BAP1 Malignant Pleural Mesothelioma Mutations in Caenorhabditis elegans Reveal Synthetic Lethality between ubh-4/BAP1 and the Proteasome Subunit rpn-9/PSMD13

Our plain-English summary of BAP1 Malignant Pleural Mesothelioma Mutations in Caenorhabditis elegans Reveal Synthetic Lethality between ubh-4/BAP1 and the Proteasome Subunit rpn-9/PSMD13, by C. Martínez-Fernández, S. Jha, E. Aliagas, et al (Cells, 2023).

The study

• Authors: C. Martínez-Fernández, S. Jha, E. Aliagas, C.I. Holmberg, E. Nadal, J. Cerón
• Journal: Cells
• Published: 2023;12(6)
• Cited by: 6 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

The deubiquitinase BAP1 (BRCA1-associated protein 1) is associated with BAP1 tumor predisposition syndrome (TPDS). BAP1 is a tumor suppressor gene whose alterations in cancer are commonly caused by gene mutations leading to protein loss of function. By CRISPR-Cas, we have generated mutations in ubh-4, the BAP1 ortholog in Caenorhabditis elegans, to model the functional impact of BAP1 mutations. We have found that a mimicked BAP1 cancer missense mutation (UBH-4 A87D; BAP1 A95D) resembles the phenotypes of ubh-4 deletion mutants. Despite ubh-4 being ubiquitously expressed, the gene is not essential for viability and its deletion causes only mild phenotypes without affecting 20S proteasome levels. Such viability facilitated an RNAi screen for ubh-4 genetic interactors that identified rpn-9, the ortholog of human PSMD13, a gene encoding subunit of the regulatory particle of the 26S proteasome. ubh-4[A87D], similarly to ubh-4 deletion, cause a synthetic genetic interaction with rpn-9 inactivation affecting body size, lifespan, and the development of germ cells. Finally, we show how ubh-4 inactivation sensitizes animals to the chemotherapeutic agent Bortezomib, which is a proteasome inhibitor. Thus, we have established a model to study BAP1 cancer-related mutations in C. elegans, and our data points toward vulnerabilities that should be studied to explore therapeutic opportunities within the complexity of BAP1 tumors.

In plain English

This was a laboratory study in the nematode Caenorhabditis elegans designed to model mutations of the human tumour suppressor BAP1, which is altered in malignant pleural mesothelioma. Using CRISPR-Cas, the authors made deletion alleles of ubh-4 (the worm ortholog, sharing 33.14% identity with BAP1 and 47.13% with UCHL5) and worm versions of two BAP1 cancer missense mutations, F81V and A95D (worm F73V and A87D). ubh-4 was expressed in all developmental stages, yet deletion animals were viable with only a slight reduction in progeny and no change in 20S proteasome tissue levels. An RNA interference screen of 150 selected genes in ubh-4(cer27) animals identified rpn-9, ortholog of human PSMD13, a 19S proteasome regulatory subunit, as a genetic interactor: rpn-9 RNAi reduced brood size in the mutants (p less than 0.01 for hatched larvae), in one experiment scoring an average of 20 animals. Double mutants of rpn-9(gk401) with the ubh-4 deletion or A87D had shorter bodies, shortened survival and smaller germlines; F73V animals did not. ubh-4 deletion animals were more sensitive to the proteasome inhibitor Bortezomib on days two and three of adulthood.

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 experimental study in Caenorhabditis elegans using CRISPR-Cas genome editing, an RNAi genetic-interaction screen, fluorescent reporters and drug exposure
• Who was studied: C. elegans strains (wild-type N2 and CRISPR-generated or CGC-provided mutant strains) studied in the laboratory; no human participants
• Exposure: Genetic alterations (ubh-4 deletion alleles cer27, cer150, cer140; missense alleles F73V and A87D mimicking BAP1 F81V and A95D; rpn-9 deletion gk401 and rpn-9 RNAi) and chemical exposure to the proteasome inhibitor Bortezomib at 5, 10, 15, 20 and 30 micromolar
• Main results:
  • UBH-4 was reported as the ortholog of human UCHL5 and BAP1, sharing 47.13% and 33.14% identity respectively
  • ubh-4 null and missense mutants showed no overt phenotypes, only a slight progeny reduction in cer27 and F73V(cer25)
  • In the RNAi screen in ubh-4(cer27) animals, hatched larvae differed between wild-type and cer27 under rpn-9(RNAi) at p less than 0.01
  • The rpn-9 RNAi brood-size comparison was based on an average of 20 animals scored, and the experiment was performed once
  • rpn-9(gk401) animals were already smaller than wild-type, and were smaller still when combined with the ubh-4 deletion (cer140) or the A87D allele (cer198)
  • Survival was markedly reduced in rpn-9(gk401) double mutants with the ubh-4 deletion or A87D, but not with F73V
  • Double mutants of rpn-9 with ubh-4 deletion or A87D had thinner, smaller germlines than single mutants
  • Animals carrying the ubh-4 deletion allele were sensitive to Bortezomib at days two and three of adulthood
  • The worm version of BAP1 F81V (F73V) produced no detected phenotype in the rpn-9 mutant background
• The authors' conclusion: The authors concluded that C. elegans is a usable model for exploring BAP1 aberrations recurrent in malignant pleural mesothelioma and for investigating drug targets, and they hypothesised that precise targeting of PSMD13 could be a potential therapeutic strategy in BAP1 mutant tumours
• Limitations the authors state:
  • The authors did not quantify the aberrant germline nuclei
  • The authors stated that conserved residues may not have the same functional relevance in worms as in humans
  • The authors stated that the mechanism behind the UBH-4/BAP1 and RPN-9/PSMD13 interaction remains unclear and is only hypothesised
  • The authors noted that proteasome-centred therapeutic intervention would need caution because the ubiquitin proteasome system affects many cellular pathways

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, Pleural Mesothelioma, BAP1 Tumor Predisposition Syndrome, Tumor Suppressor Gene.

Related studies

• Synthetic lethality in malignant pleural mesothelioma with PARP1 inhibition — G. Srinivasan, G.S. Sidhu, et al. (2017)
• Malignant cells from pleural fluids in malignant mesothelioma patients reveal novel mutations — S. Sneddon, I. Dick, et al. (2018)
• Withaferin A inhibits the proteasome activity in mesothelioma in vitro and in vivo — H. Yang, Y. Wang, et al. (2012)
• Proteasome stress sensitizes malignant pleural mesothelioma cells to bortezomib-induced apoptosis — F. Cerruti, G. Jocollè, et al. (2017)
• MRTX1719 Is an MTA-Cooperative PRMT5 Inhibitor That Exhibits Synthetic Lethality in Preclinical Models and Patients with MTAP-Deleted Cancer — L.D. Engstrom, R. Aranda, et al. (2023)
• Whole-exome sequencing reveals frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1 in malignant pleural mesothelioma — G. Guo, J. Chmielecki, et al. (2015)

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