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References
Оглавление1 Alberti, C. and Cochella, L. (2017). A framework for understanding the roles of miRNAs in animal development. Development 144: 2548–2559.
2 Ambros, V. (2004). The functions of animal microRNAs. Nature 431: 350–355.
3 Asakura, K., Kadota, T., Matsuzaki, J., Yoshida, Y., Yamamoto, Y., Nakagawa, K., Takizawa, S., Aoki, Y., Nakamura, E., Miura, J., Sakamoto, H., Kato, K., Watanabe, S.I., and Ochiya, T. (2020). A miRNA-based diagnostic model predicts resectable lung cancer in humans with high accuracy. Commun. Biol. 3: 134.
4 Asano, N., Matsuzaki, J., Ichikawa, M., Kawauchi, J., Takizawa, S., Aoki, Y., Sakamoto, H., Yoshida, A., Kobayashi, E., Tanzawa, Y., Nakayama, R., Morioka, H., Matsumoto, M., Nakamura, M., Kondo, T., Kato, K., Tsuchiya, N., Kawai, A., and Ochiya, T. (2019). A serum microRNA classifier for the diagnosis of sarcomas of various histological subtypes. Nat. Commun. 10: 1299.
5 Baek, R., Varming, K., and Jorgensen, M.M. (2016). Does smoking, age or gender affect the protein phenotype of extracellular vesicles in plasma? Transfus. Apher. Sci. 55: 44–52.
6 Bala, S., Petrasek, J., Mundkur, S., Catalano, D., Levin, I., Ward, J., Alao, H., Kodys, K., and Szabo, G. (2012). Circulating microRNAs in exosomes indicate hepatocyte injury and inflammation in alcoholic, drug-induced, and inflammatory liver diseases. Hepatology 56: 1946–1957.
7 Baran, J., Baj-Krzyworzeka, M., Weglarczyk, K., Szatanek, R., Zembala, M., Barbasz, J., Czupryna, A., Szczepanik, A., and Zembala, M. (2010). Circulating tumour-derived microvesicles in plasma of gastric cancer patients. Cancer Immunol. Immunother. 59: 841–850.
8 Birbrair, A., Zhang, T., Wang, Z.M., Messi, M.L., Mintz, A., and Delbono, O. (2015). Pericytes at the intersection between tissue regeneration and pathology. Clin. Sci. (Lond) 128: 81–93.
9 Birbrair, A., Zhang, T., Wang, Z.M., Messi, M.L., Olson, J.D., Mintz, A., and Delbono, O. (2014). Type-2 pericytes participate in normal and tumoral angiogenesis. Am. J. Physiol. Cell. Physiol. 307: C25–38.
10 Bohnsack, M.T., Czaplinski, K., and Gorlich, D. (2004). Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10: 185–191.
11 Borchert, G.M., Lanier, W., and Davidson, B.L. (2006). RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13: 1097–1101.
12 Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R.L., Torre, L.A., and Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 68: 394–424.
13 Carmeliet, P. and Jain, R.K. (2000). Angiogenesis in cancer and other diseases. Nature 407: 249–257.
14 Cazzoli, R., Buttitta, F., Di Nicola, M., Malatesta, S., Marchetti, A., Rom, W.N., and Pass, H.I. (2013). microRNAs derived from circulating exosomes as noninvasive biomarkers for screening and diagnosing lung cancer. J. Thorac. Oncol. 8: 1156–1162.
15 Chan, Y.K., Zhang, H., Liu, P., Tsao, S.W., Lung, M.L., Mak, N.K., Ngok-Shun Wong, R., and Ying-Kit Yue, P. (2015). Proteomic analysis of exosomes from nasopharyngeal carcinoma cell identifies intercellular transfer of angiogenic proteins. Int. J. Cancer 137: 1830–1841.
16 Chen, L. and Han, X. (2015). Anti-PD-1/PD-L1 therapy of human cancer: Past, present, and future. J. Clin. Invest. 125: 3384–3391.
17 Chendrimada, T.P., Gregory, R.I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K., and Shiekhattar, R. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436: 740–744.
18 Cho, Y.E., Kim, S.H., Lee, B.H., and Baek, M.C. (2017). Circulating plasma and exosomal microRNAs as indicators of drug-induced organ injury in rodent models. Biomol. Ther. (Seoul) 25: 367–373.
19 Choi, D.S., Park, J.O., Jang, S.C., Yoon, Y.J., Jung, J.W., Choi, D.Y., Kim, J.W., Kang, J.S., Park, J., Hwang, D., Lee, K.H., Park, S.H., Kim, Y.K., Desiderio, D.M., Kim, K.P., and Gho, Y.S. (2011). Proteomic analysis of microvesicles derived from human colorectal cancer ascites. Proteomics 11: 2745–2751.
20 Chopra, P., Roy, S., Ramalingaswami, V., and Nayak, N.C. (1972). Mechanism of carbon tetrachloride hepatotoxicity. An in vivo study of its molecular basis in rats and monkeys. Lab. Invest. 26: 716–727.
21 Clark, D.J., Fondrie, W.E., Yang, A., and Mao, L. (2016). Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes. J. Proteomics 133: 161–169.
22 Colombo, M., Raposo, G., and Thery, C. (2014). Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annu. Rev. Cell. Dev. Biol. 30: 255–289.
23 Conde-Vancells, J., Rodriguez-Suarez, E., Embade, N., Gil, D., Matthiesen, R., Valle, M., Elortza, F., Lu, S.C., Mato, J.M., and Falcon-Perez, J.M. (2008). Characterization and comprehensive proteome profiling of exosomes secreted by hepatocytes. J. Proteome. Res. 7: 5157–5166.
