Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection
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...
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BMC
2025-02-01
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| Series: | BMC Cancer |
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| Online Access: | https://doi.org/10.1186/s12885-025-13617-y |
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| author | Agnieszka Kraft Michaela B. Kirschner Vanessa Orlowski Manuel Ronner Caroline Bodmer Valentina Boeva Isabelle Opitz Mayura Meerang |
| author_facet | Agnieszka Kraft Michaela B. Kirschner Vanessa Orlowski Manuel Ronner Caroline Bodmer Valentina Boeva Isabelle Opitz Mayura Meerang |
| author_sort | Agnieszka Kraft |
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| description | 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. |
| format | Article |
| id | doaj-art-29280558b3d142da85e80d693db7ddb0 |
| institution | Kabale University |
| issn | 1471-2407 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj-art-29280558b3d142da85e80d693db7ddb02025-02-09T12:41:46ZengBMCBMC Cancer1471-24072025-02-0125111710.1186/s12885-025-13617-yExploring RNA cargo in extracellular vesicles for pleural mesothelioma detectionAgnieszka Kraft0Michaela B. Kirschner1Vanessa Orlowski2Manuel Ronner3Caroline Bodmer4Valentina Boeva5Isabelle Opitz6Mayura Meerang7Department of Thoracic Surgery, University Hospital ZurichDepartment of Thoracic Surgery, University Hospital ZurichDepartment of Thoracic Surgery, University Hospital ZurichDepartment of Thoracic Surgery, University Hospital ZurichDepartment of Thoracic Surgery, University Hospital ZurichInstitute for Machine Learning, Department of Computer Science, ETH ZurichDepartment of Thoracic Surgery, University Hospital ZurichDepartment of Thoracic Surgery, University Hospital ZurichAbstract 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.https://doi.org/10.1186/s12885-025-13617-yPleural mesotheliomaBiomarkersExtracellular vesiclesTranscriptomicsDiagnosis |
| spellingShingle | Agnieszka Kraft Michaela B. Kirschner Vanessa Orlowski Manuel Ronner Caroline Bodmer Valentina Boeva Isabelle Opitz Mayura Meerang Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection BMC Cancer Pleural mesothelioma Biomarkers Extracellular vesicles Transcriptomics Diagnosis |
| title | Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection |
| title_full | Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection |
| title_fullStr | Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection |
| title_full_unstemmed | Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection |
| title_short | Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection |
| title_sort | exploring rna cargo in extracellular vesicles for pleural mesothelioma detection |
| topic | Pleural mesothelioma Biomarkers Extracellular vesicles Transcriptomics Diagnosis |
| url | https://doi.org/10.1186/s12885-025-13617-y |
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