BAP1 and USP1 cooperate to regulate FANCD2 stability and cell proliferation in mesothelioma cells

Our plain-English summary of BAP1 and USP1 cooperate to regulate FANCD2 stability and cell proliferation in mesothelioma cells, by K. Suzuki, S. Kiyonari, J. Nishino, et al (Cell Death & Disease, 2026).

The study

• Authors: K. Suzuki, S. Kiyonari, J. Nishino, M. Takahashi, Y. Kato, M. Amano, A. Ogiso, T. Akashi, T. Maeda, N. Kaneda, T. Miida, Y. Kondo, K. Kadomatsu, M. Kato, K. Aoyama, H. Murakami, Y. Sekido, Y. Murakami-Tonami
• Journal: Cell Death & Disease
• Published: 2026;17(1)
• Cited by: 1 article, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

BRCA1-associated protein 1 (BAP1) is frequently inactivated in pleural mesothelioma and functions as a tumor suppressor through its deubiquitinating activity. In this study, we investigated the context-dependent interplay between BAP1 and ubiquitin-specific protease 1 (USP1) in mesothelioma cells, focusing on their roles in regulating FANCD2, cell proliferation, and DNA damage responses. Genetic suppression of USP1 selectively inhibited cell proliferation in BAP1-deficient mesothelioma cells, whereas reintroduction of wild-type BAP1 rescued this growth defect; notably, a catalytically inactive BAP1 mutant failed to do so, indicating that BAP1 deubiquitinase activity is required for this compensation. In contrast, depletion of FANCD2 suppressed cell proliferation irrespective of BAP1 status, underscoring the essential role of FANCD2 in mesothelioma cell survival. Although both BAP1 and USP1 were capable of deubiquitinating FANCD2 in vitro, USP1 suppression in mesothelioma cells did not provide clear biochemical evidence of altered FANCD2 ubiquitination. Instead, USP1 knockdown was associated with reduced FANCD2 transcript and protein levels, without markedly affecting FANCD2 mRNA stability. At the cellular level, USP1 depletion impaired FANCD2 focus formation and reduced its colocalization with γ-H2AX in BAP1-deficient cells, consistent with defective DNA damage signaling. Despite these changes, homologous recombination (HR) efficiency was largely preserved, whereas non-homologous end joining activity was modestly increased upon USP1 suppression. Consistent with these in vitro findings, USP1 knockdown suppressed tumor growth in an intrathoracic xenograft model. Collectively, our results indicate that BAP1 and USP1 appear to regulate FANCD2 through distinct, context-dependent mechanisms, with USP1 primarily influencing FANCD2 expression and BAP1 modulating FANCD2 function at the post-translational level. Together, these findings identify USP1 as a context-dependent therapeutic vulnerability in BAP1-deficient mesothelioma and support a working model in which USP1-dependent maintenance of FANCD2 function becomes critical in the absence of functional BAP1.

© 2026. The Author(s).

In plain English

This was a laboratory study in mesothelioma cell lines, mouse xenografts and public tumour datasets, testing whether the deubiquitinating enzyme USP1 is selectively needed by mesothelioma cells that have lost BAP1 (a gene often inactivated in pleural mesothelioma, a cancer the authors note is primarily associated with asbestos exposure). Knocking down USP1 with shRNA slowed growth of BAP1-deficient H28 cells but not of H28 cells re-expressing wild-type BAP1; a catalytically inactive BAP1 mutant (C91S) did not restore growth. Knocking down FANCD2 slowed growth whether or not BAP1 was present. In a cell-free assay, purified wild-type BAP1 deubiquitinated a FANCD2 probe, while the C91S mutant did not. BAP1-mutant H28 cells were not notably sensitive to PARP inhibitors. In separate reporter cell lines, homologous recombination in DR-U2OS cells showed no significant change after BAP1 overexpression or USP1 knockdown, while non-homologous end joining in H1299dA3-1 cells increased modestly after USP1 knockdown. USP1 knockdown reduced tumour growth in an intrathoracic xenograft model using BAP1-mutated H226 cells. In TCGA pleural mesothelioma data, lower USP1 expression was linked to better survival only among BAP1-mutant cases.