24 Coufal, N.G., Garcia-Perez, J.L., Peng, G.E., Yeo, G.W., Mu, Y., Lovci, M.T., Morell, M., O’Shea, K.S., Moran, J.V., and Gage, F.H. (2009). L1 retrotransposition in human neural progenitor cells. Nature 460: 1127–1131.
25 Cufaro, M.C., Pieragostino, D., Lanuti, P., Rossi, C., Cicalini, I., Federici, L., De Laurenzi, V., and Del Boccio, P. (2019). Extracellular vesicles and their potential use in monitoring cancer progression and therapy: The contribution of proteomics. J. Oncol. 2019: 1639854.
26 De Wever, O., Van Bockstal, M., Mareel, M., Hendrix, A., and Bracke, M. (2014). Carcinoma-associated fibroblasts provide operational flexibility in metastasis. Semin. Cancer Biol. 25: 33–46.
27 Deng, T., Zhang, H., Yang, H., Wang, H., Bai, M., Sun, W., Wang, X., Si, Y., Ning, T., Zhang, L., Li, H., Ge, S., Liu, R., Lin, D., Li, S., Ying, G., and Ba, Y. (2020). Exosome miR-155 derived from gastric carcinoma promotes angiogenesis by targeting the c-MYB/VEGF axis of endothelial cells. Mol. Ther. Nucleic Acids 19: 1449–1459.
28 Denli, A.M., Tops, B.B., Plasterk, R.H., Ketting, R.F., and Hannon, G.J. (2004). Processing of primary microRNAs by the microprocessor complex. Nature 432: 231–235.
29 Eichelser, C., Stuckrath, I., Muller, V., Milde-Langosch, K., Wikman, H., Pantel, K., and Schwarzenbach, H. (2014). Increased serum levels of circulating exosomal microRNA-373 in receptor-negative breast cancer patients. Oncotarget 5: 9650–9663.
30 Ekstrom, E.J., Bergenfelz, C., Von Bulow, V., Serifler, F., Carlemalm, E., Jonsson, G., Andersson, T., and Leandersson, K. (2014). WNT5A induces release of exosomes containing pro-angiogenic and immunosuppressive factors from malignant melanoma cells. Mol. Cancer 13: 88.
31 Fang, T., Lv, H., Lv, G., Li, T., Wang, C., Han, Q., Yu, L., Su, B., Guo, L., Huang, S., Cao, D., Tang, L., Tang, S., Wu, M., Yang, W., and Wang, H. (2018). Tumor-derived exosomal miR-1247-3p induces cancer-associated fibroblast activation to foster lung metastasis of liver cancer. Nat. Commun. 9: 191.
32 Farkash, E.A., Kao, G.D., Horman, S.R., and Prak, E.T. (2006). Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay. Nucleic Acids Res. 34: 1196–1204.
33 Fu, H., Yang, H., Zhang, X., Wang, B., Mao, J., Li, X., Wang, M., Zhang, B., Sun, Z., Qian, H., and Xu, W. (2018). Exosomal TRIM3 is a novel marker and therapy target for gastric cancer. J. Exp. Clin. Cancer Res. 37: 162.
34 Garcia-Perez, J.L., Morell, M., Scheys, J.O., Kulpa, D.A., Morell, S., Carter, C.C., Hammer, G.D., Collins, K.L., O’Shea, K.S., Menendez, P., and Moran, J.V. (2010). Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466: 769–773.
35 Gener Lahav, T., Adler, O., Zait, Y., Shani, O., Amer, M., Doron, H., Abramovitz, L., Yofe, I., Cohen, N., and Erez, N. (2019). Melanoma-derived extracellular vesicles instigate proinflammatory signaling in the metastatic microenvironment. Int. J. Cancer 145: 2521–2534.
36 Giusti, I., Delle Monache, S., Di Francesco, M., Sanita, P., D’Ascenzo, S., Gravina, G.L., Festuccia, C., and Dolo, V. (2016). From glioblastoma to endothelial cells through extracellular vesicles: Messages for angiogenesis. Tumour Biol. 37: 12743–12753.
37 Gould, S.J. and Raposo, G. (2013). As we wait: Coping with an imperfect nomenclature for extracellular vesicles. J. Extracell Vesicles 2. doi: 10.3402/jev.v2i0.20389.
38 Gregory, R.I., Yan, K.P., Amuthan, G., Chendrimada, T., Doratotaj, B., Cooch, N., and Shiekhattar, R. (2004). The microprocessor complex mediates the genesis of microRNAs. Nature 432: 235–240.
39 Gueta, K., Molotski, N., Gerchikov, N., Mor, E., Savion, S., Fein, A., Toder, V., Shomron, N., and Torchinsky, A. (2010). Teratogen-induced alterations in microRNA-34, microRNA-125b and microRNA-155 expression: Correlation with embryonic p53 genotype and limb phenotype. BMC Dev. Biol. 10: 20.
40 Hammond, S.M., Bernstein, E., Beach, D., and Hannon, G.J. (2000). An RNA-directed nuclease mediates post-transcriptional gene silencing in drosophila cells. Nature 404: 293–296.
41 Han, J., Lee, Y., Yeom, K.H., Kim, Y.K., Jin, H., and Kim, V.N. (2004). The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18: 3016–3027.
42 Han, J., Lee, Y., Yeom, K.H., Nam, J.W., Heo, I., Rhee, J.K., Sohn, S.Y., Cho, Y., Zhang, B.T., and Kim, V.N. (2006). Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887–901.
43 Harding, C. and Stahl, P. (1983). Transferrin recycling in reticulocytes: PH and iron are important determinants of ligand binding and processing. Biochem. Biophys. Res. Commun. 113: 650–658.
