Abstract
Extracellular RNA (exRNA) has recently expanded as a highly important area of study in biomarker discovery and cancer therapeutics. exRNA consists of diverse RNA subpopulations that are normally protected from degradation by incorporation into membranous vesicles or by lipid/protein association. They are found circulating in biofluids, and have proven highly promising for minimally invasive diagnostic and prognostic purposes, particularly in oncology. Recent work has made progress in our understanding of exRNAs—from their biogenesis, compartmentalization, and vesicle packaging to their various applications as biomarkers and therapeutics, as well as the new challenges that arise in isolation and purification for accurate and reproducible analysis. Here we review the most recent advancements in exRNA research.
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References
Di Vizio D et al (2012) Large oncosomes in human prostate cancer tissues and in the circulation of mice with metastatic disease. Am J Pathol 181(5):1573–1584
Minciacchi VR, Freeman MR, Di Vizio D (2015) Extracellular vesicles in cancer: exosomes, microvesicles and the emerging role of large oncosomes. Semin Cell Dev Biol 40:41–51
Yanez-Mo M et al (2015) Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles 4:27066
Costa-Silva B et al (2015) Pancreatic cancer exosomes initiate pre-metastatic niche formation in the liver. Nat Cell Biol 17(6):816–826
Skog J et al (2008) Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat Cell Biol 10(12):1470–1476
Chen WW et al (2013) BEAMing and droplet digital PCR analysis of mutant IDH1 mRNA in glioma patient serum and cerebrospinal fluid extracellular vesicles. Mol Ther Nucleic Acids 2:e109
Balaj L et al (2011) Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences. Nat Commun 2:180
Lasser C et al (2011) Human saliva, plasma and breast milk exosomes contain RNA: uptake by macrophages. J Transl Med 9:9
Turchinovich A et al (2011) Characterization of extracellular circulating microRNA. Nucleic Acids Res 39(16):7223–7233
Vickers KC et al (2011) MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol 13(4):423–433
Crescitelli R et al (2013) Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes. J Extracell Vesicles 2
Lasser C et al (2017) Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing. RNA Biol 14(1):58–72
Bellingham SA, Coleman BM, Hill AF (2012) Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion-infected neuronal cells. Nucleic Acids Res 40(21):10937–10949
Michell DL et al (2016) Isolation of high-density lipoproteins for non-coding small RNA quantification. J Vis Exp (117)
Arroyo JD et al (2011) Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A 108(12):5003–5008
Cha DJ et al (2015) KRAS-dependent sorting of miRNA to exosomes. Elife 4:e07197
Villarroya-Beltri C et al (2013) Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat Commun 4:2980
Shurtleff MJ et al (2016) Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. Elife 5
Yuan T et al (2016) Plasma extracellular RNA profiles in healthy and cancer patients. Sci Rep 6:19413
Wei Z et al (2016) Fetal bovine serum RNA interferes with the cell culture derived extracellular RNA. Sci Rep 6:31175
Musilova K, Mraz M (2015) MicroRNAs in B-cell lymphomas: how a complex biology gets more complex. Leukemia 29(5):1004–1017
Ebert MS, Sharp PA (2012) Roles for microRNAs in conferring robustness to biological processes. Cell 149(3):515–524
Friedman RC et al (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1):92–105
Rodriguez A et al (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14(10A):1902–1910
Pratt AJ, MacRae IJ (2009) The RNA-induced silencing complex: a versatile gene-silencing machine. J Biol Chem 284(27):17897–17901
Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9(2):102–114
Eulalio A et al (2009) Deadenylation is a widespread effect of miRNA regulation. RNA 15(1):21–32
Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297(5589):2056–2060
Nielsen CB et al (2007) Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13(11):1894–1910
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233
Chen X et al (2012) Secreted microRNAs: a new form of intercellular communication. Trends Cell Biol 22(3):125–132
Vickers KC, Remaley AT (2012) Lipid-based carriers of microRNAs and intercellular communication. Curr Opin Lipidol 23(2):91–97
Melman YF et al (2015) Circulating MicroRNA-30d is associated with response to cardiac resynchronization therapy in heart failure and regulates cardiomyocyte apoptosis: a translational pilot study. Circulation 131(25):2202–2216
Sharp SJ et al (1985) Structure and transcription of eukaryotic tRNA genes. CRC Crit Rev Biochem 19(2):107–144
Hurto RL (2011) Unexpected functions of tRNA and tRNA processing enzymes. Adv Exp Med Biol 722:137–155
Nolte-'t Hoen EN et al (2012) Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res 40(18):9272–9285
Tosar JP et al (2015) Assessment of small RNA sorting into different extracellular fractions revealed by high-throughput sequencing of breast cell lines. Nucleic Acids Res 43(11):5601–5616
Baglio SR et al (2015) Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. Stem Cell Res Ther 6:127
