Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Ben Dov, Iddo Z ^a   Whalen, Veronica M ^b   Goilav, Beatrice ^c   Max, Klaas E A ^b   Tuschl, Thomas ^b  

^a HADASSAH HEBREW UNIVERSITY MEDICAL CENTER   (Israel)

^b ROCKEFELLER UNIVERSITY   (United States)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; MICRORNA; RIBOSOME RNA; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA;

ADULT; ARTICLE; CONTROLLED STUDY; EXOSOME; FEMALE; GENDER; HUMAN; MALE; MEMBRANE MICROPARTICLE; MICTURITION; MOLECULAR LIBRARY; NEXT GENERATION SEQUENCING; NORMAL HUMAN; PILOT STUDY; RNA SEQUENCE; URINALYSIS; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES; URINE; YOUNG ADULT;

ADULT; BIOMARKERS; CELL-DERIVED MICROPARTICLES; EXTRACELLULAR VESICLES; FEMALE; GENE EXPRESSION PROFILING; HEALTHY VOLUNTEERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MICRORNAS; PRINCIPAL COMPONENT ANALYSIS; YOUNG ADULT;

EID: 84958191659     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0147249     Document Type: Article

References (16)

1. Goligorsky MS, Addabbo F, O'Riordan E. Diagnostic potential of urine proteome: a broken mirror of renal diseases. Journal of the American Society of Nephrology: JASN. 2007; 18(8):2233-9. Epub 2007/07/13. doi: 10.1681/ASN.2006121399 PMID: 17625117.
2. Alvarez ML, Khosroheidari M, Kanchi Ravi R, DiStefano JK. Comparison of protein, microRNA, and mRNA yields using different methods of urinary exosome isolation for the discovery of kidney disease biomarkers. Kidney Int. 2012; 82(9):1024-32. Epub 2012/07/13. doi: 10.1038/ki.2012.256 PMID: 22785172.
3. International Federation of Clinical Chemistry (IFCC). Scientific Committee, Clinical Section. Expert Panel on Theory of Reference Values (EPTRV). IFCC Document (1982) stage 2, draft 2, 1983-10-07 with a proposal for an IFCC recommendation. The theory of reference values. Part 2. Selection of individuals for the production of reference values. Clin Chim Acta. 1984; 139(2):205F-13F. Epub 1984/05/30. PMID: 6733931.
4. Ben-Dov IZ, Tan YC, Morozov P, Wilson PD, Rennert H, Blumenfeld JD, et al. Urine microRNA as potential biomarkers of autosomal dominant polycystic kidney disease progression: description of miRNA profiles at baseline. PLoS One. 2014; 9(1):e86856. Epub 2014/02/04. doi: 10.1371/journal. pone.0086856 PMID: 24489795; PubMed Central PMCID: PMC3906110.
5. Li X, Ben-Dov IZ, Mauro M, Williams Z. Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in. BMC molecular biology. 2015; 16:9. doi: 10.1186/s12867-015-0039-3 PMID: 25943882; PubMed Central PMCID: PMC4431604.
6. Farazi TA, Horlings HM, Ten Hoeve JJ, Mihailovic A, Halfwerk H, Morozov P, et al. MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer research. 2011; 71 (13):4443-53. Epub 2011/05/19. doi: 10.1158/0008-5472.CAN-11-0608 PMID: 21586611; PubMed Central PMCID: PMC3129492.
7. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. Epub 2004/10/06. doi: 10.1186/gb-2004-5-10-r80 PMID: 15461798; PubMed Central PMCID: PMC545600.
8. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. Epub 2014/12/18. doi: 10.1186/s13059-014-0550-8 PMID: 25516281; PubMed Central PMCID: PMC4302049.
9. Wickham H. ggplot2: Elegant Graphics for Data Analysis. Berlin: Springer; 2009.
10. Emerson JW. Interactive and Dynamic Graphics for Data Analysis: With R and GGobi by COOK, D. and SWAYNE, D. Biometrics. 2008; 64(4):1301-3. doi: 10.1111/j.1541-0420.2008.01138-4.x
11. Carey V, Gentleman R, Mar J, Vertrees J, Gatto L. MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers. 1.46.0 ed. p. R package.
12. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic acids research. 2015; 43(7):e47. Epub 2015/01/22. doi: 10.1093/nar/gkv007 PMID: 25605792; PubMed Central PMCID: PMC4402510.
13. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1):139-40. Epub 2009/11/17. doi: 10. 1093/bioinformatics/btp616 PMID: 19910308; PubMed Central PMCID: PMC2796818.
14. Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, et al. Mammalian 5'-capped microRNA precursors that generate a single microRNA. Cell. 2013; 155(7):1568-80. Epub 2013/12/24. doi: 10.1016/j.cell. 2013.11.027 PMID: 24360278; PubMed Central PMCID: PMC3899828.
15. Nissan X, Denis JA, Saidani M, Lemaitre G, Peschanski M, Baldeschi C. miR-203 modulates epithelial differentiation of human embryonic stem cells towards epidermal stratification. Dev Biol. 2011; 356 (2):506-15. Epub 2011/06/21. doi: 10.1016/j.ydbio.2011.06.004 PMID: 21684271.
16. Swayne D, Buja A. Exploratory Visual Analysis of Graphs in GGOBI. In: Antoch J, editor. COMPSTAT 2004-Proceedings in Computational Statistics: Physica-Verlag HD; 2004. p. 477-88.