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Inhibition of USP7 Destabilizes the Noncanonical PRC1.1 Complex and Induces Neuroblastoma Differentiation
Emily A Cmarik1,2,3, Abhishek Wahi1,2, Sayali S Chandekar1,2
1Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.
Abstract:
Pediatric cancers are frequently driven by genomic alterations that result in impaired differentiation during development. To identify complex-level dependencies required for differentiation in neuroblastoma, a pediatric cancer of the developing peripheral nervous system, we curated a list of protein complexes using the CORUM database and mined the Dependency Map using gene set enrichment analysis. This analysis identified the noncanonical polycomb repressive complex 1.1 (PRC1.1) complex, which represses transcriptional activity through ubiquitination of histone 2A, lysine 119 (H2AK119Ub), as a selectively enriched dependency in neuroblastoma. Knockout of PRC1.1 subunits reduced neuroblastoma growth by inducing a neuronal differentiation program. Although no known direct inhibitors of PRC1.1 exist, codependency analysis identified that the deubiquitinase USP7 strongly correlated with PRC1.1 dependency. Treatment with XL177A, a small molecule inhibitor of USP7, significantly reduced neuroblastoma growth in both cellular and animal models. Integrated RNA and chromatin immunoprecipitation sequencing showed that both PRC1.1 knockout and USP7 inhibition resulted in highly correlated transcriptional alterations and reduced H2AK119Ub deposition on chromatin, suggesting that USP7 inhibition reduced neuroblastoma growth through a PRC1.1-dependent mechanism. Mechanistically, global proteomics and ubiquitinomics revealed that USP7 inhibition disrupted noncanonical PRC1 complex assembly, resulting in the destabilization of PRC1.1 and subsequent proteolysis. Our findings expand our understanding of the chromatin complexes required to maintain a dedifferentiated state in neuroblastoma and suggest the therapeutic potential for USP7 inhibitors in the treatment of this disease.
Implications:
Our study reveals the potential for utilizing USP7 inhibitors to target epigenetic repression of differentiation programs in neuroblastoma by reducing PRC1 activity.
Insights
Targeting the non-canonical PRC1.1 complex in neuroblastoma, a pediatric cancer, can induce differentiation. USP7 inhibition disrupts PRC1.1, offering a potential therapeutic strategy for neuroblastoma treatment.
Area of Science:
- Oncology
- Epigenetics
- Developmental Biology
Background:
- Pediatric cancers like neuroblastoma often stem from disrupted cellular differentiation.
- Genomic alterations impairing differentiation are key drivers in neuroblastoma development.
Purpose of the Study:
- To identify protein complexes crucial for differentiation in neuroblastoma.
- To explore therapeutic strategies targeting identified dependencies.
Main Methods:
- Utilized CORUM database for protein complexes and Dependency Map (DepMap) for gene set enrichment analysis.
- Performed gene knockout studies, co-dependency analysis, and small molecule inhibition (USP7 inhibitor XL177A).
- Integrated RNA-sequencing, ChIP-sequencing, global proteomics, and ubiquitinomics.
Main Results:
- Identified the non-canonical PRC1.1 complex as a key dependency in neuroblastoma, repressing differentiation.
- PRC1.1 subunit knockout induced neuronal differentiation and reduced tumor growth.
- USP7 inhibition with XL177A mimicked PRC1.1 knockout effects, reducing neuroblastoma growth in vitro and in vivo.
- USP7 inhibition disrupted PRC1.1 complex assembly, leading to its destabilization and proteolysis, reducing H2AK119Ub deposition.
Conclusions:
- USP7 inhibition represents a promising therapeutic approach for neuroblastoma by targeting PRC1.1-mediated epigenetic repression.
- Understanding PRC1.1 complex function is crucial for developing new treatments for neuroblastoma.
- USP7 inhibitors can reactivate differentiation programs in neuroblastoma cells.
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