44 Hergenreider, E., Heydt, S., Treguer, K., Boettger, T., Horrevoets, A.J., Zeiher, A.M., Scheffer, M.P., Frangakis, A.S., Yin, X., Mayr, M., Braun, T., Urbich, C., Boon, R.A., and Dimmeler, S. (2012). Atheroprotective communication between endothelial cells and smooth muscle cells through miRNAs. Nat. Cell Biol. 14: 249–256.
45 Hsu, Y.L., Hung, J.Y., Chang, W.A., Lin, Y.S., Pan, Y.C., Tsai, P.H., Wu, C.Y., and Kuo, P.L. (2017). Hypoxic lung cancer-secreted exosomal miR-23a increased angiogenesis and vascular permeability by targeting prolyl hydroxylase and tight junction protein ZO-1. Oncogene 36: 4929–4942.
46 Hutvagner, G., Mclachlan, J., Pasquinelli, A.E., Balint, E., Tuschl, T., and Zamore, P.D. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834–838.
47 Imbeaud, S., Graudens, E., Boulanger, V., Barlet, X., Zaborski, P., Eveno, E., Mueller, O., Schroeder, A., and Auffray, C. (2005). Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res. 33: e56.
48 Irie, M., Yoshikawa, M., Ono, R., Iwafune, H., Furuse, T., Yamada, I., Wakana, S., Yamashita, Y., Abe, T., Ishino, F., and Kaneko-Ishino, T. (2015). Cognitive function related to the Sirh11/Zcchc16 gene acquired from an ltr retrotransposon in eutherians. PLoS Genet. 11: e1005521.
49 Ivancevic, A.M., Kortschak, R.D., Bertozzi, T., and Adelson, D.L. (2018). Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. Genome Biol. 19: 85.
50 Iwasaki, S., Kobayashi, M., Yoda, M., Sakaguchi, Y., Katsuma, S., Suzuki, T., and Tomari, Y. (2010). Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol. Cell 39: 292–299.
51 Jonas, S. and Izaurralde, E. (2015). Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet. 16: 421–433.
52 Kalluri, R. (2016). The biology and function of exosomes in cancer. J. Clin. Invest. 126: 1208–1215.
53 Kalluri, R. and Zeisberg, M. (2006). Fibroblasts in cancer. Nat. Rev. Cancer 6: 392–401.
54 Kawamura, Y., Sanchez Calle, A., Yamamoto, Y., Sato, T.A., and Ochiya, T. (2019). Extracellular vesicles mediate the horizontal transfer of an active LINE-1 retrotransposon. J. Extracell Vesicles 8: 1643214.
55 Khan, S., Jutzy, J.M., Valenzuela, M.M., Turay, D., Aspe, J.R., Ashok, A., Mirshahidi, S., Mercola, D., Lilly, M.B., and Wall, N.R. (2012). Plasma-derived exosomal survivin, a plausible biomarker for early detection of prostate cancer. PLoS One 7: e46737.
56 Kozomara, A., Birgaoanu, M., and Griffiths-Jones, S. (2019). miRBase: From microRNA sequences to function. Nucleic Acids Res. 47: D155–D162.
57 Kwak, P.B. and Tomari, Y. (2012). The N domain of Argonaute drives duplex unwinding during RISC assembly. Nat. Struct. Mol. Biol. 19: 145–151.
58 Lee, R.C., Feinbaum, R.L., and Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854.
59 Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S., and Kim, V.N. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415–419.
60 Lee, Y., Jeon, K., Lee, J.T., Kim, S., and Kim, V.N. (2002). MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J. 21: 4663–4670.
61 Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H., and Kim, V.N. (2004). MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23: 4051–4060.
62 Li, M., Yu, D., Williams, K.J., and Liu, M.L. (2010). Tobacco smoke induces the generation of procoagulant microvesicles from human monocytes/macrophages. Arterioscler Thromb Vasc. Biol. 30: 1818–1824.
63 Li, S., Zhao, Y., Chen, W., Yin, L., Zhu, J., Zhang, H., Cai, C., Li, P., Huang, L., and Ma, P. (2018). Exosomal ephrinA2 derived from serum as a potential biomarker for prostate cancer. J. Cancer 9: 2659–2665.
64 Li, Z., Ma, Y.Y., Wang, J., Zeng, X.F., Li, R., Kang, W., and Hao, X.K. (2016). Exosomal microRNA-141 is upregulated in the serum of prostate cancer patients. Onco. Targets Ther. 9: 139–148.
65 Lobb, R.J., Becker, M., Wen, S.W., Wong, C.S., Wiegmans, A.P., Leimgruber, A., and Moller, A. (2015). Optimized exosome isolation protocol for cell culture supernatant and human plasma. J. Extracell Vesicles 4: 27031.
66 Logozzi, M., De Milito, A., Lugini, L., Borghi, M., Calabro, L., Spada, M., Perdicchio, M., Marino, M.L., Federici, C., Iessi, E., Brambilla, D., Venturi, G., Lozupone, F., Santinami, M., Huber, V., Maio, M., Rivoltini, L., and Fais, S. (2009). High levels of exosomes expressing CD63 and caveolin-1 in plasma of melanoma patients. PLoS One 4: e5219.
67 Lu, Q., Zhang, J., Allison, R., Gay, H., Yang, W.X., Bhowmick, N.A., Frelix, G., Shappell, S., and Chen, Y.H. (2009). Identification of extracellular delta-catenin accumulation for prostate cancer detection. Prostate 69: 411–418.
68 Macfarlane, L.A. and Murphy, P.R. (2010). MicroRNA: Biogenesis, function and role in cancer. Curr. Genom. 11: 537–561.
