microRNA-497-5p-based screening identifies a novel synthetic lethal-type interaction via PKMYT1 and WEE1 in pleural mesothelioma

Our plain-English summary of microRNA-497-5p-based screening identifies a novel synthetic lethal-type interaction via PKMYT1 and WEE1 in pleural mesothelioma, by N. Pruett, S. Wilferd, A. Singh, et al (Molecular Therapy. Nucleic Acids, 2025).

The study

• Authors: N. Pruett, S. Wilferd, A. Singh, A.Y. Choi, S. Dixit, V. Singh, C. Nguyen, O. Lin, D.S. Schrump, C.L. Plaisier, C.D. Hoang
• Journal: Molecular Therapy. Nucleic Acids
• Published: 2025;36(3):102610
• Cited by: 4 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Diffuse pleural mesothelioma (DPM) is an incurable surface neoplasm governed by tumor suppressor losses with limited therapeutic options. Despite the advantages of leveraging the tumor suppressive activity of microRNA (miRNA/miR), clinical translation remains limited due to incomplete understanding of their context-specific gene targets. Here, we employed a biotinylated-miRNA pull-down approach to systematically identify direct targets of miR-497-5p, an miRNA markedly downregulated in DPM. Surprisingly, multiple identified targets were not predicted by in silico algorithms. Using patient samples, cell lines, murine xenograft models, and our localized nanoparticle miRNA delivery platform, we validated miR-497-5p anti-tumor mechanisms, which consisted of pro-apoptotic and anti-cell-cycle effects. Of multiple additional gene associations to DPM biology, we identified a synthetic lethal-type interaction whereby miR-497-5p co-inhibits PKMYT1 and WEE1 cell-cycle kinases (G2/M regulators). They were significantly overexpressed (poorly prognostic) in DPM, suggesting an efficacious treatment regimen to be explored. We demonstrate the utility of experimentally deriving the miR-497-5p targetome, explaining its pathophysiological role in DPM and why it is a rational therapeutic for further development.

In plain English

This laboratory study examined microRNA-497-5p (miR-497-5p) in diffuse pleural mesothelioma (DPM). Using TCGA mesothelioma data (survival available for 85 of 87 patients), the authors reported that miR-497-5p had the lowest expression of the miR-15/107 family and that higher expression of miR-107 (Z = -2.42), miR-497-5p (Z = -2.28) and miR-195-5p (Z = -2.07) was associated with better prognosis. In surgical specimens, mean miR-497-5p was decreased by -4.2-fold in DPM tumours (n = 50) versus un-matched normal pleurae (n = 26) (p less than 0.001). Re-expressing miR-497-5p in DPM cell lines reduced cell abundance and colony and sphere formation, and increased apoptosis (p less than 0.001) and G1 arrest (p less than 0.0001). A biotinylated-miRNA pull-down identified 1,468 directly bound transcripts at 12 h, of which 1,343 were not predicted by TargetScan. Directly bound targets included PKMYT1 and WEE1 (WEE1 was also a TargetScan prediction), and both were overexpressed in DPM tumours. Combined sub-lethal RP-6306 and adavosertib killed DPM cells. In mice, single miR-497-5p doses slowed xenograft growth, and in the intrapleural model median survival was 37 versus 32 days (p less than 0.02).

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 combining public tumour database analysis, human tissue measurements, cell-line experiments, a biotinylated-miRNA pull-down with RNA sequencing, and mouse xenograft experiments
• Who was studied: TCGA mesothelioma cohort (survival data for 85 of 87 patients); surgical specimens of DPM tumour and non-malignant pleura; DPM and normal pleural cell lines; male NSG mice bearing MB52 xenografts (five mice per group)
• Exposure: Re-expression of miR-497-5p (mimic transfection in cells; atelocollagen- or surface-fill hydrogel-delivered mimic in mice), and pharmacological inhibition with RP-6306 (anti-PKMYT1) and adavosertib (anti-WEE1)
• Main results:
  • In TCGA mesothelioma specimens, higher miR-107, miR-497-5p and miR-195-5p expression was significantly associated with better prognosis; higher miR-424-5p with worse prognosis
  • miR-497-5p expression was lower in DPM tumours (n = 50) than in un-matched normal pleurae (n = 26)
  • In DPM cells, miR-497-5p re-expression increased apoptosis and G1 arrest compared with negative control
  • The pull-down identified 1,468 directly bound transcripts at 12 h; 1,279 genes were downregulated at 72 h; TargetScan predicted 1,732 targets
  • 1,343 genes bound at 12 h were not predicted by TargetScan
  • Direct targets bound at 12 h included PKMYT1 and WEE1; WEE1 was also a TargetScan-predicted target
  • PKMYT1 and WEE1 mRNA were higher in DPM tumours (n = 51) than un-matched normal pleura
  • Combining sub-lethal doses of the two inhibitors was highly toxic to DPM cells
  • In the subcutaneous xenograft model, tumour growth and weight were lower with miR-497-5p than control
  • In the orthotopic (intrapleural) model, median overall survival was 37 days with miR-497-5p versus 32 days with control
• The authors' conclusion: The authors concluded that miR-497-5p acts as a tumour suppressor in DPM with pro-apoptotic and anti-cell-cycle effects, that its co-inhibition of PKMYT1 and WEE1 constitutes a synthetic lethal-type mechanism, and that miRNA-based therapy warrants further study in DPM
• Limitations the authors state:
  • The 'high-probability' targets overlapping with TargetScan predictions still require validation to confirm lowered transcript abundance
  • Most available tumour specimens were of epithelioid histology because surgical resection is rarely performed on non-epithelioid subtypes

Topics

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

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