Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes
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Evaluation Summary:
To better understand proteins and pathways regulated by deubiquitinating enzymes (DUBs), this study has assembled a database that integrates existing datasets with additional knock-out experiments. Co-dependent genes as well as protein-protein interactions and co-expression were taken into account. The combined data confirms known functions and highlights potential new functions of DUBs. This will be a useful resource for investigators aiming to elucidate DUB functions, as well as for research efforts to develop therapies for the treatment of different cancer types through targeting DUBs.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)
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Abstract
Deubiquitinating enzymes (DUBs), ~100 of which are found in human cells, are proteases that remove ubiquitin conjugates from proteins, thereby regulating protein turnover. They are involved in a wide range of cellular activities and are emerging therapeutic targets for cancer and other diseases. Drugs targeting USP1 and USP30 are in clinical development for cancer and kidney disease respectively. However, the majority of substrates and pathways regulated by DUBs remain unknown, impeding efforts to prioritize specific enzymes for research and drug development. To assemble a knowledgebase of DUB activities, co-dependent genes, and substrates, we combined targeted experiments using CRISPR libraries and inhibitors with systematic mining of functional genomic databases. Analysis of the Dependency Map, Connectivity Map, Cancer Cell Line Encyclopedia, and multiple protein-protein interaction databases yielded specific hypotheses about DUB function, a subset of which were confirmed in follow-on experiments. The data in this paper are browsable online in a newly developed DUB Portal and promise to improve understanding of DUBs as a family as well as the activities of incompletely characterized DUBs (e.g. USPL1 and USP32) and those already targeted with investigational cancer therapeutics (e.g. USP14, UCHL5, and USP7).
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Evaluation Summary:
To better understand proteins and pathways regulated by deubiquitinating enzymes (DUBs), this study has assembled a database that integrates existing datasets with additional knock-out experiments. Co-dependent genes as well as protein-protein interactions and co-expression were taken into account. The combined data confirms known functions and highlights potential new functions of DUBs. This will be a useful resource for investigators aiming to elucidate DUB functions, as well as for research efforts to develop therapies for the treatment of different cancer types through targeting DUBs.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the …
Evaluation Summary:
To better understand proteins and pathways regulated by deubiquitinating enzymes (DUBs), this study has assembled a database that integrates existing datasets with additional knock-out experiments. Co-dependent genes as well as protein-protein interactions and co-expression were taken into account. The combined data confirms known functions and highlights potential new functions of DUBs. This will be a useful resource for investigators aiming to elucidate DUB functions, as well as for research efforts to develop therapies for the treatment of different cancer types through targeting DUBs.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)
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Reviewer #1 (Public Review):
In this manuscript, the Sorger lab examines RNA expression in cell lines lacking most of the DUBs, and uses this data set, along with published data, to generate hypotheses about these molecules. While most DUBs are unlikely to have direct roles in transcriptional regulation, these data can still be used to correlate inactivation of the DUB to the inactivation of other genes. Using other published RNA seq. experiments, they find similarities between the transcriptional effects of knocking down DUBS and other genes. They then discuss these in light of published literature and datasets, primarily confirming previously suggested activities.
The ways in which the authors carry out this study is reminiscent of the ways in which many scientists initially analyze their datasets (be they expression, protein …
Reviewer #1 (Public Review):
In this manuscript, the Sorger lab examines RNA expression in cell lines lacking most of the DUBs, and uses this data set, along with published data, to generate hypotheses about these molecules. While most DUBs are unlikely to have direct roles in transcriptional regulation, these data can still be used to correlate inactivation of the DUB to the inactivation of other genes. Using other published RNA seq. experiments, they find similarities between the transcriptional effects of knocking down DUBS and other genes. They then discuss these in light of published literature and datasets, primarily confirming previously suggested activities.
The ways in which the authors carry out this study is reminiscent of the ways in which many scientists initially analyze their datasets (be they expression, protein abundance, PTM levels or CRISPR screening data) when they first have the data in hand: they look to DepMAP and BioGrid and other sites that consolidate data and try to come up with some hypothesis. However, for most investigators, this is the beginning of the investigation, whereas here it is the entire study. While they occasionally repeat the transcriptional analysis on members of the pathway in question to confirm that a particular DUB's knockout mirrors that of another gene, this is just confirming their original observation. For example, knockout of the DUB USP8 yielded similar expression changes as those associated with over activation of the NF-kB pathway. USP8 was previously shown to function in the ESCRT pathway, which is known to regulate the NF-kB pathway. The authors further confirm this by examining expression in other ESCRT mutants. As with many of the DUB interactions, they also show that this genetic interaction can be seen on DepMap. Finally, the investigators compare transcriptional output of mutants to that of cells treated with a few small molecule inhibitors. Not surprisingly, some correlate well with their presumed target, while others do not.