69 Madhavan, B., Yue, S., Galli, U., Rana, S., Gross, W., Muller, M., Giese, N.A., Kalthoff, H., Becker, T., Buchler, M.W., and Zoller, M. (2015). Combined evaluation of a panel of protein and miRNA serum-exosome biomarkers for pancreatic cancer diagnosis increases sensitivity and specificity. Int. J. Cancer 136: 2616–2627.
70 Manterola, L., Guruceaga, E., Gallego Perez-Larraya, J., Gonzalez-Huarriz, M., Jauregui, P., Tejada, S., Diez-Valle, R., Segura, V., Sampron, N., Barrena, C., Ruiz, I., Agirre, A., Ayuso, A., Rodriguez, J., Gonzalez, A., Xipell, E., Matheu, A., Lopez De Munain, A., Tunon, T., Zazpe, I., Garcia-Foncillas, J., Paris, S., Delattre, J.Y., and Alonso, M.M. (2014). A small noncoding RNA signature found in exosomes of GBM patient serum as a diagnostic tool. Neuro Oncol 16: 520–527.
71 Mathivanan, S., Ji, H., and Simpson, R.J. (2010). Exosomes: Extracellular organelles important in intercellular communication. J. Proteomics 73: 1907–1920.
72 Melo, S.A., Luecke, L.B., Kahlert, C., Fernandez, A.F., Gammon, S.T., Kaye, J., Lebleu, V.S., Mittendorf, E.A., Weitz, J., Rahbari, N., Reissfelder, C., Pilarsky, C., Fraga, M.F., Piwnica-Worms, D., and Kalluri, R. (2015). Glypican-1 identifies cancer exosomes and detects early pancreatic cancer. Nature 523: 177–182.
73 Mittelbrunn, M., Gutierrez-Vazquez, C., Villarroya-Beltri, C., Gonzalez, S., Sanchez-Cabo, F., Gonzalez, M.A., Bernad, A., and Sanchez-Madrid, F. (2011). Unidirectional transfer of microRNA-loaded exosomes from T cells to antigen-presenting cells. Nat. Commun. 2: 282.
74 Mizutani, K., Terazawa, R., Kameyama, K., Kato, T., Horie, K., Tsuchiya, T., Seike, K., Ehara, H., Fujita, Y., Kawakami, K., Ito, M., and Deguchi, T. (2014). Isolation of prostate cancer-related exosomes. Anticancer Res. 34: 3419–3423.
75 Mobarrez, F., Antoniewicz, L., Bosson, J.A., Kuhl, J., Pisetsky, D.S., and Lundback, M. (2014). The effects of smoking on levels of endothelial progenitor cells and microparticles in the blood of healthy volunteers. PLoS One 9: e90314.
76 Montecalvo, A., Larregina, A.T., Shufesky, W.J., Stolz, D.B., Sullivan, M.L., Karlsson, J.M., Baty, C.J., Gibson, G.A., Erdos, G., Wang, Z., Milosevic, J., Tkacheva, O.A., Divito, S.J., Jordan, R., Lyons-Weiler, J., Watkins, S.C., and Morelli, A.E. (2012). Mechanism of transfer of functional microRNAs between mouse dendritic cells via exosomes. Blood 119: 756–766.
77 Mor, E., He, L., Torchinsky, A., and Shomron, N. (2014). MicroRNA-34a is dispensable for p53 function as teratogenesis inducer. Arch. Toxicol. 88: 1749–1763.
78 Munro, T.P., Magee, R.J., Kidd, G.J., Carson, J.H., Barbarese, E., Smith, L.M., and Smith, R. (1999). Mutational analysis of a heterogeneous nuclear ribonucleoprotein A2 response element for RNA trafficking. J. Biol. Chem. 274: 34389–34395.
79 Naruse, M., Ono, R., Irie, M., Nakamura, K., Furuse, T., Hino, T., Oda, K., Kashimura, M., Yamada, I., Wakana, S., Yokoyama, M., Ishino, F., and Kaneko-Ishino, T. (2014). Sirh7/Ldoc1 knockout mice exhibit placental P4 overproduction and delayed parturition. Development 141: 4763–4771.
80 Nawaz, M., Shah, N., Zanetti, B.R., Maugeri, M., Silvestre, R.N., Fatima, F., Neder, L., and Valadi, H. (2018). Extracellular vesicles and matrix remodeling enzymes: the emerging roles in extracellular matrix remodeling, progression of diseases and tissue repair. Cells 7 (10): 167.
81 Negrier, S., Gravis, G., Perol, D., Chevreau, C., Delva, R., Bay, J.O., Blanc, E., Ferlay, C., Geoffrois, L., Rolland, F., Legouffe, E., Sevin, E., Laguerre, B., and Escudier, B. (2011). Temsirolimus and bevacizumab, or sunitinib, or interferon alfa and bevacizumab for patients with advanced renal cell carcinoma (TORAVA): A randomised phase 2 trial. Lancet. Oncol. 12: 673–680.
82 Ogata-Kawata, H., Izumiya, M., Kurioka, D., Honma, Y., Yamada, Y., Furuta, K., Gunji, T., Ohta, H., Okamoto, H., Sonoda, H., Watanabe, M., Nakagama, H., Yokota, J., Kohno, T., and Tsuchiya, N. (2014). Circulating exosomal microRNAs as biomarkers of colon cancer. PLoS One 9: e92921.
83 Okada, C., Yamashita, E., Lee, S.J., Shibata, S., Katahira, J., Nakagawa, A., Yoneda, Y., and Tsukihara, T. (2009). A high-resolution structure of the pre-microRNA nuclear export machinery. Science 326: 1275–1279.
