Ahadi A, Brennan S, Kennedy PJ, Hutvagner G, Tran N. 2016. Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes. Sci Rep 6: 24922.
Batagov AO, Kurochkin IV. 2013. Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3′-un-translated regions. Biol Direct 8: 12.
Berrondo C, Flax J, Kucherov V, Siebert A, Osinski T, Rosenberg A, Fucile C, Richheimer S, Beckham CJ. 2016. Expression of the long non-coding RNA HOTAIR correlates with disease progression in bladder cancer and is contained in bladder cancer patient urinary exosomes. PLoS One 11: e0147236.
Beuck C, Williamson JR, Wüthrich K, Serrano P. 2016. The acidic domain is a unique structural feature of the splicing factor SYNCRIP. Protein Sci 25: 1545–1550.
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120.
Cambier L, de Couto G, Ibrahim A, Echavez AK, Valle J, Liu W, Kreke M, Smith RR, Marbán L, Marbán E. 2017. Y RNA fragment in extracellular vesicles confers cardioprotection via modulation of IL-10 expression and secretion. EMBO Mol Med 9: 337–352.
Chakrabortty SK, Prakash A, Nechooshtan G, Hearn S, Gingeras TR. 2015. Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA 21: 1966–1979.
Challagundla KB, Wise PM, Neviani P, Chava H, Murtadha M, Xu T, Kennedy R, Ivan C, Zhang X, Vannini I, et al. 2015. Exosome-mediated transfer of microRNAs within the tumor microenvironment and neuroblastoma resistance to chemotherapy. J Natl Cancer Inst 107: djv135.
Chen M, Xu R, Ji H, Greening DW, Rai A, Izumikawa K, Ishikawa H, Takahashi N, Simpson RJ. 2016. Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line. Sci Rep 6: 38397.
Choi KS, Mizutani A, Lai MMC. 2004. SYNCRIP, a member of the heterogeneous nuclear ribonucleoprotein family, is involved in mouse hepatitis virus RNA synthesis. J Virol 78: 13153–13162.
Crescitelli R, Lässer C, Szabó TG, Kittel A, Eldh M, Dianzani I, Buzás EI, Lötvall J. 2013. Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes. J Extracell Vesicles 2: 20677.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15–21.
Duning K, Buck F, Barnekow A, Kremerskothen J. 2008. SYNCRIP, a component of dendritically localized mRNPs, binds to the translation regulator BC200 RNA. J Neurochem 105: 351–359.
Eliseeva IA, Kim ER, Guryanov SG, Ovchinnikov LP, Lyabin DN. 2011. Y-box-binding protein 1 (YB-1) and its functions. Biochemistry 76: 1402–1433.
Enderle D, Spiel A, Coticchia CM, Berghoff E, Mueller R, Schlumpberger M, Sprenger-Haussels M, Shaffer JM, Lader E, Skog J, et al. 2015. Characterization of RNA from exosomes and other extracellular vesicles isolated by a novel spin column-based method. PLoS One 10: e0136133.
Farris AD, O’Brien CA, Harley JB. 1995. Y3 is the most conserved small RNA component of Ro ribonucleoprotein complexes in vertebrate species. Gene 154: 193–198.
Friand V, David G, Zimmermann P. 2015. Syntenin and syndecan in the biogenesis of exosomes. Biol Cell 107: 331–341.
Fritz JV, Heintz-Buschart A, Ghosal A, Wampach L, Etheridge A, Galas D, Wilmes P. 2016. Sources and functions of extracellular small RNAs in human circulation. Annu Rev Nutr 36: 301–336.
Gao Y, Wang J, Zhao F. 2015. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol 16: 4.
Gezer U, Özgür E, Cetinkaya M, Işin M, Dalay N. 2014. Long non-coding RNAs with low expression levels in cells are enriched in secreted exosomes. Cell Biol Int 38: 1076–1079.
Guo T, Kong J, Liu Y, Li Z, Xia J, Zhang Y, Zhao S, Li F, Li J, Gu C. 2017. Transcriptional activation of NANOG by YBX1 promotes lung cancer stem-like properties and metastasis. Biochem Biophys Res Commun 487: 153–159.
Hannafon BN, Ding WQ. 2013. Intercellular communication by exosome-derived microRNAs in cancer. Int J Mol Sci 14: 14240–14269.
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576–589.
Hewson C, Capraro D, Burdach J, Whitaker N, Morris KV. 2016. Extracellular vesicle associated long non-coding RNAs functionally enhance cell viability. Non-Coding RNA Res 1: 3–11.
Işin M, Uysaler E, Özgür E, Köseoglu H, Şanlı Ö, Yücel ÖB, Gezer U, Dalay N. 2015. Exosomal lncRNA-p21 levels may help to distinguish prostate cancer from benign disease. Front Genet 6: 168.
