Restoration of BAP1 activity via base editing suppresses anchorage-independent survival in kidney cancer

Our plain-English summary of Restoration of BAP1 activity via base editing suppresses anchorage-independent survival in kidney cancer, by D. Lee, B. Lee, J. Lee, et al (Cancer Cell International, 2025).

The study

• Authors: D. Lee, B. Lee, J. Lee, J. Kwon
• Journal: Cancer Cell International
• Published: 2025;25(1):444
• Cited by: 2 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

BAP1, a deubiquitinase with a ubiquitin C-terminal hydrolase domain, functions as a tumor suppressor involved in diverse cellular processes, including DNA repair, genome stability, and apoptosis. Inactivating mutations in BAP1-particularly missense and deletion variants-are recurrent across multiple cancers, with a high prevalence in clear cell renal cell carcinoma (ccRCC), mesothelioma, and uveal melanoma. Among these, the Glu31Lys mutation in ccRCC impairs BAP1's enzymatic activity, protein stability, and DNA repair functions. Here, we investigated the physiological impact of this recurrent mutation using isogenic KMRC-20 ccRCC cell clones in which the Glu31Lys substitution was precisely corrected to wild-type glutamate via CRISPR-Cas9-mediated adenine base editing. BAP1 reactivation restored anchorage-dependent growth in KMRC-20 cells-a hallmark of non-transformed epithelial cells-and increased apoptosis under non-adherent conditions, indicating reinstated sensitivity to anoikis. Mechanistically, this phenotypic switch was accompanied by post-transcriptional downregulation of N-cadherin and β-catenin under anchorage-free conditions, implicating BAP1 in the regulation of adhesion- and Wnt-related survival pathways. Furthermore, transcriptomic profiling revealed broad gene expression changes upon BAP1 restoration, suggesting that these combined alterations contribute to the re-establishment of anchorage-dependent growth in KMRC-20 cells. These findings uncover a previously unrecognized role for BAP1 in suppressing anchorage-independent survival, providing new insights into BAP1-driven tumorigenesis and underscoring the therapeutic potential of precise gene editing to restore tumor suppressor function in ccRCC.

© 2025. The Author(s).

In plain English

This was a laboratory study in cultured human cells. The authors worked with KMRC-20, a clear cell renal cell carcinoma (ccRCC) cell line whose only BAP1 coding change is the Glu31Lys mutation, and used CRISPR-Cas9 adenine base editing (ABE7.10max with the VRQR Cas9 variant) to change the mutant AAG codon back to GAG (wild-type glutamate). Two independent sets of three corrected single-cell clones were made (E8, D2, B5 by lentivirus; 1-1, 1-3, 1-34 by transient transfection). Sequencing indicated all three BAP1 alleles were edited in the triploid cells, with no changes at the top three predicted off-target sites. The corrected clones regained BAP1 deubiquitinase activity, showed reduced H2A-Ub and higher BAP1 protein levels, but grew and cycled much like the parental cells in standard culture. In soft agar, colony formation was markedly reduced (clones 1-3 and 1-34 formed virtually no colonies), and apoptosis rose on ultra-low attachment plates. N-cadherin and beta-catenin protein, but not mRNA, fell under non-adherent conditions. The authors concluded BAP1 suppresses anchorage-independent survival. Mesothelioma is mentioned only as background.

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 cell-culture experiment using CRISPR-Cas9-mediated adenine base editing to create isogenic revertant clones of a kidney cancer cell line
• Who was studied: KMRC-20 clear cell renal cell carcinoma cells (JCRB Cell Bank, Japan) and derived single-cell clones; HEK293T, HCT116 and HeLa cells also used; work done in a laboratory in Seoul, Korea
• Exposure: Correction of the endogenous BAP1 Glu31Lys (AAG) mutation to wild-type glutamate (GAG) by adenine base editing; and a further edit converting GAG to GGG (glycine) in the 1-1-G31 control clone
• Main results:
  • Three edited clones (E8, D2, B5) were isolated and sequencing indicated all three BAP1 alleles were corrected, with no detectable off-target substitutions at the top three predicted sites
  • BAP1 from parental KMRC-20 cells showed no detectable deubiquitinase activity, while BAP1 from all three revertant clones showed activity; H2A-Ub was reduced and BAP1 protein levels raised in revertants
  • Correction of the mutation had little effect on growth, cell cycle or short-term viability of the revertant clones compared with parental KMRC-20 cells
  • In soft agar, all three first-set revertant clones formed markedly fewer colonies than parental cells, clone B5 almost none; in the second set, clone 1-1 was markedly reduced and clones 1-3 and 1-34 formed virtually no colonies
  • Under ultra-low attachment conditions, cell death (mainly apoptosis) and PARP1 cleavage were increased in the revertant clones versus parental cells; no difference was seen under adherent conditions
  • N-cadherin and beta-catenin protein fell in revertant clones under non-adherent conditions while vimentin was unchanged; mRNA levels of both genes were largely unchanged, indicating post-transcriptional regulation
  • Re-inactivating BAP1 in the 1-1-G31 clone restored N-cadherin and beta-catenin to parental-like levels and reduced PARP1 cleavage under ULA conditions
  • RNA-sequencing of parental cells and clones 1-1 and 1-34 showed the revertant clones clustered separately, with genes altered at least two-fold and enrichment for Wnt signaling, epithelial cell proliferation, cell adhesion and apoptosis
• The authors' conclusion: The authors concluded that a single recurrent BAP1 point mutation in ccRCC may compromise tumor suppressor function including anchorage-dependent cell death, and that correcting it by base editing restored BAP1 function and revealed a role in suppressing anchorage-independent survival through post-transcriptional downregulation of N-cadherin and beta-catenin
• Limitations the authors state:
  • The mechanism of the N-cadherin and beta-catenin downregulation was not resolved and no direct BAP1 targets were identified, which the authors call a key limitation
  • The authors state it is unclear whether the transcriptome changes come directly from BAP1 reactivation or indirectly from altered adhesion signaling

Topics

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

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