84 Ono, R., Ishii, M., Fujihara, Y., Kitazawa, M., Usami, T., Kaneko-Ishino, T., Kanno, J., Ikawa, M., and Ishino, F. (2015). Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes. Sci. Rep. 5: 12281.
85 Ono, R., Kobayashi, S., Wagatsuma, H., Aisaka, K., Kohda, T., Kaneko-Ishino, T., and Ishino, F. (2001). A retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics 73: 232–237.
86 Ono, R., Kuroki, Y., Naruse, M., Ishii, M., Iwasaki, S., Toyoda, A., Fujiyama, A., Shaw, G., Renfree, M.B., Kaneko-Ishino, T., and Ishino, F. (2011). Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event. DNA Res. 18: 211–219.
87 Ono, R., Nakamura, K., Inoue, K., Naruse, M., Usami, T., Wakisaka-Saito, N., Hino, T., Suzuki-Migishima, R., Ogonuki, N., Miki, H., Kohda, T., Ogura, A., Yokoyama, M., Kaneko-Ishino, T., and Ishino, F. (2006). Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality. Nat. Genet. 38: 101–106.
88 Ono, R., Shiura, H., Aburatani, H., Kohda, T., Kaneko-Ishino, T., and Ishino, F. (2003). Identification of a large novel imprinted gene cluster on mouse proximal chromosome 6. Genome Res. 13: 1696–1705.
89 Ono, R., Yasuhiko, Y., Aisaki, K.I., Kitajima, S., Kanno, J., and Hirabayashi, Y. (2019). Exosome-mediated horizontal gene transfer occurs in double-strand break repair during genome editing. Commun. Biol. 2: 57.
90 Ono, R., Yoshioka, Y., Furukawa, Y., Naruse, M., Kuwagata, M., Ochiya, T., Kitajima, S., and Hirabayashi, Y. (2020). Novel hepatotoxicity biomarkers of extracellular vesicle (EV)-associated miRNAs induced by CCl4. Toxicol. Rep. 7: 685–692.
91 Ostertag, E.M., Prak, E.T., Deberardinis, R.J., Moran, J.V., and Kazazian, H.H.J.R. (2000). Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res. 28: 1418–1423.
92 Paggetti, J., Haderk, F., Seiffert, M., Janji, B., Distler, U., Ammerlaan, W., Kim, Y.J., Adam, J., Lichter, P., Solary, E., Berchem, G., and Moussay, E. (2015). Exosomes released by chronic lymphocytic leukemia cells induce the transition of stromal cells into cancer-associated fibroblasts. Blood 126: 1106–1117.
93 Pan, B.T. and Johnstone, R.M. (1983). Fate of the transferrin receptor during maturation of sheep reticulocytes in vitro: Selective externalization of the receptor. Cell 33: 967–978.
94 Pan, B.T., Teng, K., Wu, C., Adam, M., and Johnstone, R.M. (1985). Electron microscopic evidence for externalization of the transferrin receptor in vesicular form in sheep reticulocytes. J. Cell Biol. 101: 942–948.
95 Pegtel, D.M., Cosmopoulos, K., Thorley-Lawson, D.A., Van Eijndhoven, M.A., Hopmans, E.S., Lindenberg, J.L., De Gruijl, T.D., Wurdinger, T., and Middeldorp, J.M. (2010). Functional delivery of viral miRNAs via exosomes. Proc. Natl. Acad. Sci. USA 107: 6328–6333.
96 Peinado, H., Aleckovic, M., Lavotshkin, S., Matei, I., Costa-Silva, B., Moreno-Bueno, G., Hergueta-Redondo, M., Williams, C., Garcia-Santos, G., Ghajar, C., Nitadori-Hoshino, A., Hoffman, C., Badal, K., Garcia, B.A., Callahan, M.K., Yuan, J., Martins, V.R., Skog, J., Kaplan, R.N., Brady, M.S., Wolchok, J.D., Chapman, P.B., Kang, Y., Bromberg, J., and Lyden, D. (2012). Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET. Nat. Med. 18: 883–891.
97 Pu, C., Huang, H., Wang, Z., Zou, W., Lv, Y., Zhou, Z., Zhang, Q., Qiao, L., Wu, F., and Shao, S. (2018). Extracellular vesicle-associated miR-21 and miR-144 are markedly elevated in serum of patients with hepatocellular carcinoma. Front. Physiol. 9: 930.
98 Que, R., Ding, G., Chen, J., and Cao, L. (2013). Analysis of serum exosomal microRNAs and clinicopathologic features of patients with pancreatic adenocarcinoma. World J. Surg. Oncol. 11: 219.
99 Rabinowits, G., Gercel-Taylor, C., Day, J.M., Taylor, D.D., and Kloecker, G.H. (2009). Exosomal microRNA: A diagnostic marker for lung cancer. Clin. Lung. Cancer 10: 42–46.
100 Raimondo, F., Morosi, L., Corbetta, S., Chinello, C., Brambilla, P., Della Mina, P., Villa, A., Albo, G., Battaglia, C., Bosari, S., Magni, F., and Pitto, M. (2013). Differential protein profiling of renal cell carcinoma urinary exosomes. Mol. Biosyst. 9: 1220–1233.
101 Rasanen, K. and Vaheri, A. (2010). Activation of fibroblasts in cancer stroma. Exp. Cell Res. 316: 2713–2722.
102 Rodriguez, M., Silva, J., Lopez-Alfonso, A., Lopez-Muniz, M.B., Pena, C., Dominguez, G., Garcia, J.M., Lopez-Gonzalez, A., Mendez, M., Provencio, M., Garcia, V., and Bonilla, F. (2014). Different exosome cargo from plasma/bronchoalveolar lavage in non-small-cell lung cancer. Genes. Chromosomes Cancer 53: 713–724.