Jenjaroenpun P, Kremenska Y, Nair VM, Kremenskoy M, Joseph B, Kurochkin IV. 2013. Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing. PeerJ 1: e201.
Ji R, Zhang B, Zhang X, Xue J, Yuan X, Yan Y, Wang M, Zhu W, Qian H, Xu W. 2015. Exosomes derived from human mesenchymal stem cells confer drug resistance in gastric cancer. Cell Cycle 14: 2473–2483.
Joyce DP, Kerin MJ, Dwyer RM. 2016. Exosome-encapsulated microRNAs as circulating biomarkers for breast cancer. Int J Cancer 139: 1443–1448.
Jung K, Wu F, Wang P, Ye X, Abdulkarim BS, Lai R. 2014. YB-1 regulates Sox2 to coordinately sustain stemness and tumorigenic properties in a phenotypically distinct subset of breast cancer cells. BMC Cancer 14: 328.
Kaudewitz D, Skroblin P, Bender LH, Barwari T, Willeit P, Pechlaner R, Sunderland NP, Willeit K, Morton AC, Armstrong PC, et al. 2016. Association of microRNAs and YRNAs with platelet function. Circ Res 118: 420–432.
Keerthikumar S, Chisanga D, Ariyaratne D, Al Saffar H, Anand S, Zhao K, Samuel M, Pathan M, Jois M, Chilamkurti N, et al. 2016. ExoCarta: a web-based compendium of exosomal cargo. J Mol Biol 428: 688–692.
Kosaka N, Yoshioka Y, Hagiwara K, Tominaga N, Ochiya T. 2013. Functional analysis of exosomal microRNA in cell-cell communication research. Methods Mol Biol 1024: 1–10.
Kossinova OA, Gopanenko AV, Tamkovich SN, Krasheninina OA, Tupikin AE, Kiseleva E, Yanshina DD, Malygin AA, Ven’yaminova AG, Kabilov MR, et al. 2017. Cytosolic YB-1 and NSUN2 are the only proteins recognizing specific motifs present in mRNAs enriched in exosomes. Biochim Biophys Acta 1865: 664–673.
Kozomara A, Griffiths-Jones S. 2014. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42: D68–D73
Kuchler L, Giegerich AK, Sha LK, Knape T, Wong MSK, Schröder K, Brandes RP, Heide H, Wittig I, Brüne B, et al. 2014. SYNCRIP-dependent Nox2 mRNA destabilization impairs ROS formation in M2-polarized macrophages. Antioxid Redox Signal 21: 2483–2497.
Lang HL, Hu GW, Chen Y, Liu Y, Tu W, Lu YM, Wu L, Xu GH. 2017. Glioma cells promote angiogenesis through the release of exosomes containing long non-coding RNA POU3F3. Eur Rev Med Pharmacol Sci 21: 959–972.
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
Lázaro-Ibáñez E, Lunavat TR, Jang SC, Escobedo-Lucea C, Oliver-De La Cruz J, Siljander P, Lötvall J, Yliperttula M. 2017. Distinct prostate cancer-related mRNA cargo in extracellular vesicle subsets from prostate cell lines. BMC Cancer 17: 92.
Lerner MR, Boyle JA, Hardin JA, Steitz JA. 1981. Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus. Science 211: 400–402.
Lévesque K, Halvorsen M, Abrahamyan L, Chatel-Chaix L, Poupon V, Gordon H, DesGroseillers L, Gatignol A, Mouland AJ. 2006. Trafficking of HIV-1 RNA is mediated by heterogeneous nuclear ribonucleoprotein A2 expression and impacts on viral assembly. Traffic 7: 1177–1193.
Li L, Li C, Wang S, Wang Z, Jiang J, Wang W, Li X, Chen J, Liu K, Li C, et al. 2016. Exosomes derived from hypoxic oral squamous cell carcinoma cells deliver miR-21 to normoxic cells to elicit a prometa-static phenotype. Cancer Res 76: 1770–1780.
Li Q, Shao Y, Zhang X, Zheng T, Miao M, Qin L, Wang B, Ye G, Xiao B, Guo J. 2015. Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer. Tumour Biol 36: 2007–2012.
Lim JP, Shyamasundar S, Gunaratne J, Scully OJ, Matsumoto K, Bay BH. 2017. YBX1 gene silencing inhibits migratory and invasive potential via CORO1C in breast cancer in vitro. BMC Cancer 17: 201.
Liu HM, Aizaki H, Choi KS, Machida K, Ou JJH, Lai MMC. 2009. SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interacting protein) is a host factor involved in hepatitis C virus RNA replication. Virology 386: 249–256.