Li M et al (2014) Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers. Philos Trans R Soc Lond Ser B Biol Sci 369(1652)
Vojtech L et al (2014) Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. Nucleic Acids Res 42(11):7290–7304
Lunavat TR et al (2015) Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells—evidence of unique microRNA cargos. RNA Biol 12(8):810–823
Lee YS et al (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23(22):2639–2649
Ivanov P et al (2011) Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 43(4):613–623
Sobala A, Hutvagner G (2013) Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells. RNA Biol 10(4):553–563
Freedman JE et al (2016) Diverse human extracellular RNAs are widely detected in human plasma. Nat Commun 7:11106
Meister G (2013) Argonaute proteins: functional insights and emerging roles. Nat Rev Genet 14(7):447–459
Hayashi R et al (2016) Genetic and mechanistic diversity of piRNA 3′-end formation. Nature 539(7630):588–592
Chuma S, Pillai RS (2009) Retrotransposon silencing by piRNAs: ping-pong players mark their sub-cellular boundaries. PLoS Genet 5(12):e1000770
Kowalski MP, Krude T (2015) Functional roles of non-coding Y RNAs. Int J Biochem Cell Biol 66:20–29
Chen X et al (2013) An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA. Cell 153(1):166–177
Krude T et al (2009) Y RNA functions at the initiation step of mammalian chromosomal DNA replication. J Cell Sci 122(Pt 16):2836–2845
Nicolas FE et al (2012) Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. FEBS Lett 586(8):1226–1230
Meiri E et al (2010) Discovery of microRNAs and other small RNAs in solid tumors. Nucleic Acids Res 38(18):6234–6246
Chakrabortty SK et al (2015) Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA 21(11):1966–1979
Kohn M et al (2015) The Y3** ncRNA promotes the 3′ end processing of histone mRNAs. Genes Dev 29(19):1998–2003
Wei Z, Batagov AO, Schinelli S, Wang J, Wang Y, El Fatimy R, Rabinovsky R, Balaj L, Chen CC, Hochberg F, Carter B, Breakefield XO, Krichevsky AM (2017) Coding and noncoding landscape of extracellular RNA released by human glioma stem cells. Nat Commun 8(1):1145
Yeri A et al (2017) Total extracellular small RNA profiles from plasma, saliva, and urine of healthy subjects. Sci Rep 7:44061
Huang X et al (2013) Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics 14:319
Hansen TB et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384–388
Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nat Rev Genet 15(6):423–437
Smith MA et al (2013) Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res 41(17):8220–8236
Johnsson P et al (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840(3):1063–1071
Kogure T et al (2013) Extracellular vesicle-mediated transfer of a novel long noncoding RNA TUC339: a mechanism of intercellular signaling in human hepatocellular cancer. Genes Cancer 4(7–8):261–272
Maxwell ES, Fournier MJ (1995) The small nucleolar RNAs. Annu Rev Biochem 64:897–934
Appaiah HN et al (2011) Persistent upregulation of U6:SNORD44 small RNA ratio in the serum of breast cancer patients. Breast Cancer Res 13(5):R86
Chen LL (2016) The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol 17(4):205–211
Memczak S et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333–338
Turchinovich A, Burwinkel B (2012) Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma. RNA Biol 9(8):1066–1075
Shelke GV et al (2014) Importance of exosome depletion protocols to eliminate functional and RNA-containing extracellular vesicles from fetal bovine serum. J Extracell Vesicles 3
Mitchell PS et al (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105(30):10513–10518
Brunet-Vega A et al (2015) Variability in microRNA recovery from plasma: comparison of five commercial kits. Anal Biochem 488:28–35
Li X, Mauro M, Williams Z (2015) Comparison of plasma extracellular RNA isolation kits reveals kit-dependent biases. Biotechniques 59(1):13–17
Royo F et al (2016) Different EV enrichment methods suitable for clinical settings yield different subpopulations of urinary extracellular vesicles from human samples. J Extracell Vesicles 5:29497
Van Deun J et al (2014) The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling. J Extracell Vesicles 3
Laurent LC et al (2015) Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. J Extracell Vesicles 4:26533
Tanriverdi K et al (2016) Comparison of RNA isolation and associated methods for extracellular RNA detection by high-throughput quantitative polymerase chain reaction. Anal Biochem 501:66–74
Gardiner C et al (2016) Techniques used for the isolation and characterization of extracellular vesicles: results of a worldwide survey. J Extracell Vesicles 5:32945
Jeppesen DK et al (2014) Comparative analysis of discrete exosome fractions obtained by differential centrifugation. J Extracell Vesicles 3:25011
Yuana Y et al (2014) Co-isolation of extracellular vesicles and high-density lipoproteins using density gradient ultracentrifugation. J Extracell Vesicles 3
Boing AN et al (2014) Single-step isolation of extracellular vesicles by size-exclusion chromatography. J Extracell Vesicles 3
Vergauwen G et al (2017) Confounding factors of ultrafiltration and protein analysis in extracellular vesicle research. Sci Rep 7(1):2704
