메뉴 건너뛰기




Volumn 12, Issue 8, 2015, Pages 810-823

Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells – Evidence of unique microRNA cargos

Author keywords

Cancer; Extracellular RNA; Malignant melanoma; Membrane vesicles; Next generation sequencing; Non coding RNA

Indexed keywords

MICRORNA; MICRORNA 155 5P; MICRORNA 199A 3P; MICRORNA 214 3P; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA; MIRN15 MICRORNA, HUMAN; MIRN199 MICRORNA, HUMAN; MIRN214 MICRORNA, HUMAN; SMALL UNTRANSLATED RNA;

EID: 84944445453     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.1080/15476286.2015.1056975     Document Type: Article
Times cited : (156)

References (63)
  • 3
    • 33847220364 scopus 로고    scopus 로고
    • Melanoma biology and new targeted therapy
    • PMID:17314971
    • Gray-Schopfer V, Wellbrock C, Marais R. Melanoma biology and new targeted therapy. Nature 2007; 445:851-7; PMID:17314971; http://dx.doi.org/10.1038/nature05661
    • (2007) Nature , vol.445 , pp. 851-857
    • Gray-Schopfer, V.1    Wellbrock, C.2    Marais, R.3
  • 4
    • 79960984966 scopus 로고    scopus 로고
    • Tumorderived exosomes confer antigen-specific immunosuppression in a murine delayed-type hypersensitivity model
    • PMID:21829629
    • Yang C, Kim SH, Bianco NR, Robbins PD. Tumorderived exosomes confer antigen-specific immunosuppression in a murine delayed-type hypersensitivity model. PloS One 2011; 6:e22517; PMID:21829629; http://dx.doi.org/10.1371/journal.pone.0022517
    • (2011) PloS One , vol.6
    • Yang, C.1    Kim, S.H.2    Bianco, N.R.3    Robbins, P.D.4
  • 5
    • 84896818399 scopus 로고    scopus 로고
    • Regulation of immune responses by extracellular vesicles
    • PMID:24566916
    • Robbins PD, Morelli AE. Regulation of immune responses by extracellular vesicles. Nat Rev Immunol 2014; 14:195-208; PMID:24566916; http://dx.doi.org/10.1038/nri3622
    • (2014) Nat Rev Immunol , vol.14 , pp. 195-208
    • Robbins, P.D.1    Morelli, A.E.2
  • 8
    • 84895475039 scopus 로고    scopus 로고
    • Role of exosomes in myocardial remodeling
    • PMID:24436427
    • Waldenstrom A, Ronquist G. Role of exosomes in myocardial remodeling. Circ Res 2014; 114:315-24; PMID:24436427; http://dx.doi.org/10.1161/CIRCRESAHA.114.300584
    • (2014) Circ Res , vol.114 , pp. 315-324
    • Waldenstrom, A.1    Ronquist, G.2
  • 9
    • 34249302620 scopus 로고    scopus 로고
    • Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells
    • PMID:17486113
    • Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, Lotvall JO. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 2007; 9:654-9; PMID:17486113; http://dx.doi.org/10.1038/ncb1596
    • (2007) Nat Cell Biol , vol.9 , pp. 654-659
    • Valadi, H.1    Ekstrom, K.2    Bossios, A.3    Sjostrand, M.4    Lee, J.J.5    Lotvall, J.O.6
  • 10
    • 43049139913 scopus 로고    scopus 로고
    • Intercellular transfer of the oncogenic receptor EGFRvIII by microvesicles derived from tumour cells
    • PMID:18425114
    • Al-Nedawi K, Meehan B, Micallef J, Lhotak V, May L, Guha A, Rak J. Intercellular transfer of the oncogenic receptor EGFRvIII by microvesicles derived from tumour cells. Nature cell biology 2008; 10:619-24; PMID:18425114; http://dx.doi.org/10.1038/ncb1725
    • (2008) Nature cell biology , vol.10 , pp. 619-624
    • Al-Nedawi, K.1    Meehan, B.2    Micallef, J.3    Lhotak, V.4    May, L.5    Guha, A.6    Rak, J.7
  • 11
    • 84896772471 scopus 로고    scopus 로고