Almost all of the connections drawn here are confirmations. In some cases, the connections are well-established, whereas others are less understood. However, there is no follow-up on any potential biology. For this reason, most of the paper jumps from topic to topic with a few paragraphs on each area of biology. Given that the technique carried out (transcriptional profiling of mutants) has been carried out extensively for more than a decade, their starting dataset is not particularly novel, making this a rather modest resource for the community.
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Reviewer #2 (Public Review):
Deubiquitinating enzymes (DUBs) are ~100 proteases that remove ubiquitin from proteins, thereby regulating protein turnover. DUB inhibition can potentially provide new avenues for regulating targets with small molecules. Towards this end, the study has assembled a knowledgebase of DUB activities, co-dependent genes and substrates by combining targeted experiments using CRISPR libraries and inhibitors with mining of functional genomic databases, including the Dependency Map, Connectivity Map, Cancer Cell Line Encyclopedia, and protein-protein interaction databases. Study data are browsable online via the DUB Portal.
Strengths
The study provides useful, new information on a number of DUBs, Better understanding the substrates and pathways regulated by DUBs could help future research efforts towards targeting …
Reviewer #2 (Public Review):
Deubiquitinating enzymes (DUBs) are ~100 proteases that remove ubiquitin from proteins, thereby regulating protein turnover. DUB inhibition can potentially provide new avenues for regulating targets with small molecules. Towards this end, the study has assembled a knowledgebase of DUB activities, co-dependent genes and substrates by combining targeted experiments using CRISPR libraries and inhibitors with mining of functional genomic databases, including the Dependency Map, Connectivity Map, Cancer Cell Line Encyclopedia, and protein-protein interaction databases. Study data are browsable online via the DUB Portal.
Strengths
The study provides useful, new information on a number of DUBs, Better understanding the substrates and pathways regulated by DUBs could help future research efforts towards targeting these newly identified relationships or DUBs themselves through the design of new small molecules.
The study mines multiple already existing databases to better understand DUB activities, which is a great way of utilizing these already existing resources.
The DUB Portal enables easy, interactive exploration of study findings.
Weaknesses
The study somewhat over-reaches in its implications. For example, the abstract states that through DUBs, previously thought to be undruggable targets, such as c-Myc can be targeted. However, what new biology regarding Myc is uncovered is somewhat unclear.
It is somewhat unclear how some of the thresholds are selected in the study results section.
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Reviewer #3 (Public Review):
The manuscript prepared by the teams of Sarah Buhrlage and Peter Sorger describes a systematic bioinformatics approach to report on the therapeutic potential of the family of deubiquitylating enzymes (DUBs).
DUBs have attracted recent attention, not only in terms of progress in understanding their biology, but also as drug targets for a variety of human disease conditions, such as cancer, neurodegeneration and immune disorders. Therefore, a comprehensive evaluation of their potential as key modulators in human diseases is timely.
The authors have collected available public data, in combination with some selected experiments, to create a 'DUB knowledge base' including function, CRISPR library screens for DUB essentiality (DepMap), co-dependent genes, DUB-protein interaction networks and substrates.
DUBs …
Reviewer #3 (Public Review):
The manuscript prepared by the teams of Sarah Buhrlage and Peter Sorger describes a systematic bioinformatics approach to report on the therapeutic potential of the family of deubiquitylating enzymes (DUBs).
DUBs have attracted recent attention, not only in terms of progress in understanding their biology, but also as drug targets for a variety of human disease conditions, such as cancer, neurodegeneration and immune disorders. Therefore, a comprehensive evaluation of their potential as key modulators in human diseases is timely.
The authors have collected available public data, in combination with some selected experiments, to create a 'DUB knowledge base' including function, CRISPR library screens for DUB essentiality (DepMap), co-dependent genes, DUB-protein interaction networks and substrates.
DUBs reflect a relevant family of enzymes, and one of their hallmarks is the relatively low level of critical mutations in humans. The fact that many DUB KO mice models show lethality in early development stages (e.g. 20 DUBs out of 82 with complete penetrance mentioned by the authors) is consistent with this observation.
Inherent to covering a broad range of information and touching on many aspects of DUB biology, each piece of information in the paper appears somewhat shallow. In aggregate, though, this study represents one of the largest assemblies of available information on DUBs compiled in one resource, reflecting a useful contribution to the field.
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