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.
Symbol | Name | DepMap Correlation | Evidence | CCLE Correlation | CCLE Z-score | CCLE p-value (adj) | CCLE Significant | CMAP Score | CMAP Type |
---|---|---|---|---|---|---|---|---|---|
MDM2 | MDM2 proto-oncogene | 0.499 | BioGRID IntAct Pathway Commons INDRA (37) Reactome (14) | 0.17 | 0.82 | 3.76e-02 | |||
TP53 | tumor protein p53 | -0.44 | BioGRID IntAct Pathway Commons INDRA (49) Reactome (16) | -0.01 | -0.16 | 8.62e-01 | |||
PPM1D | protein phosphatase, Mg2+/Mn2+ dependent 1D | 0.4 | Reactome (3) | 0.11 | 0.54 | 2.79e-01 | |||
TP53BP1 | tumor protein p53 binding protein 1 | -0.377 | IntAct INDRA (1) Reactome (3) | 0.01 | -0.01 | 8.49e-01 | |||
C16orf72 | HUWE1 associated protein modifying stress responses | 0.359 | 0.34 | 1.81 | 6.71e-04 | ||||
CDKN1A | cyclin dependent kinase inhibitor 1A | -0.342 | INDRA (5) Reactome (9) | -0.01 | -0.12 | 9.48e-01 | |||
USP28 | ubiquitin specific peptidase 28 | -0.331 | INDRA (1) Reactome (4) | 0.16 | 0.79 | 6.28e-03 |
Gene set enrichment analysis was done on the genes correlated with USP7using 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 |
---|---|---|---|---|---|
GO:0010212 | response to ionizing radiation | Biological Process | 1.61e-10 | 8.11e-08 | 9.67e-09 |
GO:0009314 | response to radiation | Biological Process | 1.68e-10 | 8.45e-08 | 9.67e-09 |
GO:0031570 | DNA integrity checkpoint | Biological Process | 2.24e-10 | 1.13e-07 | 9.67e-09 |
GO:0071478 | cellular response to radiation | Biological Process | 5.69e-10 | 2.87e-07 | 1.84e-08 |
GO:0000075 | cell cycle checkpoint | Biological Process | 1.09e-09 | 5.47e-07 | 2.81e-08 |
GO:0071479 | cellular response to ionizing radiation | Biological Process | 2.68e-09 | 1.35e-06 | 5.72e-08 |
GO:0072331 | signal transduction by p53 class mediator | Biological Process | 3.09e-09 | 1.56e-06 | 5.72e-08 |
GO:0034644 | cellular response to UV | Biological Process | 4.15e-09 | 2.09e-06 | 6.71e-08 |
GO:0071214 | cellular response to abiotic stimulus | Biological Process | 8.08e-09 | 4.07e-06 | 1.16e-07 |
GO:0030330 | DNA damage response, signal transduction by p53 class mediator | Biological Process | 1.37e-08 | 6.90e-06 | 1.77e-07 |
GO:0071482 | cellular response to light stimulus | Biological Process | 2.93e-08 | 1.48e-05 | 3.45e-07 |
GO:0042770 | signal transduction in response to DNA damage | Biological Process | 3.32e-08 | 1.67e-05 | 3.58e-07 |
GO:0009411 | response to UV | Biological Process | 3.97e-08 | 2.00e-05 | 3.96e-07 |
GO:0031668 | cellular response to extracellular stimulus | Biological Process | 5.54e-07 | 2.79e-04 | 5.12e-06 |
GO:0097193 | intrinsic apoptotic signaling pathway | Biological Process | 7.61e-07 | 3.84e-04 | 5.80e-06 |
GO:0002039 | p53 binding | Molecular Function | 7.62e-07 | 3.84e-04 | 5.80e-06 |
GO:0009416 | response to light stimulus | Biological Process | 1.05e-06 | 5.28e-04 | 7.54e-06 |
GO:0072395 | signal transduction involved in cell cycle checkpoint | Biological Process | 1.13e-06 | 5.69e-04 | 7.70e-06 |
GO:0072332 | intrinsic apoptotic signaling pathway by p53 class mediator | Biological Process | 1.27e-06 | 6.42e-04 | 8.25e-06 |
GO:0071496 | cellular response to external stimulus | Biological Process | 1.39e-06 | 7.02e-04 | 8.58e-06 |