103 Sandfeld-Paulsen, B., Jakobsen, K.R., Baek, R., Folkersen, B.H., Rasmussen, T.R., Meldgaard, P., Varming, K., Jorgensen, M.M., and Sorensen, B.S. (2016). Exosomal proteins as diagnostic biomarkers in lung cancer. J. Thorac. Oncol. 11: 1701–1710.
104 Sato, S., Vasaikar, S., Eskaros, A., Kim, Y., Lewis, J.S., Zhang, B., Zijlstra, A., and Weaver, A.M. (2019). EPHB2 carried on small extracellular vesicles induces tumor angiogenesis via activation of ephrin reverse signaling. JCI Insight 4.
105 Sekita, Y., Wagatsuma, H., Nakamura, K., Ono, R., Kagami, M., Wakisaka, N., Hino, T., Suzuki-Migishima, R., Kohda, T., Ogura, A., Ogata, T., Yokoyama, M., Kaneko-Ishino, T., and Ishino, F. (2008). Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta. Nat. Genet. 40: 243–248.
106 Shan, T., Chen, S., Chen, X., Lin, W.R., Li, W., Ma, J., Wu, T., Ji, H., Li, Y., Cui, X., and Kang, Y. (2017). Prometastatic mechanisms of CAF-mediated EMT regulation in pancreatic cancer cells. Int. J. Oncol. 50: 121–128.
107 Sharma, P. and Allison, J.P. (2015). The future of immune checkpoint therapy. Science 348: 56–61.
108 Shiga, K., Hara, M., Nagasaki, T., Sato, T., Takahashi, H., and Takeyama, H. (2015). Cancer-associated fibroblasts: Their characteristics and their roles in tumor growth. Cancers (Basel) 7: 2443–2458.
109 Shiino, S., Matsuzaki, J., Shimomura, A., Kawauchi, J., Takizawa, S., Sakamoto, H., Aoki, Y., Yoshida, M., Tamura, K., Kato, K., Kinoshita, T., Kitagawa, Y., and Ochiya, T. (2019). Serum miRNA-based prediction of axillary lymph node metastasis in breast cancer. Clin. Cancer Res. 25: 1817–1827.
110 Shimomura, A., Shiino, S., Kawauchi, J., Takizawa, S., Sakamoto, H., Matsuzaki, J., Ono, M., Takeshita, F., Niida, S., Shimizu, C., Fujiwara, Y., Kinoshita, T., Tamura, K., and Ochiya, T. (2016). Novel combination of serum microRNA for detecting breast cancer in the early stage. Cancer Sci. 107: 326–334.
111 Simons, M. and Raposo, G. (2009). Exosomes–vesicular carriers for intercellular communication. Curr. Opin. Cell Biol. 21: 575–581.
112 Skog, J., Wurdinger, T., Rijn, V.A.N., Meijer, S., Gainche, D.H., Sena-Esteves, L., Curry, W.T., Jr., Carter, B.S., Krichevsky, A.M., and Breakefield, X.O. (2008). Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat. Cell Biol. 10: 1470–1476.
113 Srivastava, A., Moxley, K., Ruskin, R., Dhanasekaran, D.N., Zhao, Y.D., and Ramesh, R. (2018). A non-invasive liquid biopsy screening of urine-derived exosomes for miRNAs as biomarkers in endometrial cancer patients. AAPS J. 20: 82.
114 Sruthi, T.V., Edatt, L., Raji, G.R., Kunhiraman, H., Shankar, S.S., Shankar, V., Ramachandran, V., Poyyakkara, A., and Kumar, S.V.B. (2018). Horizontal transfer of miR-23a from hypoxic tumor cell colonies can induce angiogenesis. J. Cell Physiol. 233: 3498–3514.
115 Subra, C., Grand, D., Laulagnier, K., Stella, A., Lambeau, G., Paillasse, M., De Medina, P., Monsarrat, B., Perret, B., Silvente-Poirot, S., Poirot, M., and Record, M. (2010). Exosomes account for vesicle-mediated transcellular transport of activatable phospholipases and prostaglandins. J. Lipid. Res. 51: 2105–2120.
116 Sun, B., Li, Y., Zhou, Y., Ng, T.K., Zhao, C., Gan, Q., Gu, X., and Xiang, J. (2019). Circulating exosomal CPNE3 as a diagnostic and prognostic biomarker for colorectal cancer. J. Cell. Physiol. 234: 1416–1425.
117 Taylor, D.D. and Gercel-Taylor, C. (2008). MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecol. Oncol. 110: 13–21.
