Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection

Our plain-English summary of Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection, by A. Kraft, M.B. Kirschner, V. Orlowski, et al (BMC Cancer, 2025).

The study

• Authors: A. Kraft, M.B. Kirschner, V. Orlowski, M. Ronner, C. Bodmer, V. Boeva, I. Opitz, M. Meerang
• Journal: BMC Cancer
• Published: 2025;25(1):212
• Cited by: 5 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Background: Pleural Mesothelioma (PM) is a highly aggressive cancer, for which effective early detection remains a challenge due to limited screening options and low sensitivity of biomarkers discovered so far. While extracellular vesicles (EVs) have emerged as promising candidates for blood-based biomarkers, their role in PM has not been studied yet. In this study, we characterized the transcriptomic profile of EVs secreted by PM primary cells and explored their potential as a biomarker source for PM detection.

Methods: We collected cell culture supernatant from early-passage PM cell cultures derived from the pleural effusion of 4 PM patients. EVs were isolated from the supernatant using Qiagen exoEasy Maxi kit. RNA isolation from EVs was done using the mirVana PARIS kit. Finally, single-end RNA sequencing was done with Illumina Novaseq 6000.

Results: We identified a range of RNA species expressed in EVs secreted by PM cells, including protein-coding RNA (80%), long non-coding RNA (13%), pseudogenes (4.5%), and short non-coding RNA (1.6%). We detected a subset of genes associated with the previously identified epithelioid (32 genes) and sarcomatoid molecular components (36 genes) in PM-EVs. To investigate whether these markers could serve as biomarkers for PM detection in blood, we compared the RNA content of PM-EVs with the cargo of EVs isolated from the plasma of healthy donors (publicly available data). Majority of upregulated genes in PM-EVs were protein-coding and long non-coding RNAs. Interestingly, 25 of them were the sarcomatoid and epithelioid marker genes. Finally, functional analysis revealed that the PM-EV RNA cargo was associated with Epithelial-Mesenchymal transition, glycolysis, and hypoxia.

Conclusions: This is the first study to characterize the transcriptomic profile of EVs secreted by PM primary cell cultures, demonstrating their potential as biomarker source for early detection. Further investigation of the functional role of PM-EVs will provide new insights into disease biology and therapeutic avenues.

© 2025. The Author(s).

In plain English

This laboratory study in Zurich examined the RNA carried in extracellular vesicles (tiny particles released by cells) from pleural mesothelioma cells. The cells were grown from the pleural fluid of four patients: three had biphasic tumors and one an epithelioid tumor, and three were recorded as asbestos-exposed. The study did not analyze asbestos exposure. Across the four samples, 15,786 genes were detected. Of these, 80% were protein-coding, 13% long non-coding RNAs, 4.5% pseudogenes and 1.6% short non-coding RNAs. The authors compared these with publicly available data from 32 healthy-donor plasma samples. In the mesothelioma vesicles, 3,653 genes were higher and 3,413 lower, and 25 of the higher genes were markers linked to epithelioid or sarcomatoid features. Two of these RNAs, SNHG9 and GAS5, were detectable at low levels in vesicles from the plasma of four mesothelioma patients. In a public tumor database, eight of the genes were associated with worse survival. The authors concluded that the vesicles show potential as a source of diagnostic biomarkers. They noted the small sample size, the under-representation of sarcomatoid tumors and batch differences between datasets, and called for validation in larger groups.

