pre-ERCC

Papers Related to exRNA

This is not a comprehensive list, but a snapshot to serve as a guide to the published literature.  There are several other relevant published studies.   Inclusion in this list, or omission from this list of any published work does not indicate impact or significance.

Categories

  • Reviews

  • Observations/Biomarkers

  • Mechanisms & Models

  • Methods/Protocols

Reviews

Cocucci, E., Racchetti, G. & Meldolesi, J. Shedding microvesicles: artefacts no more. Trends Cell Biol 19, 43-51, doi:10.1016/J.Tcb.2008.11.003 (2009).

Etheridge, A., Gomes, Clarissa P. C., Pereira, R.W., Galas, D.J., & Wang, K. 2013. The complexity, function, and applications of RNA in circulation. Front. Genet., doi: 10.3389/fgene.2013.00115.

Fabian, M. R., Sonenberg, N. & Filipowicz, W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem, 79, 351-79.

Gerdes, H. H. & Carvalho, R.N. 2008. Intercellular transfer mediated by tunneling nanotubes. Curr Opin Cell Biol, 20, 470-5.

Kulp, A., & Kuehn, M.J. 2010. Biological Functions and Biogenesis of Secreted Bacterial Outer Membrane Vesicles. Annual Review of Microbiology, 64(1), 163–184.

Lo, Y. M. & Chiu, R.W. 2012. Genomic analysis of fetal nucleic acids in maternal blood. Annu Rev Genomics Hum Genet, 13, 285-306.

Lotvall, J. & Valadi, H. 2007. Cell to cell signalling via exosomes through esRNA. Cell Adh Migr, 1, 156-8.

Mause, S. F. & Weber, C. Microparticles: Protagonists of a Novel Communication Network for Intercellular Information Exchange. Circ Res 107, 1047-1057, doi:10.1161/Circresaha.110.226456 (2010).

Repoila, F., & Darfeuille, F. 2009. Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biology of the Cell, 101(2), 117–131.

Shifrin, D.A., Beckler, M.D., Coffey, R.J. & Tyska, M.J. Extracellular vesicles: communication, coercion, and conditioning. Mol Biol Cell 24, 1253-1259, doi:10.1091/Mbc.E12-08-0572 (2013).

Vogel, J., & Wagner, E.G.H. 2007. Target identification of small noncoding RNAs in bacteria. Current Opinion in Microbiology, 10(3), 262–270.

Observations / Biomarkers

Arroyo, J.D., Chevillet, J.R., Kroh, E.M., Ruf, I.K., Pritchard, C.C., Gibson, D.F., Mitchell, P.S., Bennett, C.F., Pogosova-Agadjanyan, E.L., Stirewalt, D.L., Tait, J.F.& Tewari, M.2011.Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma.Proc Natl Acad Sci U S A, 108: 5003-5008.

Bala, S., Petrasek, J., Mundkur, S., Catalano, D., Levin, I., Ward, J., Alao, H., Kodys, K.& Szabo, G.2012.Circulating microRNAs in exosomes indicate hepatocyte injury and inflammation in alcoholic, drug-induced, and inflammatory liver diseases.Hepatology, 56, 1946-57.

Cortez, M.A., Bueso-Ramos, C., Ferdin, J., Lopez-Berestein, G., Sood, A.K.& Calin, G.A.2011.MicroRNAs in body fluids–the mix of hormones and biomarkers.Nat Rev Clin Oncol, 8, 467-77.

Devaux, Y.et al.Use of Circulating MicroRNAs to Diagnose Acute Myocardial Infarction.Clin Chem 58, 559-567, doi:10.1373/Clinchem.2011.173823 (2012).

Gandhi, R.et al.Circulating MicroRNAs as biomarkers for disease staging in multiple sclerosis.Ann Neurol 73, 729-740, doi:10.1002/Ana.23880 (2013).

Hanke, M., Hoefig, K., Merz, H., Feller, A.C., Kausch, I., Jocham, D., Warnecke, J.M.& Sczakiel, G.2010.A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer.Urol Oncol, 28, 655-61.

Kohler, C., Barekati, Z., Radpour, R.& Zhong, X.Y.2011.Cell-free DNA in the circulation as a potential cancer biomarker.Anticancer Res, 31, 2623-8.

Laterza, O.F., Lim, L., Garrett-Engele, P.W., Vlasakova, K., Muniappa, N., Tanaka, W.K., Johnson, J.M., Sina, J.F., Fare, T.L., Sistare, F.D.& Glaab, W.E.2009.Plasma MicroRNAs as sensitive and specific biomarkers of tissue injury.Clin Chem, 55, 1977-83.

