Small RNA Transcriptomes of Two Types of Exosomes in Human Whole Saliva Determined by Next Generation Sequencing

Ogawa, Yuko; Taketomi, Yoshitaka; Murakami, Makoto; Tsujimoto, Masafumi; Yanoshita, Ryohei

doi:10.1248/bpb.b12-00607

Cited by 134 publications

(114 citation statements)

References 46 publications

(54 reference statements)

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“…16) A broad range of RNA sizes were detected in all three samples. rRNA (18s, 28s rRNA) peaks were not as high in our samples compared with those of urinary exosomes.…”

Section: Sequencing and Annotation Of Rnas From Salivary Exosomes Andmentioning

confidence: 88%

“…Isolation of total RNA from WS was performed as described previously. 16) Briefly, human WS was collected from a single healthy female volunteer of Japanese origin (38 years old) from our laboratory, and written informed consent for this specific study was obtained. Total RNA was isolated from 1 mL of WS using the RNeasy Protect Saliva Mini Kit (Qiagen, Valencia, CA, U.S.A.), according to the manufacturer's instructions.…”

Section: Methodsmentioning

confidence: 99%

“…The total RNA concentrations of exosomes I, II and WS were 0.21, 0.10 and 4.2 ng/mL of saliva, respectively. 16) RNA Library Construction and Sequencing Isolated RNA samples from exosomes I, II and WS were amplified using the RampUP RNA Amplification Kit (Genisphere, PA, U.S.A.) according to the manufacturer's protocol. Total RNA (2 ng) from exosomes I, II or WS was used for amplification.…”

Section: Methodsmentioning

confidence: 99%

“…The mean diameter of exosome I was 83.5 nm and that of exosome II was 40.5 nm as calibrated by transmission electron microscopy. We also performed proteome and small RNA transcriptome analyses 14,16) and the results showed that the protein and sncRNA components of exosomes I and II did not completely coincide with each other. The reads mapping to sncRNAs by next-generation sequencing (NGS) showed that sncRNAs of rRNAs, piRNAs, snoRNAs, short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs) and reads defined as 'repeats' included long terminal repeats (LTRs) were abundant in the two types of exosomes and WS, in addition to miRNAs.…”

mentioning

confidence: 99%

“…20) In this study, we investigated long RNA components (pcRNA and lncRNA) of exosomes I, II and WS by NGS using total RNA samples from our previous study of the small RNA transcriptome. 16) …”

mentioning

confidence: 99%

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Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva

Ogawa

Tsujimoto

Yanoshita

2016

Biological & Pharmaceutical Bulletin

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Exosomes are small extracellular vesicles containing microRNAs and mRNAs that are produced by various types of cells. We previously used ultrafiltration and size-exclusion chromatography to isolate two types of human salivary exosomes (exosomes I, II) that are different in size and proteomes. We showed that salivary exosomes contain large repertoires of small RNAs. However, precise information regarding long RNAs in salivary exosomes has not been fully determined. In this study, we investigated the compositions of protein-coding RNAs (pcRNAs) and long non-protein-coding RNAs (lncRNAs) of exosome I, exosome II and whole saliva (WS) by next-generation sequencing technology. Although 11% of all RNAs were commonly detected among the three samples, the compositions of reads mapping to known RNAs were similar. The most abundant pcRNA is ribosomal RNA protein, and pcRNAs of some salivary proteins such as S100 calcium-binding protein A8 (protein S100-A8) were present in salivary exosomes. Interestingly, lncRNAs of pseudogenes (presumably, processed pseudogenes) were abundant in exosome I, exosome II and WS. Translationally controlled tumor protein gene, which plays an important role in cell proliferation, cell death and immune responses, was highly expressed as pcRNA and pseudogenes in salivary exosomes. Our results show that salivary exosomes contain various types of RNAs such as pseudogenes and small RNAs, and may mediate intercellular communication by transferring these RNAs to target cells as gene expression regulators.Key words exosome; transcriptome; human whole saliva; next-generation sequencing; non-coding RNA; pseudogene Human whole saliva (WS) contains an aqueous complex mixture of proteins, peptides, hormones, metabolites, DNAs and RNAs. WS contributes to maintain the integrity of the oral cavity through its lubricating, antibacterial, antiviral and buffering actions, and facilitates chewing and swallowing food. It plays an important role in front-line body defense. Because WS can be collected simply, cheaply and noninvasively, it has been used to monitor human health and disease. Because saliva contains ribonucleases and nucleases from various sources, which influence RNA stability, relatively few studies have analyzed human salivary RNA.1) Salivary nucleotides are protected from degradation by inclusion in extracellular vesicles such as exosomes. Recently, RNAs and DNAs in WS have been highlighted in the fields of biomarker research, disease diagnostics and forensic study. 2-4)Exosomes are small (30-100 nm) membrane vesicles of endocytic origin that are released into the extracellular environment upon fusion of multivesicular bodies with the plasma membrane. Exosomes are present in various body fluids including blood, breast milk, malignant ascites, urine, amniotic fluid and saliva. 5) Exosomes can contain the proteins and nucleic acids of their cell of origin and can transfer their contents to recipient cells at a distance. 5) Exosomes are now thought to be secreted by various cell types, and numerous comp...

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“…16) A broad range of RNA sizes were detected in all three samples. rRNA (18s, 28s rRNA) peaks were not as high in our samples compared with those of urinary exosomes.…”

Section: Sequencing and Annotation Of Rnas From Salivary Exosomes Andmentioning

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva

Ogawa

Tsujimoto

Yanoshita

2016

Biological & Pharmaceutical Bulletin

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MicroRNAs

Farmer¹,

Hirschi²

2017

Nutrigenomics and Proteomics in Health and Disease

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Exosomes: Isolation, Analysis, and Applications in Cancer Detection and Therapy

et al. 2018

ChemBioChem

103

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Exosomes are cell‐derived small extracellular vesicles that are naturally secreted by all types of cells and widely distributed in various biofluids. They carry a variety of key bioactive molecules (e.g., nucleic acids, proteins, growth factors, cytokines) from their parent cells and convey them to neighboring or even distant cells through circulation. In recent years, tumor‐derived exosomes have attracted great interest from investigators because they actively participate in nearly all aspects of tumor development and facilitate both tumor growth and metastasis through exosome‐mediated intercellular communication. The vesicular contents are increasingly considered potential biomarkers for tumor diagnoses and prognosis. With the progress made in isolation and analytical technologies, the functions of exosomes and their contents in tumor development are also becoming clearer. In this review article we describe the recent developments in exosome isolation techniques and analysis of exosomal contents. We also address their applications in cancer detection and therapy.

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Small RNA Transcriptomes of Two Types of Exosomes in Human Whole Saliva Determined by Next Generation Sequencing

Cited by 134 publications

References 46 publications

Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva

Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva

MicroRNAs

Exosomes: Isolation, Analysis, and Applications in Cancer Detection and Therapy

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