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: RNA sequencing of extracellular vesicles from primary mesothelioma cell cultures, compared with public RNA-sequencing data from healthy plasma vesicles, with RT-qPCR checks and a survival analysis in a public tumor database (TCGA)
• Who was studied: Primary cell cultures from the pleural effusions of 4 pleural mesothelioma patients (3 biphasic, 1 epithelioid; all male, aged 56 to 68) diagnosed at the University Hospital Zurich. Also 3 non-malignant mesothelial cell cultures, public data from 32 healthy-donor plasma vesicle samples, plasma from 4 mesothelioma patients, and the TCGA mesothelioma cohort
• Exposure: Not an asbestos exposure study; no fiber types or doses were studied. The clinical table records asbestos exposure as 'yes' for three of the four patients (PM-B2, PM-B3, PM-E1) and 'no' for one (PM-B1). The thing measured was the RNA content of vesicles released by the cells.
• Main results:
  • Of genes expressed in the mesothelioma-cell vesicles, 80% were protein-coding, 13% long non-coding RNAs, 4.5% pseudogenes and 1.6% short non-coding RNAs
  • Within 15,786 genes expressed across the 4 mesothelioma vesicle samples, 36 sarcomatoid-component and 32 epithelioid-component marker genes were detected
  • In three of the four samples, sarcomatoid markers had significantly higher expression than epithelioid markers
  • Compared with healthy plasma vesicles, 3,413 genes were lower and 3,653 higher in the mesothelioma vesicles
  • 25 sarcomatoid and epithelioid marker genes were enriched in the mesothelioma vesicles compared with healthy plasma vesicles
  • Selected markers showed only a trend toward higher expression in mesothelioma-cell vesicles than in vesicles from non-malignant mesothelial cells
  • In vesicles from the plasma of four mesothelioma patients, SNHG9 and GAS5 were detectable at low levels (mean Ct 35.5 and 30.9; beta-actin control 27.2)
  • After RNase treatment, GAS5 showed less degradation than free control RNA (Delta Ct 4.2 and 5.3, versus 14.6 and 15.7 for the luciferase control). The other four markers showed no detectable signal.
  • Genes higher in the mesothelioma vesicles were associated with epithelial-to-mesenchymal transition, glycolysis and hypoxia. Interferon response, oxidative phosphorylation and DNA repair were depleted.
  • In TCGA tumor tissue data, eight genes (CAV1, DDIT3, SNAI2, LAMC2, COL6A3, UCHL1, SRPX and SNHG9) were significantly associated with worse survival (p less than 0.05), including in models that included age and disease stage
• The authors' conclusion: The authors concluded that their work gives the first overview of the RNA cargo of vesicles secreted by pleural mesothelioma cells. In their view, it underlines the potential of these vesicles as a source of diagnostic biomarkers.
• Limitations the authors state:
  • The number of mesothelioma samples was small, possibly leading to sample-specific findings
  • The sarcomatoid subtype was underrepresented
  • The comparison with healthy plasma vesicles involved a batch effect: different sources, institutions, ages and genders. Despite normalization, this may confound the results.
  • The healthy plasma comparison rests on the assumption that mesothelioma vesicles are released into the bloodstream. Larger validation with plasma from healthy people and mesothelioma patients is needed.
  • The vesicle isolation method (ExoEasy kit rather than ultracentrifugation or size exclusion chromatography) may have affected the analysis
  • The RNase test suggested that some biomarkers may not be fully inside the vesicles, although RNase carryover could explain part of the degradation

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, Biomarker, Pleural Effusion, Epithelioid, Sarcomatoid, Hypoxia.

Related studies

• Diagnostic and Prognostic Utility of the Extracellular Vesicles Subpopulations Present in Pleural Effusion — J. Javadi, A. Görgens, et al. (2021)
• Selection of microRNAs in extracellular vesicles for diagnosis of malignant pleural mesothelioma by in vitro analysis — T. Jotatsu, H. Izumi, et al. (2020)
• Small Extracellular Vesicle-Derived Circular RNA hsa_circ_0007386 as a Biomarker for the Diagnosis of Pleural Mesothelioma — S. Zhand, J. Liao, et al. (2024)
• Critical Roles of Tumor Extracellular Vesicles in the Microenvironment of Thoracic Cancers — L. Kara-Terki, L. Treps, et al. (2020)
• Ferroptosis-dependent extracellular vesicles from macrophage contribute to asbestos-induced mesothelial carcinogenesis through loading ferritin — F. Ito, K. Kato, et al. (2021)
• Extracellular Vesicles-Based Drug Delivery Systems: A New Challenge and the Exemplum of Malignant Pleural Mesothelioma — S. Burgio, L. Noori, et al. (2020)

Browse more research in BMC Cancer, or return to medical research.