Diverse human extracellular RNAs are widely detected in human plasma

Nature Communications

Volumn 7, Issue , 2016, Pages

  Freedman, Jane E ^a   Gerstein, Mark ^b   Mick, Eric ^a   Rozowsky, Joel ^b   Levy, Daniel ^c,d   Kitchen, Robert ^b   Das, Saumya ^e   Shah, Ravi ^e   Danielson, Kirsty ^e   Beaulieu, Lea ^a   Navarro, Fabio C P ^b   Wang, Yaoyu ^f   Galeev, Timur R ^b   Holman, Alex ^f   Kwong, Raymond Y ^g   Murthy, Venkatesh ^h   Tanriverdi, Selim E ^a   Koupenova Zamor, Milka ^a   Mikhalev, Ekaterina ^a   Tanriverdi, Kahraman ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c FRAMINGHAM HEART STUDY   (United States)

^d NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^e BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^f DANA FARBER CANCER INSTITUTE   (United States)

^g BRIGHAM AND WOMEN S HOSPITAL   (United States)

^h UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PIWI INTERACTING RNA; SMALL NUCLEOLAR RNA; SMALL INTERFERING RNA;

BIOINFORMATICS; BLOOD; GENE EXPRESSION; GENETIC ANALYSIS; POLYMERASE CHAIN REACTION; PROTEIN;

AGED; ARTICLE; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; HEMOLYSIS; HUMAN; MALE; PHENOTYPE; PLASMA; POLYMERASE CHAIN REACTION; QUANTITATIVE POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; BLOOD; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; LONGITUDINAL STUDY; MIDDLE AGED; MOLECULAR GENETICS; REAL TIME POLYMERASE CHAIN REACTION; UNITED STATES;

AGED; FEMALE; GENE EXPRESSION REGULATION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LONGITUDINAL STUDIES; MALE; MICRORNAS; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; REAL-TIME POLYMERASE CHAIN REACTION; RNA, SMALL INTERFERING; RNA, SMALL NUCLEOLAR; UNITED STATES;

EID: 84964927994     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms11106     Document Type: Article

References (48)