Lawrie, C.H., Gal, S., Dunlop, H.M., Pushkaran, B., Liggins, A.P., Pulford, K., Banham, A.H., Pezzella, F., Boultwood, J., Wainscoat, J.S., Hatton, C.S.& Harris, A.L.2008.Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma.Br J Haematol, 141, 672-5.

Ma, Y., Zhang, P., Wang, F., Zhang, H., Yang, J., Peng, J., Liu, W.& Qin, H.2012.miR-150 as a potential biomarker associated with prognosis and therapeutic outcome in colorectal cancer.Gut, 61, 1447-53.

Mandel, P.& Métais, P.1948.Les acides nucléiques du plasma sanguin chez l’homme.C.R.Acad.Sci.Paris, 142, 241-243.

Mitchell, P.S., Parkin, R.K., Kroh, E.M., Fritz, B.R., Wyman, S.K., Pogosova-Agadjanyan, E.L., Peterson, A., Noteboom, J., O’Briant, K.C., Allen, A., Lin, D.W., Urban, N., Drescher, C.W., Knudsen, B.S., Stirewalt, D.L., Gentleman, R., Vessella, R.L., Nelson, P.S., Martin, D.B.& Tewari, M.2008.Circulating microRNAs as stable blood-based markers for cancer detection.Proc Natl Acad Sci U S A, 105, 10513-8.

Miyamoto, M., Yanai, M., Ookubo, S., Awasaki, N., Takami, K.& Imai, R.2008.Detection of cell-free, liver-specific mRNAs in peripheral blood from rats with hepatotoxicity: a potential toxicological biomarker for safety evaluation.Toxicol Sci, 106, 538-45.

Moltzahn, F.et al.Microfluidic-Based Multiplex qRT-PCR Identifies Diagnostic and Prognostic microRNA Signatures in the Sera of Prostate Cancer Patients.Cancer Res 71, 550-560, doi:10.1158/0008-5472.Can-10-1229 (2011).

Moussay, E., Wang, K., Cho, J., Van Moer, K., Pierson, S., Paggetti, J., Nazarov, P.V., Palissot, V., Hood, L., Berchem, G., & Galas, D.J.2011.microRNA as biomarkers and regulators in B chronic lymphocytic leukemia.PNAS, 108(16):6573-6578.

Okubo, S., Miyamoto, M., Takami, K., Kanki, M., Ono, A., Nakatsu, N., Yamada, H., Ohno, Y.& Urushidani, T.2013.Identification of novel liver-specific mRNAs in plasma for biomarkers of drug-induced liver injury and quantitative evaluation in rats treated with various hepatotoxic compounds.Toxicol Sci, 132, 21-31.

Park, N.J., Zhou, H., Elashoff, D., Henson, B.S., Kastratovic, D.A., Abemayor, E.& Wong, D.T.2009.Salivary microRNA: discovery, characterization, and clinical utility for oral cancer detection.Clin Cancer Res, 15, 5473-7.

Skog, J.et al.Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers.Nat Cell Biol 10, 1470-U1209, doi:10.1038/Ncb1800 (2008).

Su, Y.W., Chen, X., Jiang, Z.Z., Wang, T., Wang, C., Zhang, Y., Wen, J., Xue, M., Zhu, D., Zhang, Y., Su, Y.J., Xing, T.Y., Zhang, C.Y.& Zhang, L.Y.2012.A panel of serum microRNAs as specific biomarkers for diagnosis of compound- and herb-induced liver injury in rats.PLoS ONE, 7, e37395.

Sueoka, E., Sueoka, N., Iwanaga, K., Sato, A., Suga, K., Hayashi, S., Nagasawa, K.& Nakachi, K.2005.Detection of plasma hnRNP B1 mRNA, a new cancer biomarker, in lung cancer patients by quantitative real-time polymerase chain reaction.Lung Cancer, 48, 77-83.

Taylor, D.D.& Gercel-Taylor, C.2008.MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer.Gynecol Oncol, 110, 13-21.

Turchinovich, A., Weiz, L., Langheinz, A.& Burwinkel, B.2011.Characterization of extracellular circulating microRNA.Nucleic Acids Res, 39, 7223-33.

Vickers, K.C., Palmisano, B.T., Shoucri, B.M., Shamburek, R.D.& Remaley, A.T.2011.MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins.Nat Cell Biol, 13, 423-33.

Wagner, J., Riwanto, M., Besler, C., Knau, A., Fichtlscherer, S., Roxe, T., Zeiher, A.M., Landmesser, U.& Dimmeler, S.2013.Characterization of Levels and Cellular Transfer of Circulating Lipoprotein-Bound MicroRNAs.Arterioscler Thromb Vasc Biol.

