ArticleInternational journal of molecular sciences2023
Phospho-RNA-Seq Highlights Specific Small RNA Profiles in Plasma Extracellular Vesicles.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A ribozyme ligase that requires a 3' terminal phosphate on its RNA substrate.Nature communications · 2026Article
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- Residual Genetic Material in Mature Red Blood Cells.International journal of molecular sciences · 2025Review
- High-throughput assay confirmation of a T-cell receptor pre-mRNA fragment as a blood-based inflammatory breast cancer biomarker.medRxiv : the preprint server for health sciences · 2025Article
- Methodological Assessment of ExoGAG for Isolation of Cerebrospinal Fluid Extracellular Vesicles as a Source of Biomarkers.International journal of molecular sciences · 2024Article
- A Comprehensive Review on Circulating cfRNA in Plasma: Implications for Disease Diagnosis and Beyond.Diagnostics (Basel, Switzerland) · 2024Review
- Challenges in characterization of transcriptomes of extracellular vesicles and non-vesicular extracellular RNA carriers.Frontiers in molecular biosciences · 2023Review
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Authors and funding
10 authors.
Funding
Abstract
Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5'-end (5'-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.
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