Characterization of BRCA1-Associated Protein-1 (BAP1) Aggregation Properties Induced by Cancer-Associated Mutations

Our plain-English summary of Characterization of BRCA1-Associated Protein-1 (BAP1) Aggregation Properties Induced by Cancer-Associated Mutations, by L.C. Hsiao, S. Puri, M.K. Sriramoju, et al (Chembiochem, 2025).

The study

• Authors: L.C. Hsiao, S. Puri, M.K. Sriramoju, Y.S. Wang, T.N. Lee, L.H. Wang, S.D. Hsu
• Journal: Chembiochem
• Published: 2025;26(23):e202500372
• Cited by: 3 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

BRCA1-associated protein-1 (BAP1) is a tumor suppressor protein that regulates DNA transcription through its deubiquitinase activity. Cancer-associated missense mutations within its ubiquitin C-terminal hydrolase (UCH) domain result in structural destabilization and aggregation, contributing to various malignancies such as malignant mesothelioma and uveal melanoma. In this study, we investigated the aggregation mechanisms of highly destabilized BAP1-UCH variants, including N78S, C91W, F81V, and G128R, using Thioflavin T (ThT) binding assays and AmyloFit analysis. Our results reveal that all BAP1-UCH variants follow a secondary nucleation-dominated aggregation model, exhibiting strong concentration dependence and significantly higher aggregation rates, which may be responsible for their impaired nuclear import, leading to increased cytosolic retention. These findings provide critical insights into how specific mutations in BAP1 drive aggregation and compromise its tumor-suppressing functions inside the nucleus, thereby contributing to cancer progression.

© 2025 The Author(s). ChemBioChem published by Wiley‐VCH GmbH.

In plain English

This was a laboratory study of the UCH domain of the BAP1 protein. It looked at how four cancer-associated mutations (N78S, C91W, F81V and G128R) affect the protein's tendency to clump together, or aggregate. It did not study asbestos, patients or tumours. The authors mention malignant mesothelioma only as background. They purified the normal (wild-type) fragment and the four variants and tracked aggregation with a dye test (ThT) and other methods. Wild-type protein needed concentrations of 10 μM and above to aggregate noticeably, while G128R aggregated readily at 1 μM. A model in which existing fibrils seed new aggregates ("secondary nucleation") best fit every variant. F81V and G128R formed clumps fastest and formed mature fibrils within 3 days. Wild type was slowest. In HeLa-Kyoto cells made to overexpress full-length BAP1, the N78S and G128R versions formed spots of clumped protein beside the nucleus; overexpressed wild type did not. Computer prediction tools did not match the experimental results. The authors concluded that aggregation-driven loss of BAP1 function might play a significant role in cancers. They cautioned that secondary nucleation is inherently random.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory (in vitro) study of purified protein fragments, with computer predictions and a cell-culture imaging experiment
• Who was studied: Purified BAP1-UCH protein domain: wild type (WT) and four cancer-associated variants (N78S, C91W, F81V, G128R). Full-length BAP1 with N78S or G128R, and WT BAP1, were overexpressed in HeLa-Kyoto cells. No human participants.
• Exposure: No asbestos or other environmental exposure was studied. The study compared cancer-associated missense mutations in the BAP1-UCH domain with the wild-type protein.
• Main results:
  • In the dye (ThT) test, wild-type protein required concentrations of 10 μM and above to show significant aggregation. G128R aggregated readily at 1 μM.
  • A secondary nucleation-dominated model best described aggregation of all the BAP1-UCH variants tested.
  • Over time, all variants lost α-helical structure while their β-sheet content increased.
  • F81V and G128R formed oligomers fastest, followed by N78S and C91W. Wild type was slowest.
  • Early in aggregation the variants formed small oligomers, which then aggregated into large soluble aggregates of 20 to 300 MDa.
  • In electron microscopy, F81V and G128R formed mature fibrils within 3 days.
  • When full-length BAP1 was overexpressed in HeLa-Kyoto cells, the N78S and G128R versions formed perinuclear puncta (spots next to the nucleus). Overexpressed wild-type BAP1 did not.
  • A sequence-based prediction tool (AGGRESCAN) predicted lower aggregation for F81V and G128R, contrary to the experiments.
  • The primary nucleation rate and order correlated with the previously measured enthalpy of unfolding. Secondary nucleation parameters did not.
• The authors' conclusion: The authors concluded that aggregation-mediated loss of function in BAP1, as with p53, might play a significant role in developing and advancing various cancers. They also suggested that large aggregates would be too big to enter the nucleus.
• Limitations the authors state:
  • The results should be read in light of the inherent randomness of secondary nucleation, reflected in variable fitted parameters.
  • Reliable measurements of F81V and G128R at high protein concentrations were challenging.
  • Data points outside the linear range of the half-time plots were excluded from model fitting.
  • Some G128R precipitated during the ThT measurements, which may have reduced the dye signal.
  • Because samples had to be filtered, aggregate sizes at later time points could not be measured by SEC-MALS.

Topics

Medical terms in this study, explained in our Lexicon: BAP1, Mesothelioma.

Related studies

• Prevalence of BRCA-1 associated protein 1 germline mutation in sporadic malignant pleural mesothelioma cases — A. Rusch, G. Ziltener, et al. (2015)
• Functional differences between wild-type and mutant-type BRCA1-associated protein 1 tumor suppressor against malignant mesothelioma cells — S. Hakiri, H. Osada, et al. (2015)
• Tumours associated with BAP1 mutations — R. Murali, T. Wiesner, et al. (2013)
• BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas — N. Leblay, F. Leprêtre, et al. (2017)
• BAP1 (BRCA1-associated protein 1) is a highly specific marker for differentiating mesothelioma from reactive mesothelial proliferations — M. Cigognetti, S. Lonardi, et al. (2015)
• A Novel BRCA1-Associated Protein-1 Isoform Affects Response of Mesothelioma Cells to Drugs Impairing BRCA1-Mediated DNA Repair — R. Parrotta, A. Okonska, et al. (2017)

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