118 Thery, C., Witwer, K.W., Aikawa, E., Alcaraz, M.J., Anderson, J.D., Andriantsitohaina, R., Antoniou, A., Arab, T., Archer, F., Atkin-Smith, G.K., Ayre, D.C., Bach, J.M., Bachurski, D., Baharvand, H., Balaj, L., Baldacchino, S., Bauer, N.N., Baxter, A.A., Bebawy, M., Beckham, C., Bedina Zavec, A., Benmoussa, A., Berardi, A.C., Bergese, P., Bielska, E., Blenkiron, C., Bobis-Wozowicz, S., Boilard, E., Boireau, W., Bongiovanni, A., Borras, F.E., Bosch, S., Boulanger, C.M., Breakefield, X., Breglio, A.M., Brennan, M.A., Brigstock, D.R., Brisson, A., Broekman, M.L., Bromberg, J.F., Bryl-Gorecka, P., Buch, S., Buck, A.H., Burger, D., Busatto, S., Buschmann, D., Bussolati, B., Buzas, E.I., Byrd, J.B., Camussi, G., Carter, D.R., Caruso, S., Chamley, L.W., Chang, Y.T., Chen, C., Chen, S., Cheng, L., Chin, A.R., Clayton, A., Clerici, S.P., Cocks, A., Cocucci, E., Coffey, R.J., Cordeiro da Silva, A., Couch, Y., Coumans, F.A., Coyle, B., Crescitelli, R., Criado, M.F., D’Souza-Schorey, C., Das, S., Datta Chaudhuri, A., De Candia, P., De Santana, E.F., De Wever, O., Del Portillo, H.A., Demaret, T., Deville, S., Devitt, A., Dhondt, B., Di Vizio, D., Dieterich, L.C., Dolo, V., Dominguez Rubio, A.P., Dominici, M., Dourado, M.R., Driedonks, T.A., Duarte, F.V., Duncan, H.M., Eichenberger, R.M., Ekstrom, K., El Andaloussi, S., Elie-Caille, C., Erdbrugger, U., Falcon-Perez, J.M., Fatima, F., Fish, J.E., Flores-Bellver, M., Forsonits, A., Frelet-Barrand, A. et al. (2018). Minimal information for studies of extracellular vesicles 2018 (MISEV2018): A position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J. Extracell Vesicles 7: 1535750.
119 Thery, C., Zitvogel, L., and Amigorena, S. (2002). Exosomes: Composition, biogenesis and function. Nat. Rev. Immunol. 2: 569–579.
120 Tian, Y., Ma, L., Gong, M., Su, G., Zhu, S., Zhang, W., Wang, S., Li, Z., Chen, C., Li, L., Wu, L., and Yan, X. (2018). Protein profiling and sizing of extracellular vesicles from colorectal cancer patients via flow cytometry. ACS Nano 12: 671–680.
121 Tommelein, J., Verset, L., Boterberg, T., Demetter, P., Bracke, M., and De Wever, O. (2015). Cancer-associated fibroblasts connect metastasis-promoting communication in colorectal cancer. Front. Oncol. 5: 63.
122 Topalian, S.L. (2017). Targeting immune checkpoints in cancer therapy. JAMA 318: 1647–1648.
123 Topalian, S.L., Drake, C.G., and Pardoll, D.M. (2015). Immune checkpoint blockade: A common denominator approach to cancer therapy. Cancer Cell 27: 450–461.
124 Ueda, K., Ishikawa, N., Tatsuguchi, A., Saichi, N., Fujii, R., and Nakagawa, H. (2014). Antibody-coupled monolithic silica microtips for highthroughput molecular profiling of circulating exosomes. Sci. Rep. 4: 6232.
125 Urabe, F., Kosaka, N., Yoshioka, Y., Egawa, S., and Ochiya, T. (2017). The small vesicular culprits: The investigation of extracellular vesicles as new targets for cancer treatment. Clin. Transl. Med. 6: 45.
126 Usuba, W., Urabe, F., Yamamoto, Y., Matsuzaki, J., Sasaki, H., Ichikawa, M., Takizawa, S., Aoki, Y., Niida, S., Kato, K., Egawa, S., Chikaraishi, T., Fujimoto, H., and Ochiya, T. (2019). Circulating miRNA panels for specific and early detection in bladder cancer. Cancer Sci. 110: 408–419.
127 Vaidyanathan, K. and Vasudevan, D.M. (2012). Organ specific tumor markers: What’s new? Indian J. Clin. Biochem. 27: 110–120.
128 Valadi, H., Ekstrom, K., Bossios, A., Sjostrand, M., Lee, J.J., and Lotvall, J.O. (2007). Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat. Cell Biol. 9: 654–659.
129 van der Pol, E., Boing, A.N., Harrison, P., Sturk, A., and Nieuwland, R. (2012). Classification, functions, and clinical relevance of extracellular vesicles. Pharmacol. Rev. 64: 676–705.
130 Villarroya-Beltri, C., Gutierrez-Vazquez, C., Sanchez-Cabo, F., Perez-Hernandez, D., Vazquez, J., Martin-Cofreces, N., Martinez-Herrera, D.J., Pascual-Montano, A., Mittelbrunn, M., and Sanchez-Madrid, F. (2013). Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat. Commun. 4: 2980.
131 Wang, H., Yang, H., Shivalila, C.S., Dawlaty, M.M., Cheng, A.W., Zhang, F., and Jaenisch, R. (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153: 910–918.
132 Wang, J., De Veirman, K., Faict, S., Frassanito, M.A., Ribatti, D., Vacca, A., and Menu, E. (2016). Multiple myeloma exosomes establish a favourable bone marrow microenvironment with enhanced angiogenesis and immunosuppression. J. Pathol. 239: 162–173.
133 Watson, C.N., Belli, A., and Pietro, D.I. (2019). Small non-coding RNAs: New class of biomarkers and potential therapeutic targets in neurodegenerative disease. Front. Genet. 10: 364.
134 Welslau, M., Dieras, V., Sohn, J.H., Hurvitz, S.A., Lalla, D., Fang, L., Althaus, B., Guardino, E., and Miles, D. (2014). Patient-reported outcomes from EMILIA, a randomized phase 3 study of trastuzumab emtansine (T-DM1) versus capecitabine and lapatinib in human epidermal growth factor receptor 2-positive locally advanced or metastatic breast cancer. Cancer 120: 642–651.
135 Witwer, K.W., Buzas, E.I., Bemis, L.T., Bora, A., Lasser, C., Lotvall, J., Nolte-’t Hoen, E.N., Piper, M.G., Sivaraman, S., Skog, J., Thery, C., Wauben, M.H., and Hochberg, F. (2013). Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. J. Extracell. Vesicles 2.