    • Dll4-containing exosomes induce capillary sprout retraction in a 3D microenvironment
    • PMID:24504253
    • Sharghi-Namini S, Tan E, Ong LL, Ge R, Asada HH. Dll4-containing exosomes induce capillary sprout retraction in a 3D microenvironment. Sci Rep 2014; 4:4031; PMID:24504253; http://dx.doi.org/10.1038/srep04031
    • (2014) Sci Rep , vol.4 , pp. 4031
    • Sharghi-Namini, S.1    Tan, E.2    Ong, L.L.3    Ge, R.4    Asada, H.H.5
  • 12
    • 84904385898 scopus 로고    scopus 로고
    • Renal tumor-derived exosomes inhibit hepaCAM expression of renal carcinoma cells in ap-AKT-dependent manner
    • PMID:24645843
    • Jiang XL, Zhang Y, Tan B, Luo CL, Wu XH. Renal tumor-derived exosomes inhibit hepaCAM expression of renal carcinoma cells in ap-AKT-dependent manner. Neoplasma 2014; 61:416-23; PMID:24645843; http://dx.doi.org/10.4149/neo_2014_051
    • (2014) Neoplasma , vol.61 , pp. 416-423
    • Jiang, X.L.1    Zhang, Y.2    Tan, B.3    Luo, C.L.4    Wu, X.H.5
  • 13
    • 84881102179 scopus 로고    scopus 로고
    • Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition
    • PMID:23645497
    • Tauro BJ, Mathias RA, Greening DW, Gopal SK, Ji H, Kapp EA, Coleman BM, Hill AF, Kusebauch U,Hallows JL, et al. Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition. Mol Cell Proteomics 2013; 12:2148-59; PMID:23645497; http://dx.doi.org/10.1074/mcp.M112.027086
    • (2013) Mol Cell Proteomics , vol.12 , pp. 2148-2159
    • Tauro, B.J.1    Mathias, R.A.2    Greening, D.W.3    Gopal, S.K.4    Ji, H.5    Kapp, E.A.6    Coleman, B.M.7    Hill, A.F.8    Kusebauch, U.9    Hallows, J.L.10
  • 17
    • 0347755643 scopus 로고    scopus 로고
    • The microRNA Registry
    • PMID:14681370
    • Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004:D109-11; PMID:14681370; http://dx.doi.org/10.1093/nar/gkh023
    • (2004) Nucleic Acids Res , pp. D109-D111
    • Griffiths-Jones, S.1
  • 18
    • 22144461002 scopus 로고    scopus 로고
    • miRNAs, cancer, and stem cell division
    • PMID:16009126
    • Croce CM, Calin GA. miRNAs, cancer, and stem cell division. Cell 2005; 122:6-7; PMID:16009126; http://dx.doi.org/10.1016/j.cell.2005.06.036
    • (2005) Cell , vol.122 , pp. 6-7
    • Croce, C.M.1    Calin, G.A.2
  • 19
    • 77955902024 scopus 로고    scopus 로고
    • The widespread regulation of microRNA biogenesis, function and decay
    • PMID:20661255
    • Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010; 11:597-610; PMID:20661255
    • (2010) Nat Rev Genet , vol.11 , pp. 597-610
    • Krol, J.1    Loedige, I.2    Filipowicz, W.3
  • 20
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • PMID:15211354
    • He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004; 5:522-31; PMID:15211354; http://dx.doi.org/10.1038/nrg1379
    • (2004) Nat Rev Genet , vol.5 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 22
    • 84870599244 scopus 로고    scopus 로고
    • Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion-infected neuronal cells
    • PMID:22965126
    • Bellingham SA, Coleman BM, Hill AF. Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion-infected neuronal cells. Nucleic Acids Res 2012; 40:10937-49; PMID:22965126; http://dx.doi.org/10.1093/nar/gks832
    • (2012) Nucleic Acids Res , vol.40 , pp. 10937-10949
    • Bellingham, S.A.1    Coleman, B.M.2    Hill, A.F.3
  • 23
    • 84867546396 scopus 로고    scopus 로고
    • Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions
    • PMID:22821563