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 in human mesothelioma cell lines with biochemical and reporter assays, plus a mouse intrathoracic xenograft experiment and analysis of public TCGA-MESO and GTEx datasets
• Who was studied: Human mesothelioma cell lines (NCI-H28, NCI-H226, NCI-H2373, NCI-H2452, ACC-MESO-1) and engineered derivatives; NOG mice given intrathoracic transplants; DNA-repair reporter cell lines DR-U2OS and H1299dA3-1; public TCGA-MESO and GTEx lung data
• Exposure: Genetic manipulation rather than an environmental exposure: shRNA knockdown of USP1, FANCD2 or BAP1; overexpression of wild-type BAP1 or catalytically inactive BAP1(C91S); pharmacological USP1-UAF1 inhibition with ML323 and PARP inhibitors MC2050 and 3-ABA
• Main results:
  • USP1 knockdown reduced proliferation of BAP1-deficient H28-Venus cells but not of H28 cells expressing wild-type BAP1
  • The catalytically inactive BAP1(C91S) mutant did not rescue the growth defect caused by USP1 knockdown in H28 cells
  • FANCD2 knockdown suppressed proliferation in both BAP1-deficient and BAP1-expressing H28 cells
  • In the cell-free fluorescence polarization assay, purified wild-type BAP1 deubiquitinated the FANCD2 probe at 1.25 to 5 micromolar, while the C91S mutant did not
  • BAP1-mutant H28 cells showed no significant sensitivity to the two PARP inhibitors tested
  • In the DR-U2OS homologous recombination reporter cells, neither BAP1 overexpression nor USP1 knockdown produced a significant change in HR activity
  • In the H1299dA3-1 non-homologous end joining reporter cells, USP1 knockdown modestly increased NHEJ activity
  • USP1 knockdown reduced FANCD2 transcript levels in H28-Venus and H28-BAP1 cells
  • USP1 knockdown reduced total FANCD2 protein in H28 cells
  • No consistent accumulation of ubiquitinated FANCD2 was detected after USP1 knockdown
  • In BAP1-deficient H28-Venus cells, USP1 knockdown reduced colocalization of FANCD2 foci with gamma-H2AX
  • In the intrathoracic xenograft model with BAP1-mutated H226 cells, USP1 knockdown reduced tumour growth and tumour burden
  • In TCGA-MESO BAP1 wild-type cases, overall survival did not differ between high and low USP1 expression (log-rank p = 0.94)
  • In TCGA-MESO BAP1-mutated cases, lower USP1 mRNA expression was associated with improved overall survival (log-rank p = 0.038)
• The authors' conclusion: The authors concluded that BAP1 and USP1 regulate FANCD2 through distinct layers, with USP1 influencing FANCD2 expression and BAP1 acting post-translationally, and that USP1 is a context-dependent vulnerability in BAP1-deficient mesothelioma
• Limitations the authors state:
  • The authors state they found no clear biochemical evidence that USP1 directly regulates FANCD2 ubiquitination in mesothelioma cells
  • The authors describe their in vivo analyses as preliminary, with dosing, specificity, off-target effects and tolerability still to be assessed
  • The authors note the histological origin of the H226 cells used in the xenograft model has been debated and that the model was supplementary
  • The authors note the in vitro deubiquitination assay used a minimal peptide substrate, so activity reflects simplified conditions
  • The authors state that the genome-wide shRNA screen that identified USP1 is not shown

Topics

The National Library of Medicine indexes this study under subjects our site covers: Mesothelioma.

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

Related studies

• BAP1 regulates IP3R3-mediated Ca2+ flux to mitochondria suppressing cell transformation — A. Bononi, C. Giorgi, et al. (2017)
• 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)
• Loss of the deubiquitylase BAP1 alters class I histone deacetylase expression and sensitivity of mesothelioma cells to HDAC inhibitors — J.J. Sacco, J. Kenyani, et al. (2015)
• BAP1 and YY1 regulate expression of death receptors in malignant pleural mesothelioma — Y. Ishii, K.K. Kolluri, et al. (2021)
• BAP1 (BRCA1-associated protein 1) is a highly specific marker for differentiating mesothelioma from reactive mesothelial proliferations — M. Cigognetti, S. Lonardi, et al. (2015)
• BAP1 immunohistochemistry and p16 FISH to separate benign from malignant mesothelial proliferations — B.S. Sheffield, H.C. Hwang, et al. (2015)

Browse more research in Cell Death & Disease, or return to medical research.