GO:0071158 | positive regulation of cell cycle arrest | Biological Process | 1.54e-06 | 7.77e-04 | 9.07e-06 |
GO:0090400 | stress-induced premature senescence | Biological Process | 2.33e-06 | 1.18e-03 | 1.31e-05 |
GO:0071156 | regulation of cell cycle arrest | Biological Process | 3.54e-06 | 1.79e-03 | 1.83e-05 |
GO:0044774 | mitotic DNA integrity checkpoint | Biological Process | 3.44e-06 | 1.74e-03 | 1.83e-05 |
GO:1902807 | negative regulation of cell cycle G1/S phase transition | Biological Process | 6.19e-06 | 3.12e-03 | 3.08e-05 |
GO:0090399 | replicative senescence | Biological Process | 7.57e-06 | 3.82e-03 | 3.63e-05 |
GO:0009267 | cellular response to starvation | Biological Process | 9.52e-06 | 4.80e-03 | 4.40e-05 |
GO:0007093 | mitotic cell cycle checkpoint | Biological Process | 1.27e-05 | 6.39e-03 | 5.66e-05 |
GO:0046827 | positive regulation of protein export from nucleus | Biological Process | 1.75e-05 | 8.80e-03 | 7.53e-05 |
GO:0042594 | response to starvation | Biological Process | 1.84e-05 | 9.29e-03 | 7.58e-05 |
GO:0006367 | transcription initiation from RNA polymerase II promoter | Biological Process | 1.87e-05 | 9.44e-03 | 7.58e-05 |
GO:1902806 | regulation of cell cycle G1/S phase transition | Biological Process | 2.25e-05 | 1.14e-02 | 8.84e-05 |
GO:0071480 | cellular response to gamma radiation | Biological Process | 3.37e-05 | 1.70e-02 | 1.28e-04 |
GO:0010165 | response to X-ray | Biological Process | 3.86e-05 | 1.95e-02 | 1.43e-04 |
GO:0097718 | disordered domain specific binding | Molecular Function | 4.12e-05 | 2.07e-02 | 1.44e-04 |
GO:0007050 | cell cycle arrest | Biological Process | 4.08e-05 | 2.06e-02 | 1.44e-04 |
GO:0006352 | DNA-templated transcription, initiation | Biological Process | 4.34e-05 | 2.19e-02 | 1.48e-04 |
GO:1901988 | negative regulation of cell cycle phase transition | Biological Process | 5.22e-05 | 2.63e-02 | 1.73e-04 |
GO:0044839 | cell cycle G2/M phase transition | Biological Process | 5.46e-05 | 2.75e-02 | 1.77e-04 |
GO:0031647 | regulation of protein stability | Biological Process | 5.90e-05 | 2.97e-02 | 1.86e-04 |
GO:0046825 | regulation of protein export from nucleus | Biological Process | 6.47e-05 | 3.26e-02 | 1.99e-04 |
GO:0044843 | cell cycle G1/S phase transition | Biological Process | 7.04e-05 | 3.55e-02 | 2.12e-04 |
GO:0090068 | positive regulation of cell cycle process | Biological Process | 7.33e-05 | 3.70e-02 | 2.15e-04 |
GO:0070646 | protein modification by small protein removal | Biological Process | 7.48e-05 | 3.77e-02 | 2.15e-04 |
GO:0042771 | intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator | Biological Process | 7.84e-05 | 3.95e-02 | 2.21e-04 |
GO:0044389 | ubiquitin-like protein ligase binding | Molecular Function | 8.01e-05 | 4.04e-02 | 2.21e-04 |
GO:2000379 | positive regulation of reactive oxygen species metabolic process | Biological Process | 8.57e-05 | 4.32e-02 | 2.31e-04 |
The following table shows the significantly differentially expressed genes after knocking out USP7 using CRISPR-Cas9.
There were too few differentially expressed genes to run a meaningful GSEA.
INDRA was used to automatically assemble known mechanisms related to USP7 from literature and knowledge bases. The first section shows only DUB activity and the second shows all other results.