Transcriptional perturbation of protein arginine methyltransferase-5 exhibits MTAP-selective oncosuppression

Our plain-English summary of Transcriptional perturbation of protein arginine methyltransferase-5 exhibits MTAP-selective oncosuppression, by S. Busacca, Q. Zhang, A. Sharkey, et al (Scientific Reports, 2021).

The study

• Authors: S. Busacca, Q. Zhang, A. Sharkey, A.G. Dawson, D.A. Moore, D.A. Waller, A. Nakas, C. Jones, K. Cain, J.L. Luo, A. Salcedo, I.C. Salaroglio, C. Riganti, J. Le Quesne, T. John, P.C. Boutros, S.D. Zhang, D.A. Fennell
• Journal: Scientific Reports
• Published: 2021;11(1):7434
• Cited by: 7 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

We hypothesized that small molecule transcriptional perturbation could be harnessed to target a cellular dependency involving protein arginine methyltransferase 5 (PRMT5) in the context of methylthioadenosine phosphorylase (MTAP) deletion, seen frequently in malignant pleural mesothelioma (MPM). Here we show, that MTAP deletion is negatively prognostic in MPM. In vitro, the off-patent antibiotic Quinacrine efficiently suppressed PRMT5 transcription, causing chromatin remodelling with reduced global histone H4 symmetrical demethylation. Quinacrine phenocopied PRMT5 RNA interference and small molecule PRMT5 inhibition, reducing clonogenicity in an MTAP-dependent manner. This activity required a functional PRMT5 methyltransferase as MTAP negative cells were rescued by exogenous wild type PRMT5, but not a PRMT5E444Q methyltransferase-dead mutant. We identified c-jun as an essential PRMT5 transcription factor and a probable target for Quinacrine. Our results therefore suggest that small molecule-based transcriptional perturbation of PRMT5 can leverage a mutation-selective vulnerability, that is therapeutically tractable, and has relevance to 9p21 deleted cancers including MPM.

In plain English

This study combined malignant pleural mesothelioma (MPM) tumour samples with laboratory work on cell lines. Asbestos was not studied. Of 79 tumours from surgery, 33 (42%) had lost the MTAP gene. Median overall survival was shorter with MTAP deletion: 12.5 months (95% CI 6.8 to 18.2) versus 17.6 months (95% CI 6.5 to 28.7), p = 0.042. In a separate group of 100 patients, 63% had MTAP deletion; median survival was 8.7 months (95% CI 4.6 to 12.8) versus 22.7 months (95% CI 11.4 to 33.9), p = 0.021. In cell lines, silencing PRMT5 reduced growth selectively in MTAP-negative cells. The antibiotic quinacrine, found through a computer drug screen, lowered PRMT5 mRNA in all three cell lines but caused growth arrest only in MTAP-negative cells. Adding back working PRMT5, but not an inactive mutant, reversed this growth arrest. Quinacrine appeared to act through the transcription factor c-JUN. The authors noted that because MTAP was usually lost with CDKN2A, its separate effect could not be judged. The authors concluded their results were a proof of concept suggesting a repurposing potential that warrants further study.

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 mesothelioma cell lines, combined with a survival analysis of patient tumour samples (a discovery cohort and a separate validation cohort)
• Who was studied: 79 malignant pleural mesothelioma tumour samples from patients having extended pleurectomy decortication, under UK ethics approvals (London-Fulham, Northampton, Leicester). There was also a separate validation cohort of 100 patients from an earlier published study, and the MPM cell lines NCI-H2052 and NCI-H2591 (MTAP negative) and MPP89 (MTAP positive). Study dates are not given.
• Exposure: Asbestos exposure was not studied. The patient analysis compared tumours with and without MTAP gene deletion. The laboratory exposures were PRMT5 silencing by RNA interference, the PRMT5 inhibitor EPZ015666, and quinacrine at 500 nM, 1 µM and 2 µM.
• Main results:
  • In the 79-patient cohort, 42% (33 samples) had MTAP deletion. MTAP deletion was associated with shorter median overall survival than wild-type MTAP: 12.5 (95% CI 6.8 to 18.2) versus 17.6 (95% CI 6.5 to 28.7) months, p = 0.042, HR 0.609 (95% CI 0.376 to 0.987).
  • In the 100-patient validation cohort, 63% (63 samples) had MTAP deletion. MTAP deletion was associated with shorter overall survival than wild-type MTAP: 8.7 (95% CI 4.6 to 12.8) versus 22.7 (95% CI 11.4 to 33.9) months, p = 0.021, HR 0.599 (95% CI 0.386 to 0.930).
  • In a Cox multivariate analysis, iMig stage (HR 1.36, 95% CI 1.11 to 1.68, p = 0.003) and MTAP status (HR 1.41, 95% CI 1.03 to 1.93, p = 0.032) remained statistically significant. Age did not (HR 1.32, 95% CI 0.97 to 1.79, p = 0.08). The article does not state which cohort this analysis used.
  • In cell lines, silencing PRMT5 reduced clonogenic (colony-forming) growth selectively in MTAP-negative cell lines.
  • Quinacrine at 1 µM for 72 h reduced PRMT5 mRNA in all three cell lines tested, including the MTAP-positive line MPP89 (NCI-H2052 p = 0.0308; NCI-H2591 p = 0.0063; MPP89 p = 0.005).
  • Quinacrine caused growth arrest in MTAP-negative cells but not in MTAP-positive cells. It did not directly affect PRMT5 enzymatic activity.
  • Overexpressing wild-type PRMT5 rescued MTAP-negative cells from quinacrine. A methyltransferase-dead PRMT5 mutant (E444Q) did not.
  • No apoptosis (cell death) or cell cycle disturbance was seen after quinacrine treatment.
  • Quinacrine suppressed c-JUN mRNA in MTAP-negative cells, suggesting it acts on PRMT5 indirectly through c-JUN. It did not suppress c-JUN mRNA in MTAP-positive cells.
• The authors' conclusion: The authors concluded that their results provide a proof of concept for using small molecule transcriptional perturbation to exploit a vulnerability created by a somatic mutation. They suggested a potential to repurpose quinacrine that warrants further study.
• Limitations the authors state:
  • Because MTAP was co-deleted with CDKN2A, which has also been shown to be negatively prognostic, the authors could not separate the effect of MTAP alone.
  • Whether quinacrine works through the RNA splicing and p53 pathway described for other PRMT5 inhibitors was not tested and needs further work.

Topics

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

Related studies

• CDKN2A and MTAP deletions in peritoneal mesotheliomas are correlated with loss of p16 protein expression and poor survival — A.M. Krasinskas, D.L. Bartlett, et al. (2010)
• Correlation of methylthioadenosine phosphorylase (MTAP) protein expression with MTAP and CDKN2A copy number in malignant pleural mesothelioma — D.B. Chapel, A.M. Dubuc, et al. (2021)
• Prevalence of S-methyl-5'-thioadenosine Phosphorylase (MTAP) Deficiency in Human Cancer: A Tissue Microarray Study on 13,067 Tumors From 149 Different Tumor Types — N. Gorbokon, N. Wößner, et al. (2024)
• Immunohistochemical detection of MTAP and BAP1 protein loss for mesothelioma diagnosis: Comparison with 9p21 FISH and BAP1 immunohistochemistry — T. Hida, M. Hamasaki, 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)
• Usefulness of methylthioadenosine phosphorylase and BRCA-associated protein 1 immunohistochemistry in the diagnosis of malignant mesothelioma in effusion cytology specimens — K.B. Berg, A.M. Churg, et al. (2020)

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