Gamez-Valero A et al (2016) Size-exclusion chromatography-based isolation minimally alters extracellular vesicles’ characteristics compared to precipitating agents. Sci Rep 6:33641
Kanwar SS et al (2014) Microfluidic device (ExoChip) for on-chip isolation, quantification and characterization of circulating exosomes. Lab Chip 14(11):1891–1900
Balaj L et al (2015) Heparin affinity purification of extracellular vesicles. Sci Rep 5:10266
Enderle D et al (2015) Characterization of RNA from exosomes and other extracellular vesicles isolated by a novel spin column-based method. PLoS One 10(8):e0136133
Gallart-Palau X et al (2015) Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR). Sci Rep 5:14664
Shih CL et al (2016) Development of a magnetic bead-based method for the collection of circulating extracellular vesicles. New Biotechnol 33(1):116–122
Puhka M et al (2017) KeepEX, a simple dilution protocol for improving extracellular vesicle yields from urine. Eur J Pharm Sci 98:30–39
Turchinovich A, Weiz L, Burwinkel B (2013) Isolation of circulating microRNA associated with RNA-binding protein. Methods Mol Biol 1024:97–107
Thery C, Ostrowski M, Segura E (2009) Membrane vesicles as conveyors of immune responses. Nat Rev Immunol 9(8):581–593
Schipper HM et al (2007) MicroRNA expression in Alzheimer blood mononuclear cells. Gene Regul Syst Bio 1:263–274
Karlsson O et al (2016) Detection of long non-coding RNAs in human breastmilk extracellular vesicles: implications for early child development. Epigenetics:0
Machtinger R et al (2017) Extracellular microRNAs in follicular fluid and their potential association with oocyte fertilization and embryo quality: an exploratory study. J Assist Reprod Genet 34(4):525–533
Dear JW, Street JM, Bailey MA (2013) Urinary exosomes: a reservoir for biomarker discovery and potential mediators of intrarenal signalling. Proteomics 13(10–11):1572–1580
Quinn JF et al (2015) Extracellular RNAs: development as biomarkers of human disease. J Extracell Vesicles 4:27495
March-Villalba JA et al (2012) Cell-free circulating plasma hTERT mRNA is a useful marker for prostate cancer diagnosis and is associated with poor prognosis tumor characteristics. PLoS One 7(8):e43470
Xie Z et al (2013) Salivary microRNAs as promising biomarkers for detection of esophageal cancer. PLoS One 8(4):e57502
Xie Z et al (2015) Salivary microRNAs show potential as a noninvasive biomarker for detecting resectable pancreatic cancer. Cancer Prev Res (Phila) 8(2):165–173
Akers JC et al (2013) MiR-21 in the extracellular vesicles (EVs) of cerebrospinal fluid (CSF): a platform for glioblastoma biomarker development. PLoS One 8(10):e78115
Akat KM et al (2014) Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers. Proc Natl Acad Sci U S A 111(30):11151–11156
de Gonzalo-Calvo D et al (2016) Circulating long-non coding RNAs as biomarkers of left ventricular diastolic function and remodelling in patients with well-controlled type 2 diabetes. Sci Rep 6:37354
Ben-Dov IZ et al (2016) Cell and microvesicle urine microRNA deep sequencing profiles from healthy individuals: observations with potential impact on biomarker studies. PLoS One 11(1):e0147249
Rodosthenous RS, Burris HH, Sanders AP, Just AC, Dereix AE, Svensson K, Solano M, Téllez-Rojo MM, Wright RO, Baccarelli AA (2017) Second trimester extracellular microRNAs in maternal blood and fetal growth: an exploratory study. Epigenetics 12(9):804–810
Tsochandaridis M, Nasca L, Toga C, Levy-Mozziconacci A (2015) Circulating MicroRNAs as clinical biomarkers in the predictions of pregnancy complications. BioMed Res Int 2015:294954
Ohno S et al (2013) Systemically injected exosomes targeted to EGFR deliver antitumor microRNA to breast cancer cells. Mol Ther 21(1):185–191
Zhang Y et al (2014) Microvesicle-mediated delivery of transforming growth factor beta1 siRNA for the suppression of tumor growth in mice. Biomaterials 35(14):4390–4400
Jinek M, Doudna JA (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature 457(7228):405–412
Lai RC, Yeo RW, Lim SK (2015) Mesenchymal stem cell exosomes. Semin Cell Dev Biol 40:82–88
Shimbo K et al (2014) Exosome-formed synthetic microRNA-143 is transferred to osteosarcoma cells and inhibits their migration. Biochem Biophys Res Commun 445(2):381–387
Lou G et al (2015) Exosomes derived from miR-122-modified adipose tissue-derived MSCs increase chemosensitivity of hepatocellular carcinoma. J Hematol Oncol 8:122
Greco KA et al (2016) PLK-1 silencing in bladder cancer by siRNA delivered with exosomes. Urology 91:241.e1–241.e7
Mizrak A et al (2013) Genetically engineered microvesicles carrying suicide mRNA/protein inhibit schwannoma tumor growth. Mol Ther 21(1):101–108
Acknowledgements
B.G. is an Edward R. and Anne G. Lefler Center Postdoctoral Fellow. The authors declare no conflicts of interest.
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Sadik, N. et al. (2018). Extracellular RNAs: A New Awareness of Old Perspectives. In: Patel, T. (eds) Extracellular RNA. Methods in Molecular Biology, vol 1740. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7652-2_1
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DOI: https://doi.org/10.1007/978-1-4939-7652-2_1
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