    • Nolte-'t Hoen EN, Buermans HP, Waasdorp M, Stoorvogel W, Wauben MH, t Hoen PA. 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 2012; 40:9272-85; PMID:22821563; http://dx.doi.org/10.1093/nar/gks658
    • (2012) Nucleic Acids Res , vol.40 , pp. 9272-9285
    • Nolte-'t Hoen, E.N.1    Buermans, H.P.2    Waasdorp, M.3    Stoorvogel, W.4    Wauben, M.H.5    t Hoen, P.A.6
  • 24
    • 84902471813 scopus 로고    scopus 로고
    • Epstein-Barr virus-encoded small RNAs (EBERs) are present in fractions related to exosomes released by EBV-transformed cells
    • PMID:24896633
    • Ahmed W, Philip PS, Tariq S, Khan G. Epstein-Barr virus-encoded small RNAs (EBERs) are present in fractions related to exosomes released by EBV-transformed cells. PloS One 2014; 9:e99163; PMID:24896633; http://dx.doi.org/10.1371/journal.pone.0099163
    • (2014) PloS One , vol.9
    • Ahmed, W.1    Philip, P.S.2    Tariq, S.3    Khan, G.4
  • 26
    • 84925267233 scopus 로고    scopus 로고
    • EVpedia: A community web portal for extracellular vesicles research
    • PMID25388151
    • Kim DK, Lee J, Kim SR, Choi DS, Yoon YJ, Kim JH, et al. EVpedia: a community web portal for extracellular vesicles research. Bioinformatics 2015; 31(6); 933-9; PMID25388151; http://dx.doi.org/10.1093/bioinformatics/btu741
    • (2015) Bioinformatics , vol.31 , Issue.6 , pp. 933-939
    • Kim, D.K.1    Lee, J.2    Kim, S.R.3    Choi, D.S.4    Yoon, Y.J.5    Kim, J.H.6
  • 27
    • 84925267233 scopus 로고    scopus 로고
    • EVpedia: A community web portal for extracellular vesicles research
    • PMID 25388151
    • Kim DK, Lee J, Kim SR, Choi DS, Yoon YJ, Kim JH, et al. EVpedia: a community web portal for extracellular vesicles research. Bioinformatics 2015; 31(6): 933-9; PMID 25388151; http://dx.doi.org/10.1093/bioinformatics/btu741
    • (2015) Bioinformatics , vol.31 , Issue.6 , pp. 933-939
    • Kim, D.K.1    Lee, J.2    Kim, S.R.3    Choi, D.S.4    Yoon, Y.J.5    Kim, J.H.6
  • 28
    • 84924330606 scopus 로고    scopus 로고
    • A functional extracellular transcriptome in animals? implications for biology, disease and medicine
    • PMID:25723626
    • Tewari M. A functional extracellular transcriptome in animals? implications for biology, disease and medicine. Genome Biol 2015; 16:47; PMID:25723626; http://dx.doi.org/10.1186/s13059-015-0613-5
    • (2015) Genome Biol , vol.16 , pp. 47
    • Tewari, M.1
  • 30
    • 0345599951 scopus 로고    scopus 로고
    • Lipid raft-associated protein sorting in exosomes
    • PMID:12881314
    • de Gassart A, Geminard C, Fevrier B, Raposo G, Vidal M. Lipid raft-associated protein sorting in exosomes. Blood 2003; 102:4336-44; PMID:12881314; http://dx.doi.org/10.1182/blood-2003-03-0871
    • (2003) Blood , vol.102 , pp. 4336-4344
    • de Gassart, A.1    Geminard, C.2    Fevrier, B.3    Raposo, G.4    Vidal, M.5
  • 33
  • 37
    • 84883466769 scopus 로고    scopus 로고
    • The hypoxia-induciblemicroRNA cluster miR-199a approximately 214 targets myocardial PPARdelta and impairs mitochondrial fatty acid oxidation
    • PMID:24011070
    • el Azzouzi H, Leptidis S, Dirkx E, Hoeks J, van Bree B, Brand K, McClellan EA, Poels E, Sluimer JC, van den HoogenhofMM, et al. The hypoxia-induciblemicroRNA cluster miR-199a approximately 214 targets myocardial PPARdelta and impairs mitochondrial fatty acid oxidation. Cell Metab 2013; 18:341-54; PMID:24011070; http://dx.doi.org/10.1016/j.cmet.2013.08.009
    • (2013) Cell Metab , vol.18 , pp. 341-354