Wang, G.K., Zhu, J.Q., Zhang, J.T., Li, Q., Li, Y., He, J., Qin, Y.W.& Jing, Q.2010.Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans.Eur Heart J, 31, 659-66.

Wang, K., Li, H., Yuan, Y., Etheridge, A., Zhou, Y., Huang, D., Wilmes, P.& Galas, D.2012.The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS ONE, 7, e51009.

Wang, K.Yuan, Y., Cho, J-H., McClarty, S., Baxter, D.Galas, D.J.2012.Comparing the MicroRNA spectrum between serum and plasma.PLoS ONE, 7 (7), e41561

Wang, K., Zhang, S., Marzolf, B., Troisch, P., Brightman, A., Hu, Z., Hood, L.E.& Galas, D.J.2009.Circulating microRNAs, potential biomarkers for drug-induced liver injury.Proc Natl Acad Sci U S A, 106, 4402-7.

Weber, J.A., Baxter, D.H., Zhang, S., Huang, D.Y., Huang, K.H., Lee, M.J., Galas, D.J.& Wang, K.2010.The microRNA spectrum in 12 body fluids.Clin Chem, 56, 1733-41.

Witwer, K.W., McAlexander, M.A., Queen, S.E., and Adams R.J.2013.Real-time PCR and droplet digital PCR for plant miRNAs in mammalian blood provide little evidence for general uptake of dietary miRNAs.RNA Biology, 10:7, 1-7.

Wu, L., Zhou, H., Lin, H., Qi, J., Zhu, C., Gao, Z.& Wang, H.2012.Circulating microRNAs are elevated in plasma from severe preeclamptic pregnancies.Reproduction, 143, 389-97.

Zhang, X., Wang, C., Wang, L., Du, L., Wang, S., Zheng, G., Li, W., Zhuang, X., Zhang, X.& Dong, Z.2012b.Detection of circulating Bmi-1 mRNA in plasma and its potential diagnostic and prognostic value for uterine cervical cancer.Int J Cancer, 131, 165-72.

Zhao, H., Shen, J., Medico, L., Wang, D., Ambrosone, C.B.& Liu, S.2010.A pilot study of circulating miRNAs as potential biomarkers of early stage breast cancer.PLoS ONE, 5, e13735.

Zhao, Z., Zhao, Q., Warrick, J., Lockwood, C.M., Woodworth, A., Moley, K.H.& Gronowski, A.M.2012.Circulating microRNA miR-323-3p as a biomarker of ectopic pregnancy.Clin Chem, 58, 896-905.

Zhong, X.Y., Holzgreve, W.& Huang, D.J.2008.Isolation of cell-free RNA from maternal plasma.Methods Mol Biol, 444, 269-73.

Mechanisms & Models

Alexopoulou, L., Holt, A.C., Medzhitov, R., & Flavell, R.A. Recognition of double-stranded RNA and activation of NF-[kappa]B by Toll-like receptor 3. Nature(2001) 413: 732–738.

Bomberger, J.M., MacEachran, D.P., Coutermarsh, B.A., Ye, S., O’Toole, G.A., & Stanton, B.A.2009.Long-Distance Delivery of Bacterial Virulence Factors by Pseudomonas aeruginosa Outer Membrane Vesicles.PLoS Pathog, 5(4), e1000382.

Camussi, G., Deregibus, M.C., Bruno, S., Grange, C., Fonsato, V.& Tetta, C.2011.Exosome/microvesicle-mediated epigenetic reprogramming of cells.Am J Cancer Res, 1, 98-110.

Care, A., Catalucci, D., Felicetti, F., Bonci, D., Addario, A., Gallo, P., Bang, M.L., Segnalini, P., Gu, Y., Dalton, N.D., Elia, L., Latronico, M.V., Hoydal, M., Autore, C., Russo, M.A., Dorn, G.W., 2nd, Ellingsen, O., Ruiz-Lozano, P., Peterson, K.L., Croce, C.M., Peschle, C.& Condorelli, G.2007.MicroRNA-133 controls cardiac hypertrophy.Nat Med, 13, 613-8.

Chabelskaya, S., Gaillot, O., & Felden, B.2010.A Staphylococcus aureus Small RNA Is Required for Bacterial Virulence and Regulates the Expression of an Immune-Evasion Molecule.PLoS Pathog, 6(6), e1000927.

Chendrimada, T.P., Finn, K.J., Ji, X., Baillat, D., Gregory, R.I., Liebhaber, S.A., Pasquinelli, A.E.& Shiekhattar, R.2007.MicroRNA silencing through RISC recruitment of eIF6.Nature, 447, 823-8.

