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Pediatric brain tumor cell lines exhibit miRNA-depleted, Y RNA-enriched extracellular vesicles

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Abstract

Background

Medulloblastoma (MB) and diffuse infiltrative pontine glioma (DIPG) are malignant pediatric tumors. Extracellular vesicles (EVs) and their bioactive cargoes have been implicated in tumorigenesis. Most studies have focused on adult tumors, therefore the role of EVs and the noncoding RNA (ncRNA) landscape in pediatric brain tumors is not fully characterized. The overall aim of this pilot study was to isolate EVs from MB and DIPG patient-derived cell lines and to explore the small ncRNA transcriptome.

Methods

EVs from 3 DIPG and 4 MB patient-derived cell lines were analyzed. High-throughput next generation sequencing interrogated the short non-coding RNA (ncRNA) transcriptome. Known and novel miRNAs were quantified. Differential expression analysis, in silico target prediction, and functional gene enrichment were performed.

Results

EV secretomes from MB and DIPG patient-derived cell lines demonstrated discrete ncRNA biotypes. Notably, miRNAs were depleted and Y RNAs were enriched in EV samples. Hierarchical cluster analysis revealed high discrimination in miRNA expression between DIPG and MB cell lines and RNA-Seq identified novel miRNAs not previously implicated in MB or DIPG pathogenesis. Known and putative target genes of dysregulated miRNAs were identified. Functional annotation analysis of the target genes for differentially expressed EV-and parental-derived miRNAs revealed significant cancer-related pathway involvement.

Conclusions

This hypothesis-generating study demonstrated that pediatric brain tumor-derived cell lines secrete EVs comprised of various ncRNA cargoes. Validation of these findings in patient samples may provide new insights into the pediatric brain tumor microenvironment and identification of novel therapeutic candidates.

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Data availability

Data available upon request from the corresponding author.

Code availability

Not applicable.

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Acknowledgements

We would like to thank Dr. Liang Zhang in Neurologic Surgery for providing DIPG samples, Dr. Michelle Monje for providing autopsy-derived DIPG-4 and DIPG-17 cell lines, Kim Klingsporn in Mayo Media Support Services for creating the manuscript figures and tables, and Lori Lynn Reinstrom for technical assistance with formatting and submission of the manuscript.

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Mayo Clinic Center for Individualized Medicine.

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Author notes

  1. Setty M. Magaña

    Present address: Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH, USA

Authors and Affiliations

  1. Departments of Neurology (SMM), Neurologic Surgery (TEP, DJD, IFP), Health Sciences Research (JEE, PAD, JEEP), Medical Genome Analysis Core (VS); Immunology (IFP), Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA

    Setty M. Magaña, Timothy E. Peterson, Jared E. Evans, Paul A. Decker, Vernadette Simon, Jeanette E. Eckel-Passow, David J. Daniels & Ian F. Parney

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  1. Setty M. Magaña
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Contributions

Conception and design: SMM, TEP, DJD, IFP. Collection and assembly of data: all authors. Data analysis and interpretation: all authors. Manuscript preparation and review, accountability for all aspects of the work: all authors.

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Correspondence to Ian F. Parney.

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Magaña, S.M., Peterson, T.E., Evans, J.E. et al. Pediatric brain tumor cell lines exhibit miRNA-depleted, Y RNA-enriched extracellular vesicles. J Neurooncol 156, 269–279 (2022). https://doi.org/10.1007/s11060-021-03914-4

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