136 Witwer, K.W., Soekmadji, C., Hill, A.F., Wauben, M.H., Buzas, E.I., Di Vizio, D., Falcon-Perez, J.M., Gardiner, C., Hochberg, F., Kurochkin, I.V., Lotvall, J., Mathivanan, S., Nieuwland, R., Sahoo, S., Tahara, H., Torrecilhas, A.C., Weaver, A.M., Yin, H., Zheng, L., Gho, Y.S., Quesenberry, P., and Thery, C. (2017). Updating the MISEV minimal requirements for extracellular vesicle studies: Building bridges to reproducibility. J Extracell Vesicles 6: 1396823.
137 Xouri, G. and Christian, S. (2010). Origin and function of tumor stroma fibroblasts. Semin. Cell Dev. Biol. 21: 40–46.
138 Yan, S., Jiang, Y., Liang, C., Cheng, M., Jin, C., Duan, Q., Xu, D., Yang, L., Zhang, X., Ren, B., and Jin, P. (2018). Exosomal miR-6803-5p as potential diagnostic and prognostic marker in colorectal cancer. J. Cell Biochem. 119: 4113–4119.
139 Yanez-Mo, M., Siljander, P.R., Andreu, Z., Zavec, A.B., Borras, F.E., Buzas, E.I., Buzas, K., Casal, E., Cappello, F., Carvalho, J., Colas, E., Cordeiro da Silva, A., Fais, S., Falcon-Perez, J.M., Ghobrial, I.M., Giebel, B., Gimona, M., Graner, M., Gursel, I., Gursel, M., Heegaard, N.H., Hendrix, A., Kierulf, P., Kokubun, K., Kosanovic, M., Kralj-Iglic, V., Kramer-Albers, E.M., Laitinen, S., Lasser, C., Lener, T., Ligeti, E., Line, A., Lipps, G., Llorente, A., Lotvall, J., Mancek-Keber, M., Marcilla, A., Mittelbrunn, M., Nazarenko, I., Nolte-’t Hoen, E.N., Nyman, T.A., O’Driscoll, L., Olivan, M., Oliveira, C., Pallinger, E., Del Portillo, H.A., Reventos, J., Rigau, M., Rohde, E., Sammar, M., Sanchez-Madrid, F., Santarem, N., Schallmoser, K., Ostenfeld, M.S., Stoorvogel, W., Stukelj, R., Van Der Grein, S.G., Vasconcelos, M.H., Wauben, M.H., and De Wever, O. (2015). Biological properties of extracellular vesicles and their physiological functions. J. Extracell. Vesicles. 4: 27066.
140 Yao, B., Qu, S., Hu, R., Gao, W., Jin, S., Liu, M., and Zhao, Q. (2019). A panel of miRNAs derived from plasma extracellular vesicles as novel diagnostic biomarkers of lung adenocarcinoma. FEBS Open. Bio. 9: 2149–2158.
141 Yi, R., Qin, Y., Macara, I.G., and Cullen, B.R. (2003). Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes. Dev. 17: 3011–3016.
142 Yokoi, A., Matsuzaki, J., Yamamoto, Y., Yoneoka, Y., Takahashi, K., Shimizu, H., Uehara, T., Ishikawa, M., Ikeda, S.I., Sonoda, T., Kawauchi, J., Takizawa, S., Aoki, Y., Niida, S., Sakamoto, H., Kato, K., Kato, T., and Ochiya, T. (2018). Integrated extracellular microRNA profiling for ovarian cancer screening. Nat. Commun. 9: 4319.
143 Yoshioka, Y., Kosaka, N., Konishi, Y., Ohta, H., Okamoto, H., Sonoda, H., Nonaka, R., Yamamoto, H., Ishii, H., Mori, M., Furuta, K., Nakajima, T., Hayashi, H., Sugisaki, H., Higashimoto, H., Kato, T., Takeshita, F., and Ochiya, T. (2014). Ultra-sensitive liquid biopsy of circulating extracellular vesicles using ExoScreen. Nat. Commun. 5: 3591.
144 You, Y., Shan, Y., Chen, J., Yue, H., You, B., Shi, S., Li, X., and Cao, X. (2015). Matrix metalloproteinase 13-containing exosomes promote nasopharyngeal carcinoma metastasis. Cancer Sci. 106: 1669–1677.
145 Yu, Y., Xiao, C.H., Tan, L.D., Wang, Q.S., Li, X.Q., and Feng, Y.M. (2014). Cancer-associated fibroblasts induce epithelial-mesenchymal transition of breast cancer cells through paracrine TGF-beta signalling. Br. J. Cancer 110: 724–732.
146 Zeng, Y. and Cullen, B.R. (2004). Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res. 32: 4776–4785.
147 Zhang, H. (2016). Three generations of epidermal growth factor receptor tyrosine kinase inhibitors developed to revolutionize the therapy of lung cancer. Drug. Des. Devel. Ther. 10: 3867–3872.
148 Zhou, C.F., Ma, J., Huang, L., Yi, H.Y., Zhang, Y.M., Wu, X.G., Yan, R.M., Liang, L., Zhong, M., Yu, Y.H., Wu, S., and Wang, W. (2019). Cervical squamous cell carcinoma-secreted exosomal miR-221-3p promotes lymphangiogenesis and lymphatic metastasis by targeting VASH1. Oncogene 38: 1256–1268.
149 Zhuang, J., Lu, Q., Shen, B., Huang, X., Shen, L., Zheng, X., Huang, R., Yan, J., and Guo, H. (2015). TGFbeta1 secreted by cancer-associated fibroblasts induces epithelial-mesenchymal transition of bladder cancer cells through lncRNA-ZEB2NAT. Sci. Rep. 5: 11924.
