RNA in Extracellular Vesicles

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 4068

Special Issue Editors


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Guest Editor
Disease Networks Research Unit, Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland
Interests: extracellular vesicles; extracellular RNA; astrocyte-derived extracellular vesicles; ncRNA; miRNA; mRNA; human sweat nucleic acids; metagenomics
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Guest Editor
HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland
Interests: extracellular vesicles; transcriptomics; RNA; mRNA; small RNA; liquid biopsies; kidney disease; diabetes; cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extracellular Vesicle (EV) RNA cargo attracts a lot of interest as a liquid biopsy offering a way to tap information about the originating tissues and physiological status of the secreting cells. EV RNA is also investigated as a dynamic intercellular or interkingdom messenger. Consequently, the EV RNA field progresses at a fast pace with regular new twists due to technical advances and challenges. For example, RNA is now recognized both inside vesicles as a protected cargo as well as bound to the surface of EV. EV have been traditionally classified based on secretion pathways: endosomal pathway or membrane budding, which may result in the packaging of different RNA species. Currently investigators explore also novel types of secreted nanoparticles such as exomeres and supermeres with potentially different RNA cargo than found from EV secreted from the same cells. In addition to its use as liquid biopsy, EV RNA may be able to modulate gene expression if taken up by cells. The purpose of this Special Issue is to present original research, critical technologies and review articles documenting different RNA types in EV and nanoparticles and their regulatory roles in recipient cells.

Dr. Genevieve Bart
Dr. Maija Puhka
Guest Editors

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Keywords

  • EV associated RNA
  • EV encapsulated RNA
  • novel RNA
  • regulatory RNA
  • ncRNA
  • mRNA
  • small RNA
  • miRNA
  • transcriptomics
  • PCR

Published Papers (2 papers)

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Research

40 pages, 7779 KiB  
Article
Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles—From Pre-Analytical Obstacles to Biomarker Research
by Karina Barreiro, Om Prakash Dwivedi, Antti Rannikko, Harry Holthöfer, Tiinamaija Tuomi, Per-Henrik Groop and Maija Puhka
Genes 2023, 14(7), 1415; https://doi.org/10.3390/genes14071415 - 08 Jul 2023
Cited by 1 | Viewed by 1475
Abstract
Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of preanalytical choices hinder biomarker studies. We aimed to assess how preanalytical variables (urine storage temperature, isolation workflow) affect diabetic kidney disease (DKD)—linked [...] Read more.
Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of preanalytical choices hinder biomarker studies. We aimed to assess how preanalytical variables (urine storage temperature, isolation workflow) affect diabetic kidney disease (DKD)—linked miRNAs or kidney—linked miRNAs and mRNAs (kidney-RNAs) in uEV isolates and to discover stable reference mRNAs across diverse uEV datasets. We studied nine raw and normalized sequencing datasets including healthy controls and individuals with prostate cancer or type 1 diabetes with or without albuminuria. We focused on kidney-RNAs reviewing literature for DKD-linked miRNAs from kidney tissue, cell culture and uEV/urine experiments. RNAs were analyzed by expression heatmaps, hierarchical clustering and selecting stable mRNAs with normalized counts (>200) and minimal coefficient of variation. Kidney-RNAs were decreased after urine storage at −20 °C vs. −80 °C. Isolation workflows captured kidney-RNAs with different efficiencies. Ultracentrifugation captured DKD -linked miRNAs that separated healthy and diabetic macroalbuminuria groups. Eleven mRNAs were stably expressed across the datasets. Hence, pre-analytical choices had variable effects on kidney-RNAs—analyzing kidney-RNAs complemented global correlation, which could fade differences in some relevant RNAs. Replicating prior DKD-marker results and discovery of candidate reference mRNAs encourages further uEV biomarker studies. Full article
(This article belongs to the Special Issue RNA in Extracellular Vesicles)
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49 pages, 10581 KiB  
Article
Human Adult Astrocyte Extracellular Vesicle Transcriptomics Study Identifies Specific RNAs Which Are Preferentially Secreted as EV Luminal Cargo
by Keerthanaa Balasubramanian Shanthi, Daniel Fischer, Abhishek Sharma, Antti Kiviniemi, Mika Kaakinen, Seppo J. Vainio and Geneviève Bart
Genes 2023, 14(4), 853; https://doi.org/10.3390/genes14040853 - 31 Mar 2023
Viewed by 1834
Abstract
Astrocytes are central nervous system (CNS)-restricted glial cells involved in synaptic function and CNS blood flow regulation. Astrocyte extracellular vesicles (EVs) participate in neuronal regulation. EVs carry RNAs, either surface-bound or luminal, which can be transferred to recipient cells. We characterized the secreted [...] Read more.
Astrocytes are central nervous system (CNS)-restricted glial cells involved in synaptic function and CNS blood flow regulation. Astrocyte extracellular vesicles (EVs) participate in neuronal regulation. EVs carry RNAs, either surface-bound or luminal, which can be transferred to recipient cells. We characterized the secreted EVs and RNA cargo of human astrocytes derived from an adult brain. EVs were isolated by serial centrifugation and characterized with nanoparticle tracking analysis (NTA), Exoview, and immuno-transmission electron microscopy (TEM). RNA from cells, EVs, and proteinase K/RNase-treated EVs was analyzed by miRNA-seq. Human adult astrocyte EVs ranged in sizes from 50 to 200 nm, with CD81 as the main tetraspanin marker and larger EVs positive for integrin β1. Comparison of the RNA between the cells and EVs identified RNA preferentially secreted in the EVs. In the case of miRNAs, enrichment analysis of their mRNA targets indicates that they are good candidates for mediating EV effects on recipient cells. The most abundant cellular miRNAs were also abundant in EVs, and the majority of their mRNA targets were found to be downregulated in mRNA-seq data, but the enrichment analysis lacked neuronal specificity. Proteinase K/RNase treatment of EV-enriched preparations identified RNAs secreted independently of EVs. Comparing the distribution of cellular and secreted RNA identifies the RNAs involved in intercellular communication via EVs. Full article
(This article belongs to the Special Issue RNA in Extracellular Vesicles)
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