Choi, D.S., Kim, D.K., Kim, Y.K.& Gho, Y.S.Proteomics, transcriptomics and lipidomics of exosomes and ectosomes.Proteomics 13, 1554-1571, doi:10.1002/Pmic.201200329 (2013).

Gong, H., Vu, G.-P., Bai, Y., Chan, E., Wu, R., Yang, E., Liu, F., et al.2011.A Salmonella Small Non-Coding RNA Facilitates Bacterial Invasion and Intracellular Replication by Modulating the Expression of Virulence Factors.PLoS Pathog, 7(9), e1002120.

Hammell, C.M., & Hannon, G.J.2012.Inducing RNAi in C.elegans by Feeding with dsRNA-expressing E.coli.Cold Spring Harbor Protocols, 2012(12), pdb.prot072348.

Hansen, D.R., Van Alfen, N.K., Gillies, K., & Powell, W.A.1985.Naked dsRNA Associated with Hypovirulence of Endothia parasitica is Packaged in Fungal Vesicles.Journal of General Virology, 66(12), 2605–2614.

Kogure, T., Lin, W.L., Yan, I.K., Braconi, C.& Patel, T.2011.Intercellular nanovesicle-mediated microRNA transfer: a mechanism of environmental modulation of hepatocellular cancer cell growth.Hepatology, 54, 1237-48.

Higashijima, A., Miura, K., Mishima, H., Kinoshita, A., Jo, O., Abe, S., Hasegawa, Y., Miura, S., Yamasaki, K., Yoshida, A., Yoshiura, K.& Masuzaki, H.2013.Characterization of placenta-specific microRNAs in fetal growth restriction pregnancy.Prenat Diagn, 33, 214-22.

Lee, E.-Y., Choi, D.-Y., Kim, D.-K., Kim, J.-W., Park, J.O., Kim, S., Kim, S.-H., et al.2009.Gram-positive bacteria produce membrane vesicles: Proteomics-based characterization of Staphylococcus aureus-derived membrane vesicles.Proteomics, 9(24), 5425–5436.

Lee, S.T., Chu, K., Jung, K.H., Kim, J.H., Huh, J.Y., Yoon, H., Park, D.K., Lim, J.Y., Kim, J.M., Jeon, D., Ryu, H., Lee, S.K., Kim, M.& Roh, J.K.2012.miR-206 regulates brain-derived neurotrophic factor in Alzheimer disease model.Ann Neurol, 72, 269-77.

Liu, A.Y., Pascal, L.E., Vencio, R.Z.& Vencio, E.F.2010.Stromal-epithelial interactions in early neoplasia.Cancer biomarkers: section A of Disease markers, 9, 141-55.

Liu, H., Wang, X., Wang, H.-D., Wu, J., Ren, J., Meng, L., Wu, Q., et al.2012.Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans.Nat Commun, 3, 1073.

Mittelbrunn, M., Gutierrez-Vazquez, C., Villarroya-Beltri, C., Gonzalez, S., Sanchez-Cabo, F., Gonzalez, M.A., Bernad, A.& Sanchez-Madrid, F.2011.Unidirectional transfer of microRNA-loaded exosomes from T cells to antigen-presenting cells.Nat Commun, 2, 282.

Parker, H., Chitcholtan, K., Hampton, M.B., & Keenan, J.I.2010.Uptake of Helicobacter pylori Outer Membrane Vesicles by Gastric Epithelial Cells.Infection and Immunity, 78(12), 5054–5061.

Ratajczak, J., Miekus, K., Kucia, M., Zhang, J., Reca, R., Dvorak, P.& Ratajczak, M.Z.2006.Embryonic stem cell-derived microvesicles reprogram hematopoietic progenitors: evidence for horizontal transfer of mRNA and protein delivery.Leukemia, 20, 847-56.

Riley D.R., Sieber K.B., Robinson K.M., White J.R., Ganesan A., Nourbakhsh S., Dunning Hotopp J.C.2013.Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples.PLoS Comput Biol, 9(6): e1003107.

Rodrigues, M.L., Franzen, A.J., Nimrichter, L., & Miranda, K.(n.d.).Vesicular mechanisms of traffic of fungal molecules to the extracellular space.Current Opinion in Microbiology, (0).doi:http://dx.doi.org/10.1016/j.mib.2013.04.002.

Schmidt, W.M., Spiel, A.O., Jilma, B., Wolzt, M.& Muller, M.2009.In vivo profile of the human leukocyte microRNA response to endotoxemia.Biochemical and biophysical research communications, 380, 437-41.