    • el Azzouzi, H.1    Leptidis, S.2    Dirkx, E.3    Hoeks, J.4    van Bree, B.5    Brand, K.6    McClellan, E.A.7    Poels, E.8    Sluimer, J.C.9    van den Hoogenhof, M.M.10
  • 38
    • 84866057221 scopus 로고    scopus 로고
    • Let-7b and microRNA-199a inhibit the proliferation of B16F10 melanoma cells
    • PMID:23162627
    • Xu D, Tan J, Zhou M, Jiang B, Xie H, Nie X, Xia K, Zhou J. Let-7b and microRNA-199a inhibit the proliferation of B16F10 melanoma cells. Oncol Lett 2012; 4:941-6; PMID:23162627
    • (2012) Oncol Lett , vol.4 , pp. 941-946
    • Xu, D.1    Tan, J.2    Zhou, M.3    Jiang, B.4    Xie, H.5    Nie, X.6    Xia, K.7    Zhou, J.8
  • 39
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • PMID:19131956
    • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44-57; PMID:19131956; http://dx.doi.org/10.1038/nprot.2008.211
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 40
    • 84872353504 scopus 로고    scopus 로고
    • Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases, and benign melanocytic nevi
    • PMID:23111773
    • Sand M, Skrygan M, Sand D, Georgas D, Gambichler T, Hahn SA, Altmeyer P, Bechara FG. Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases, and benign melanocytic nevi. Cell Tissue Res 2013; 351:85-98; PMID:23111773; http://dx.doi.org/10.1007/s00441-012-1514-5
    • (2013) Cell Tissue Res , vol.351 , pp. 85-98
    • Sand, M.1    Skrygan, M.2    Sand, D.3    Georgas, D.4    Gambichler, T.5    Hahn, S.A.6    Altmeyer, P.7    Bechara, F.G.8
  • 41
    • 80053309537 scopus 로고    scopus 로고
    • Intercellular nanovesicle-mediated microRNA transfer: A mechanism of environmental modulation of hepatocellular cancer cell growth
    • PMID:21721029
    • Kogure T, Lin WL, Yan IK, Braconi C, Patel T. Intercellular nanovesicle-mediated microRNA transfer: a mechanism of environmental modulation of hepatocellular cancer cell growth. Hepatology 2011; 54:1237-48; PMID:21721029; http://dx.doi.org/10.1002/hep.24504
    • (2011) Hepatology , vol.54 , pp. 1237-1248
    • Kogure, T.1    Lin, W.L.2    Yan, I.K.3    Braconi, C.4    Patel, T.5
  • 43
    • 84907915122 scopus 로고    scopus 로고
    • Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer
    • PMID:25116943
    • White NM, Cabanski CR, Silva-Fisher JM, Dang HX, Govindan R, Maher CA. Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. Genome Biol 2014; 15:429; PMID:25116943; http://dx.doi.org/10.1186/s13059-014-0429-8
    • (2014) Genome Biol , vol.15 , pp. 429
    • White, N.M.1    Cabanski, C.R.2    Silva-Fisher, J.M.3    Dang, H.X.4    Govindan, R.5    Maher, C.A.6
  • 44
    • 79957578583 scopus 로고    scopus 로고
    • Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
    • PMID:21356093
    • McCormick KP, Willmann MR, Meyers BC. Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence 2011; 2:2; PMID:21356093; http://dx.doi.org/10.1186/1758-907X-2-2
    • (2011) Silence , vol.2 , pp. 2
    • McCormick, K.P.1    Willmann, M.R.2    Meyers, B.C.3
  • 45
    • 43649087713 scopus 로고    scopus 로고
    • Micro-RNAs associated with metastasis in uveal melanoma identified by multiplexed microarray profiling
    • PMID:18477892
    • Worley LA, Long MD, Onken MD, Harbour JW. Micro-RNAs associated with metastasis in uveal melanoma identified by multiplexed microarray profiling. Melanoma Res 2008; 18:184-90; PMID:18477892; http://dx.doi.org/10.1097/CMR.0b013e3282feeac6
    • (2008) Melanoma Res , vol.18 , pp. 184-190