Liu T, Zhang X, Gao S, Jing F, Yang Y, Du L, Zheng G, Li P, Li C, Wang C. 2016. Exosomal long noncoding RNA CRNDE-h as a novel serum-based biomarker for diagnosis and prognosis of colorectal cancer. Oncotarget 7: 85551–85563.
Lobb RJ, van Amerongen R, Wiegmans A, Ham S, Larsen JE, Möller A. 2017. Exosomes derived from mesenchymal non-small cell lung cancer cells promote chemoresistance. Int J Cancer 141: 614–620.
Lötvall J, Hill AF, Hochberg F, Buzás EI, Di Vizio D, Gardiner C, Gho YS, Kurochkin IV, Mathivanan S, Quesenberry P, et al. 2014. Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles. J Extracell Vesicles 3: 26913.
Lv J, Huang Z, Liu H, Liu H, Cui W, Li B, He H, Guo J, Liu Q, Zhang Y, et al. 2014. Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Mol Genet Genomics 289: 1225–1235.
Mateescu B, Kowal EJK, van Balkom BWM, Bartel S, Bhattacharyya SN, Buzás EI, Buck AH, de Candia P, Chow FWN, Das S, et al. 2017. Obstacles and opportunities in the functional analysis of extracellular vesicle RNA—an ISEV position paper. J Extracell Vesicles 6: 1286095.
Mathivanan S, Ji H, Simpson RJ. 2010. Exosomes: extracellular organelles important in intercellular communication. J Proteomics 73: 1907–1920.
McCarthy DJ, Chen Y, Smyth GK. 2012. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40: 4288–4297.
Milane L, Singh A, Mattheolabakis G, Suresh M, Amiji MM. 2015. Exosome mediated communication within the tumor microenvironment. J Control Release 219: 278–294.
Miranda KC, Bond DT, Levin JZ, Adiconis X, Sivachenko A, Russ C, Brown D, Nusbaum C, Russo LM. 2014. Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA. PLoS One 9: e96094.
Momen-Heravi F, Saha B, Kodys K, Catalano D, Satishchandran A, Szabo G. 2015. Increased number of circulating exosomes and their microRNA cargos are potential novel biomarkers in alcoholic hepatitis. J Transl Med 13: 261.
Moser JJ, Eystathioy T, Chan EKL, Fritzler MJ. 2007. Markers of mRNA stabilization and degradation, and RNAi within astrocytoma GW bodies. J Neurosci Res 85: 3619–3631.
Munro TP, Magee RJ, Kidd GJ, Carson JH, Barbarese E, Smith LM, Smith R. 1999. Mutational analysis of a heterogeneous nuclear ribonucleoprotein A2 response element for RNA trafficking. J Biol Chem 274: 34389–34395.
Okoye IS, Coomes SM, Pelly VS, Czieso S, Papayannopoulos V, Tolmachova T, Seabra MC, Wilson MS. 2014. MicroRNA-contain-ing T-regulatory-cell-derived exosomes suppress pathogenic T helper 1 cells. Immunity 41: 89–103.
Øverbye A, Skotland T, Koehler CJ, Thiede B, Seierstad T, Berge V, Sandvig K, Llorente A. 2015. Identification of prostate cancer biomarkers in urinary exosomes. Oncotarget 6: 30357–30376.
Pan L, Liang W, Fu M, Huang ZH, Li X, Zhang W, Zhang P, Qian H, Jiang PC, Xu WR, et al. 2017. Exosomes-mediated transfer of long noncoding RNA ZFAS1 promotes gastric cancer progression. J Cancer Res Clin Oncol 143: 991–1004.
Peake PW, Pianta TJ, Succar L, Fernando M, Pugh DJ, McNamara K, Endre ZH. 2014. A comparison of the ability of levels of urinary biomarker proteins and exosomal mRNA to predict outcomes after renal transplantation. PLoS One 9: e98644.
Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J. 2016. ncRNA orthologies in the vertebrate lineage. Database 2016: bav127.
Provencio M, Rodríguez M, Cantos B, Sabín P, Quero C, García-Arroyo FR, Rueda A, Maximiano C, Rodríguez-Abreu D, Sánchez A, et al. 2017. mRNA in exosomas as a liquid biopsy in non-Hodgkin lymphoma: a multicentric study by the Spanish Lymphoma Oncology Group. Oncotarget 8: 50949–50957.
Qu L, Ding J, Chen C, Wu ZJ, Liu B, Gao Y, Chen W, Liu F, Sun W, Li XF, et al. 2016. Exosome-transmitted lncARSR promotes suniti-nib resistance in renal cancer by acting as a competing endogenous RNA. Cancer Cell 29: 653–668.