1. Ambros, V. MicroRNAs: tiny regulators with great potential. Cell 107, 823-826 (2001).
2. Mitchell, P. S. et al. Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Natl Acad. Sci. USA 105, 10513-10518 (2008).
3. Argyropoulos, C. et al. Urinary microRNA profiling in the nephropathy of type 1 diabetes. PloS ONE 8, e54662 (2013).
4. Laterza, O. F. et al. Plasma microRNAs as sensitive and specific biomarkers of tissue injury. Clin. Chem. 55, 1977-1983 (2009).
5. Cheng, Y. et al. A translational study of circulating cell-free microRNA-1 in acute myocardial infarction. Clin. Sci. (Lond.) 119, 87-95 (2010).
6. Calin, G. A. et al. A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N. Engl. J. Med. 353, 1793-1801 (2005).
7. Lee, L. W. et al. Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA. 16, 2170-2180 (2010).
8. Wang, K. et al. The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PloS ONE 7, e51009 (2012).
9. Bahn, J. H. et al. The landscape of microRNA, piwi-interacting RNA, and circular RNA in human saliva. Clin. Chem. 61, 221-230 (2015).
10. Cheng, L., Sharples, R. A., Scicluna, B. J. & Hill, A. F. Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood. J. Extracell. Vesicles 3 (2014).
11. Zheng, G. et al. Serum microRNA panel as biomarkers for early diagnosis of colorectal adenocarcinoma. Br. J. Cancer 111, 1985-1992 (2014).
12. Blondal, T. et al. Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods 59, S1-S6 (2012).
13. Ruby, J. G. et al. Large-scale sequencing reveals 21u-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193-1207 (2006).
14. Huang, X. et al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics 14, 319 (2013).
15. Freedman, J. E. et al. Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham Heart Study. Circulation 122, 119-129 (2010).
16. Huan, T. et al. Dissecting the roles of microRNAs in coronary heart disease via integrative genomic analyses. Arterioscler. Thromb. Vasc. Biol. 35, 1011-1021 (2015).
17. Wong, N. & Wang, X. Mirdb: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 43, D146-D152 (2015).
18. Kanehisa, M. & Goto, S. Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000).
19. Carrington, J. C. & Ambros, V. Role of microRNAs in plant and animal development. Science 301, 336-338 (2003).
20. Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818 (2003).
21. Ambros, V. MicroRNAs and developmental timing. Curr. Opin. Genet. Dev. 21, 511-517 (2011).
22. Ambros, V. The functions of animal microRNAs. Nature 431, 350-355 (2004).
23. Ambros, V. The evolution of our thinking about microRNAs. Nat. Med. 14, 1036-1040 (2008).
24. Freedman, J. E., Vitseva, O. & Tanriverdi, K. The role of the blood transcriptome in innate inflammation and stroke. Ann. NY Acad. Sci. 1207, 41-45 (2010).
25. Wang, K. et al. Comparing the microRNA spectrum between serum and plasma. PLoS ONE 7, e41561 (2012).
26. Weber, J. A. et al. The microRNA spectrum in 12 body fluids. Clin. Chem. 56, 1733-1741 (2010).
27. McManus, D. D. & Ambros, V. Circulating microRNAs in cardiovascular disease. Circulation 124, 1908-1910 (2011).
28. Diehl, P. et al. Microparticles: major transport vehicles for distinct microRNAs in circulation. Cardiovasc. Res. 93, 633-644 (2012).
29. Small, E. M. & Olson, E. N. Pervasive roles of microRNAs in cardiovascular biology. Nature 469, 336-342 (2011).
30. Freedman, J. E. A platelet transcriptome revolution. Blood 118, 3760-3761 (2011).
31. Duttagupta, R., Jiang, R., Gollub, J., Getts, R. C. & Jones, K. W. Impact of cellular miRNAs on circulating miRNA biomarker signatures. PLoS ONE 6, e20769 (2011).
32. Risitano, A., Beaulieu, L. M., Vitseva, O. & Freedman, J. E. Platelets and platelet-like particles mediate intercellular RNA transfer. Blood 119, 6288-6295 (2012).
33. Zhang, H. et al. Investigation of microRNA expression in human serum during the aging process. J. Gerontol. A Biol. Sci. Med. Sci. 70, 102-109 (2015).
34. Keam, S. P. et al. The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res. 42, 8984-8995 (2014).
35. Spornraft, M., Kirchner, B., Pfaffl, M. W. & Riedmaier, I. Comparison of the mirnome and pirnome of bovine blood and plasma by small RNA sequencing. Biotechnol. Lett. 37, 1165-1176 (2015).
36. Liao, J. et al. Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol. Cancer 9, 198 (2010).
37. Ronchetti, D. et al. The expression pattern of small nucleolar and small cajal body-specific RNAs characterizes distinct molecular subtypes of multiple myeloma. Blood Cancer J. 2, e96 (2012).
38. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
39. Hackenberg, M., Rodriguez-Ezpeleta, N. & Aransay, A. M. Miranalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res. 39, W132-W138 (2011).
40. Hackenberg, M., Sturm, M., Langenberger, D., Falcon-Perez, J. M. & Aransay, A. M. Miranalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 37, W68-W76 (2009).
41. Kozomara, A. & Griffiths-Jones, S. Mirbase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157 (2011).
42. Lorenz, R. et al. ViennaRNA package 2.0. Algorithms Mol. Biol. 6, 26 (2011).
43. Chan, P. P. & Lowe, T. M. GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37, D93-D97 (2009).
44. Pang, K. C. et al. Rnadb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res. 35, D178-D182 (2007).
45. Lestrade, L. & Weber, M. J. SnoRNA-lbme-db, a comprehensive database of human h/aca and c/d box snoRNAs. Nucleic Acids Res. 34, D158-D162 (2006).
46. Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41, D226-D232 (2013).
47. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. Edger: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
48. Hanson, M. S. et al. Phosphodiesterase 3 is present in rabbit and human erythrocytes and its inhibition potentiates iloprost-induced increases in camp. Am. J. Physiol. Heart Circ. Physiol. 295, H786-H793 (2008).