USP41 Data Analysis

HGNC Gene Name
ubiquitin specific peptidase 41
HGNC Gene Symbol
USP41
Identifiers
hgnc:20070 NCBIGene:373856 uniprot:Q3LFD5
Orthologs
mgi:1344364
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for USP41
Number of Papers
7 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

Dependency GO Term Enrichment

Gene set enrichment analysis was done on the genes correlated with USP41using 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

Literature Mining

INDRA was used to automatically assemble known mechanisms related to USP41 from literature and knowledge bases. The first section shows only DUB activity and the second shows all other results.

Deubiquitinase Activity

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

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USP41 knockdown inhibits cell proliferation and migration and induces cell apoptosis of lung cancer.

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In contrast, USP41 knockdown significantly inhibited BC colony-forming ability, proliferation, and migration.

eidos
USP41 knockdown inhibits cell proliferation and migration and induces cell apoptosis of lung cancer .

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MTT, EdU, flow cytometry, and transwell assays further determined that USP41 enhanced the proliferation and migration of lung cancer cells.

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Overexpression of USP41 greatly enhanced BC colony-forming ability, proliferation, and migration.

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Deubiquitinating enzyme USP41 promotes lung cancer cell proliferation and migration.
Bisphenol A affects USP41
2 |
Bisphenol A increases the amount of USP41. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
| 2

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USP41 knockdown promotes lung cancer cell apoptosis.

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USP41 knockdown inhibits cell proliferation and migration and induces cell apoptosis of lung cancer.
Indometacin affects USP41
2 |
Indometacin increases the amount of USP41.
1 |
Indometacin increases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available
Indometacin decreases the amount of USP41.
1 |
Indometacin decreases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available
2 |
Dexamethasone increases the amount of USP41.
1 |
Dexamethasone increases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available
Dexamethasone decreases the amount of USP41.
1 |
Dexamethasone decreases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available
3-isobutyl-1-methyl-7H-xanthine increases the amount of USP41.
1 |
1 |

ctd
No evidence text available
3-isobutyl-1-methyl-7H-xanthine decreases the amount of USP41.
1 |
1 |

ctd
No evidence text available
Urethane affects USP41
1 |
Urethane decreases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available

ctd
No evidence text available

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An independent cohort confirmed LPS induction of USP41 and IL10 genes.
Doxorubicin affects USP41
1 |
Doxorubicin decreases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available
Bis(2-ethylhexyl) phthalate increases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available

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We knocked down E-cadherin in lung cancer cell lines using siRNA, and demonstrated that E-Cadherin knockout offseted the effect of inhibition of USP41 on cell migration, and inhibition of USP41 may reverse EMT of lung cancer cells.
| 1

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These results indicated that USP41 promoted lung cancer cell migration.
USP41 affects RACK1
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USP41 increases the amount of RACK1. 1 / 1
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USP41 promoted the protein expression of RACK1 .
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| 1

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Overexpression of the Ubiquitin Specific Proteases USP43, USP41, USP27x and USP6 in Osteosarcoma Cell Lines: Inhibition of Osteosarcoma Tumor Growth and Lung Metastasis Development by the USP Antagonist PR619.
| 1

eidos
USP41 promotes breast cancer via regulating RACK1 .
RACK1 affects USP41
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RACK1 activates USP41. 1 / 1
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Knockdown of RACK1 inhibited cell growth and migration, and reversed the oncogenic function of USP41 in BC cells.
USP41 is modified
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USP41 is deubiquitinated. 1 / 1
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trips
Deubiquitinating enzyme USP41 promotes lung cancer cell proliferation and migration.
IFNA affects USP41
1 |
IFNA increases the amount of USP41. 1 / 1
1 |

bel
Table 3. Genes on chromosome 22 exhibiting IFN-sensitive expression changes
4,4'-sulfonyldiphenol decreases the amount of USP41. 1 / 1
1 |

ctd
No evidence text available