYCARD
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USP50 inhibits PYCARD. 2 / 3
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Taken together with our results that USP50 depletion decreases the formation of ASC specks as well as the secretion of IL-lbeta, our findings strongly suggest the possibility that removal of these polyubiquitin chains from ASC protein by USP50 is a crucial step for inflammasome activation.

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USP50 depletion markedly impedes the formation of ASC oligomer and IL-1beta secretion in both human THP-1 macrophages and mouse BMDMs.
USP50 affects IL1B
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USP50 inhibits IL1B. 2 / 2
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In contrast, USP50 depletion significantly decreased IL-1beta secretion, suggesting the possibility that USP50 is a positive regulator in inflammasome activation.

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USP50 depletion markedly impedes the formation of ASC oligomer and IL-1beta secretion in both human THP-1 macrophages and mouse BMDMs.
Leflunomide affects USP50
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Leflunomide decreases the amount of USP50. 1 / 1
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ctd
No evidence text available
Jinfukang affects USP50
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Jinfukang decreases the amount of USP50. 1 / 1
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ctd
No evidence text available
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Cadmium atom decreases the amount of USP50. 1 / 1
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ctd
No evidence text available
Butanal affects USP50
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Butanal decreases the amount of USP50. 1 / 1
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ctd
No evidence text available
Bisphenol A affects USP50
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Bisphenol A decreases the amount of USP50. 1 / 1
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ctd
No evidence text available
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Taken together, these findings suggest a model where USP50 and Ku70 may stabilize Mcl-1 and prevent apoptosis in the late stages of erythropoiesis.

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The deubiquitinase USP50 also contributes to NLRP3 inflammasome activation through ASC deubiquitination.
USP50 affects CPT1A
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USP50 activates CPT1A. 1 / 1
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Curcumin alleviated LPS-mediated sepsis by suppressing the activities of mitochondrial STAT3 and NF-κB. Conclusion: Our findings reveal that mitochondrial STAT3 could trigger FAO by inducing CPT1a stabilization mediated by USP50 in macrophages, at least partially.
PAX4 affects USP50
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PAX4 decreases the amount of USP50. 1 / 1
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biopax:msigdb
No evidence text available
FOXO4 affects USP50
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FOXO4 decreases the amount of USP50. 1 / 1
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biopax:msigdb
No evidence text available