Quek C, Bellingham SA, Jung CH, Scicluna BJ, Shambrook MC, Sharples RA, Cheng L, Hill AF. 2017. Defining the purity of exosomes required for diagnostic profiling of small RNA suitable for biomarker discovery. RNA Biol 14: 245–258.
Repetto E, Lichtenstein L, Hizir Z, Tekaya N, Benahmed M, Ruidavets JB, Zaragosi LE, Perret B, Bouchareychas L, Genoux A, et al. 2015. RNY-derived small RNAs as a signature of coronary artery disease. BMC Med 13: 259.
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140.
Robinson MD, Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25.
Sánchez CA, Andahur EI, Valenzuela R, Castellón EA, Fullá JA, Ramos CG, Triviño JC. 2016. Exosomes from bulk and stem cells from human prostate cancer have a differential microRNA content that contributes cooperatively over local and pre-metastatic niche. Oncotarget 7: 3993–4008.
Santangelo L, Giurato G, Cicchini C, Montaldo C, Mancone C, Tarallo R, Battistelli C, Alonzi T, Weisz A, Tripodi M. 2016. The RNA-binding protein SYNCRIP is a component of the hepatocyte exosomal machinery controlling microRNA sorting. Cell Rep 17: 799–808.
Schwarzenbach H. 2015. The clinical relevance of circulating, exosomal miRNAs as biomarkers for cancer. Expert Rev Mol Diagn 15: 1159–1169.
Shurtleff MJ, Temoche-Diaz MM, Karfilis KV, Ri S, Schekman R. 2016. Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. eLife 5: e19276.
Simons M, Raposo G. 2009. Exosomes—vesicular carriers for intercellular communication. Curr Opin Cell Biol 21: 575–581.
Skogberg G, Gudmundsdottir J, van der Post S, Sandström K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O. 2013. Characterization of human thymic exosomes. PLoS ONE 8: e67554.
Solé C, Cortés-Hernández J, Felip ML, Vidal M, Ordi-Ros J. 2015. miR-29c in urinary exosomes as predictor of early renal fibrosis in lupus nephritis. Nephrol Dial Transplant 30: 1488–1496.
Suzuki H, Matsuoka M. 2017. hnRNPA1 autoregulates its own mRNA expression to remain non-cytotoxic. Mol Cell Biochem 427: 123–131.
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.
van Balkom BWM, Eisele AS, Pegtel DM, Bervoets S, Verhaar MC. 2015. Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting. J Extracell Vesicles 4: 26760.
Villarroya-Beltri C, Gutiérrez-Vázquez C, Sánchez-Cabo F, Pérez-Hernández D, Vázquez J, Martin-Cofreces N, Martinez-Herrera DJ, Pascual-Montano A, Mittelbrunn M, Sánchez-Madrid F. 2013. Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat Commun 4: 2980.
Wang J, Zhou Y, Lu J, Sun Y, Xiao H, Liu M, Tian L. 2014. Combined detection of serum exosomal miR-21 and HOTAIR as diagnostic and prognostic biomarkers for laryngeal squamous cell carcinoma. Med Oncol 31: 148.
Wu SL, Fu X, Huang J, Jia TT, Zong FY, Mu SR, Zhu H, Yan Y, Qiu S, Wu Q, et al. 2015. Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme. Nucleic Acids Res 43: 8516–8528.
Xu JF, Wang Y, Zhang SJ, Chen Y, Gu HF, Dou XF, Xia B, Bi Q, Fan SW. 2017. Exosomes containing differential expression of microRNA and mRNA in osteosarcoma that can predict response to chemotherapy. Oncotarget 5: 75968–75978.
Yoon C, Kim J, Park G, Kim S, Kim D, Hur DY, Kim B, Kim YS. 2016. Delivery of miR-155 to retinal pigment epithelial cells mediated by Burkitt’s lymphoma exosomes. Tumour Biol 37: 313–321.
Zhang J, Kong L, Guo S, Bu M, Guo Q, Xiong Y, Zhu N, Qiu C, Yan X, Chen Q, et al. 2017. hnRNPs and ELAVL1 cooperate with uORFs to inhibit protein translation. Nucleic Acids Res 45: 2849–2864.
Zhao X, Liu Y, Yu S. 2017. Long noncoding RNA AWPPH promotes hepatocellular carcinoma progression through YBX1 and serves as a prognostic biomarker. Biochim Biophys Acta 1863: 1805–1816.
Zhou J, Gong G, Tan H, Dai F, Zhu X, Chen Y, Wang J, Liu Y, Chen P, Wu X, et al. 2015. Urinary microRNA-30a-5p is a potential biomarker for ovarian serous adenocarcinoma. Oncol Rep 33: 2915–2923.