    • Worley, L.A.1    Long, M.D.2    Onken, M.D.3    Harbour, J.W.4
  • 49
    • 79956069781 scopus 로고    scopus 로고
    • Searching for the 'melano-miRs': MiR-214 drives melanoma metastasis
    • PMID:21593728
    • Bar-Eli M. Searching for the 'melano-miRs': miR-214 drives melanoma metastasis. EMBO J 2011; 30:1880-1; PMID:21593728; http://dx.doi.org/10.1038/emboj.2011.132
    • (2011) EMBO J , vol.30 , pp. 1880-1881
    • Bar-Eli, M.1
  • 53
    • 84924534612 scopus 로고    scopus 로고
    • MicroRNA regulation of tumorigenesis, cancer progression and interpatient heterogeneity: Towards clinical use
    • PMID:25315999
    • Nana-Sinkam S, Croce CM. MicroRNA regulation of tumorigenesis, cancer progression and interpatient heterogeneity: towards clinical use. Genome Biol 2014; 15:445; PMID:25315999; http://dx.doi.org/10.1186/s13059-014-0445-8
    • (2014) Genome Biol , vol.15 , pp. 445
    • Nana-Sinkam, S.1    Croce, C.M.2
  • 54
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • PMID:21278185
    • Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27:863-4; PMID:21278185; http://dx.doi.org/10.1093/bioinformatics/btr026
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 58
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq - A Python framework to work with high-throughput sequencing data
    • PMID 25260700
    • Anders S, Pyl PT, Huber W: HTSeq - A Python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31:166; PMID 25260700; http://dx.doi.org/10.1093/bioinformatics/btu638
    • (2015) Bioinformatics , vol.31 , pp. 166
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 60
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
    • PMID:25516281
    • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol 2014; 15:550; PMID:25516281; http://dx.doi.org/10.1186/s13059-014-0550-8
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 61
    • 71549122588 scopus 로고    scopus 로고
    • Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells
    • PMID:19930720
    • Hong BS, Cho JH, Kim H, Choi EJ, Rho S, Kim J, Kim JH, Choi DS, Kim YK, Hwang D, et al. Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells. BMC Genomics 2009; 10:556; PMID:19930720; http://dx.doi.org/10.1186/1471-2164-10-556
    • (2009) BMC Genomics , vol.10 , pp. 556
    • Hong, B.S.1    Cho, J.H.2    Kim, H.3    Choi, E.J.4    Rho, S.5    Kim, J.6    Kim, J.H.7    Choi, D.S.8    Kim, Y.K.9    Hwang, D.10
  • 62
    • 84863076731 scopus 로고    scopus 로고
    • The protein interaction network of extracellular vesicles derived from human colorectal cancer cells
    • PMID:22149170
    • Choi DS, Yang JS, Choi EJ, Jang SC, Park S, Kim OY, Hwang D, Kim KP, Kim YK, Kim S, et al. The protein interaction network of extracellular vesicles derived from human colorectal cancer cells. J Proteome Res 2012; 11:1144-51; PMID:22149170; http://dx.doi.org/10.1021/pr200842h
    • (2012) J Proteome Res , vol.11 , pp. 1144-1151
    • Choi, D.S.1    Yang, J.S.2    Choi, E.J.3    Jang, S.C.4    Park, S.5    Kim, O.Y.6    Hwang, D.7    Kim, K.P.8    Kim, Y.K.9    Kim, S.10
  • 63
    • 44149083586 scopus 로고    scopus 로고
    • miRDB: A microRNA target prediction and functional annotation database with a wiki interface
    • PMID:18426918
    • Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. Rna 2008; 14:1012-7; PMID:18426918; http://dx.doi.org/10.1261/rna.965408
    • (2008) Rna , vol.14 , pp. 1012-1017
    • Wang, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.