Valadi, H., Ekstrom, K., Bossios, A., Sjostrand, M., Lee, J.J.& Lotvall, J.O.2007.Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells.Nat Cell Biol, 9, 654-9.

Vencio, E.F., Pascal, L.E., Page, L.S., Denyer, G., Wang, A.J., Ruohola-Baker, H., Zhang, S., Wang, K., Galas, D.J.& Liu, A.Y.2011.Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells.Journal of cellular physiology, 226, 1479-88.

Wang, K., Zhang, S., Weber, J., Baxter, D., & Galas, D.J.2010a.Mammalian cells in culture actively export specific microRNAs.Nucleic Acids Research, 38(20):7248-7259.

Wang, K., Zhang, S., Weber, J., Baxter, D., & Galas, D.J.2010b.Export of microRNAs and microRNA-protective protein by mammalian cells.Nucleic Acids Res, 38, 7248-59.

Yang, M., Chen, J., Su, F., Yu, B., Lin, L., Liu, Y., Huang, J.D.& Song, E.2011.Microvesicles secreted by macrophages shuttle invasion-potentiating microRNAs into breast cancer cells.Molecular cancer, 10, 117.

Zhang, L., Hou, D., Chen, X., Li, D., Zhu, L., Zhang, Y., Li, J., Bian, Z., Liang, X., Cai, X., Yin, Y., Wang, C., Zhang, T., Zhu, D., Zhang, D., Xu, J., Chen, Q., Ba, Y., Liu, J., Wang, Q., Chen, J., Wang, J., Wang, M., Zhang, Q., Zhang, J., Zen, K.& Zhang, C.Y.2012a.Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.Cell Res, 22, 107-26.

Methods/Protocols

Argyropoulos, C., Wang, K., McClarty, S., Huang, D., Bernardo, J., Ellis, D., Orchard, T., Galas, D., Johnson, J. 2013. Urinary MicroRNA Profiling in the Nephropathy of Type 1 Diabetes. PLoS ONE 8:e54662. doi: 10.1371/journal.pone.0054662.

Lee, H.-J., & Hong, S.-H. 2012. Analysis of microRNA-size, small RNAs in Streptococcus mutans by deep sequencing. FEMS Microbiology Letters, 326(2), 131–136.

Lee, L.W., Zhang, S., Etheridge, A., Ma, L., Martin, D., Galas, D. & Wang, K. 2010. Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA, 16, 2170-80.

Kang, S.M., Choi, J.W., Lee, Y., Hong, S.H., & Lee, H.-J. 2013. Identification of microRNA-Size, Small RNAs in Escherichia coli. Current Microbiology, 1–5. doi:10.1007/s00284-013-0411-9.

Kogure, T., & Patel, T.  2013.   Isolation of extracellular nanovesicle microRNA from liver cancer cells in culture.  Methods Mol Biol. 2013;1024:11-8. doi: 10.1007/978-1-62703-453-1_2.

Nolte-‘T hoen, E.N.M., Buermans, H.P.J., Wasdorp, M., Stoorvogel, W., Wauben, M.H.M., & ‘T hoen, P.A.C., Deep sequencing of RNA from immune cell-dervived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions,  Nucl Acids Res. (2012) 40: 9272-9285.

Semenov, D.V., Baryakin, D.N., Brenner, E.V., Kurilshikov, A.M., Vasiliev, G.V., Bryzgalov, L.A., Chikova, E.D., Filippova, J.A., Kuligina, E.V. & Richter, V.A. 2012. Unbiased approach to profile the variety of small non-coding RNA of human blood plasma with massively parallel sequencing technology. Expert Opin Biol Ther, 12 Suppl 1, S43-51.

Sipova, H., Zhang, S., Dudley, A.M., Galas, D.J., Wang, K. & Homola, J. 2010. Surface Plasmon Resonance Biosensor for Rapid Label-free Detection of microRNA at Sub-femtomolar Levels. Analytical Chemistry, 82(24):10110-10115.

Turchinovich A., Weiz, L., Langheinz, A., & Burwinkel B. 2011. Characterization of extracellular circulating microRNA.  Nucleic Acids Res. 39(16):7223-33. doi: 10.1093/nar/gkr254. Epub 2011 May 24.

Wang, Q.L. et al. Delivery of therapeutic agents by nanoparticles made of grapefruit-derived lipids. Nat Commun 4, 1867, doi:10.1038/Ncomms2886 (2013).

Witwer, K.W. et al. Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. J Extracell Ves 2, 20360, doi:10.3402/jev.v2i0.20360 (2013).