Genome-wide CRISPR screen identifies BUB1 kinase as a druggable vulnerability in malignant pleural mesothelioma

Our plain-English summary of Genome-wide CRISPR screen identifies BUB1 kinase as a druggable vulnerability in malignant pleural mesothelioma, by E. Cakiroglu, S. Eris, O. Oz, et al (Cell Death & Disease, 2025).

The study

• Authors: E. Cakiroglu, S. Eris, O. Oz, G. Karakülah, S. Senturk
• Journal: Cell Death & Disease
• Published: 2025;16(1):241
• Cited by: 11 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Malignant pleural mesothelioma (MPM) is a rare yet highly aggressive malignancy with a severe prognosis. Compounded by the lack of effective treatment modalities, MPM remains a formidable health challenge. Therefore, the identification of actionable liabilities is critical for advancing precision medicine to combat this lethal disease. Here, we exploit an unbiased genome-wide CRISPR screen, integrating and cross-comparing three MPM cell lines with nonmalignant mesothelial cells, to selectively map the gene targets whose depletion indicates a common dependency in MPM cells. This systematic approach unveils a cohort of verifiable genes, among which BUB1, a mitotic checkpoint serine/threonine kinase, emerges as a high-confidence hit in cancer cells. Cellular and molecular studies demonstrate that genetic depletion or pharmacological inhibition of BUB1 profoundly impairs MPM cell survival and growth while inducing G2/M cell cycle arrest, cellular senescence, and apoptosis, and attenuating functional hallmarks of aggressive cancer cells. Transcriptomic profiling of BUB1-depleted cells discloses differential gene expression signatures congruent with cell fate phenotypes, including the reprogramming of mitotic network genes. Mechanistically, BUB1 is indispensable for the proper localization of essential mitotic regulators MAD1, MAD2, and Shugoshin (SGO1), thereby ensuring the functionality of the spindle assembly checkpoint (SAC). Furthermore, BUB1 ablation leads to cytokinesis failure and multinucleation, a phenotype characterized by the downregulation of CDC20, Cyclin A, and Cyclin B, and a reciprocal upregulation of the cyclin-dependent kinase inhibitor p21. Clinically, MPM tumors exhibit elevated levels of BUB1, and high BUB1 expression is associated with shorter patient survival. Our novel findings accentuate comparative CRISPR screens as a powerful platform to explore tumor cell-selective gene essentiality and propose BUB1 kinase as a potential marker and druggable vulnerability with therapeutic implications for MPM.

© 2025. The Author(s).

In plain English

This was a laboratory study, not a study of people's exposures. The authors ran a genome-wide CRISPR knockout screen (Brunello library, 77,441 gRNAs) in three human malignant pleural mesothelioma (MPM) cell lines, H2052 (sarcomatoid), H2452 (biphasic) and H28 (epithelioid), and in one SV40-immortalised nonmalignant pleural mesothelial line, MeT-5A, selecting genes whose loss depleted the MPM cells more than that nonmalignant line, a filter that still allowed some effect in MeT-5A. Eight high-confidence genes emerged (ATG9A, BUB1, CCND1, CDK2, PIKFYVE, TMEM41B, USP17L25, VPS37A). The authors focused on BUB1. Knocking out BUB1 reduced MPM cell proliferation, colony formation, migration, invasion and spheroid formation, caused G2/M arrest, some senescence and apoptosis, disturbed MAD1, MAD2 and SGO1 localisation, and produced multinucleated cells. The BUB1 kinase inhibitor BAY-1816032 gave IC50 values of 1.2, 2.8 and 3.9 microM in H2052, H2452 and H28. In a tissue microarray and public datasets, BUB1 was higher in MPM tissue than normal mesothelium, and higher expression went with shorter overall survival. Asbestos 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 study: genome-wide CRISPR knockout screen in cancer and nonmalignant cell lines, with follow-up cell, molecular and drug experiments, transcriptomic profiling, tissue microarray immunohistochemistry and analysis of public gene expression datasets
• Who was studied: Three human MPM cell lines (H2052 sarcomatoid, H2452 biphasic, H28 epithelioid) and the nonmalignant SV40-immortalised pleural mesothelial line MeT-5A; plus a commercial tissue microarray of 40 cases (10 MPM, 17 malignant mesothelioma of other tissues, 10 normal tissues) and public datasets (TCGA MPM, GSE2549, GSE29211, GSE42977, GSE51024, GSE117668, GSE163722)
• Exposure: Not an asbestos exposure study: the 'exposures' were CRISPR/Cas9 gene knockout (notably of BUB1), ectopic BUB1 overexpression, and treatment with the selective BUB1 kinase inhibitor BAY-1816032 at 0.25 to 10 microM
• Main results:
  • The comparative screen identified eight high-confidence genes whose loss selectively depleted the MPM cell lines relative to MeT-5A, scored by at least two gRNAs
  • The hit filtering allowed a flexible response in the nonmalignant MeT-5A line, requiring only that MPM cells be depleted relative to it
  • BUB1 knockout selectively reduced proliferation of the MPM cell lines compared with MeT-5A, and reduced 2D clonogenic capacity
  • In the MPM cell lines, BUB1 loss caused G2/M arrest with S-phase accumulation, most marked in H2452
  • RNA profiling of BUB1 knockout cells found 1540, 1749 and 648 genes altered in H2052, H2452 and H28 respectively
  • BUB1 knockout cells failed to localise MAD1, MAD2 and SGO1 properly and became multinucleated, with lower CDC20, Cyclin A and Cyclin B and higher p21
  • The BUB1 inhibitor BAY-1816032 gave IC50 values of 1.2 microM (H2052), 2.8 microM (H2452) and 3.9 microM (H28) in viability assays; apoptosis induction with the drug was described as notable yet statistically insignificant
  • In the tissue microarray, MPM tissues scored mild (IRS 2 to 3) to moderate (IRS 4 to 6) BUB1 staining, while normal mesothelium was mostly negative (IRS 0 in 6 of 10 cases)
  • In the TCGA MPM dataset BUB1 expression correlated with proliferation markers: Ki67 r = 0.91 (p value = 1.08e-33) and PCNA r = 0.68 (p value = 3.09e-13)
  • In the TCGA MPM cohort and the GSE2549 dataset, higher BUB1 expression was linked with shorter overall survival
• The authors' conclusion: The authors concluded that comparative CRISPR screening can expose cancer-cell-selective vulnerabilities and proposed BUB1 kinase as a potential marker and druggable vulnerability in MPM
• Limitations the authors state:
  • The authors state the work needs testing in clinically relevant models, indicating the findings so far are from cell-based systems
  • Screen performance was lower in the H28 cell line
  • Senescence induction after BUB1 loss was modest, so it explains only part of the antiproliferative effect
  • H28 cells could not form colonies in soft agar, so anchorage-independent growth could not be assessed in that line

Topics

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

Medical terms in this study, explained in our Lexicon: Pleural Mesothelioma, Prognosis, Mesothelial Cells, Apoptosis.

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