title: Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.
abstract: Intact RNA from exosomes/microvesicles (collectively referred to as microvesicles) has sparked much interest as potential biomarkers for the non-invasive analysis of disease. Here we use the Illumina Genome Analyzer to determine the comprehensive array of nucleic acid reads present in urinary microvesicles. Extraneous nucleic acids were digested using RNase and DNase treatment and the microvesicle inner nucleic acid cargo was analyzed with and without DNase digestion to examine both DNA and RNA sequences contained in microvesicles. Results revealed that a substantial proportion (∼87%) of reads aligned to ribosomal RNA. Of the non-ribosomal RNA sequences, ∼60% aligned to non-coding RNA and repeat sequences including LINE, SINE, satellite repeats, and RNA repeats (tRNA, snRNA, scRNA and srpRNA). The remaining ∼40% of non-ribosomal RNA reads aligned to protein coding genes and splice sites encompassing approximately 13,500 of the known 21,892 protein coding genes of the human genome. Analysis of protein coding genes specific to the renal and genitourinary tract revealed that complete segments of the renal nephron and collecting duct as well as genes indicative of the bladder and prostate could be identified. This study reveals that the entire genitourinary system may be mapped using microvesicle transcript analysis and that the majority of non-ribosomal RNA sequences contained in microvesicles is potentially functional non-coding RNA, which play an emerging role in cell regulation.
authors.affiliation: Program in Membrane Biology, Division of Nephrology & Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Miranda
authors.affiliation: Program in Membrane Biology, Division of Nephrology & Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Daniel T
authors.initials: DT
authors.lastname: Bond
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Xian
authors.initials: X
authors.lastname: Adiconis
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Andrey
authors.initials: A
authors.lastname: Sivachenko
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.affiliation: Program in Membrane Biology, Division of Nephrology & Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Dennis
authors.initials: D
authors.lastname: Brown
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.affiliation: Program in Membrane Biology, Division of Nephrology & Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Leileata M
authors.initials: LM
authors.lastname: Russo
mesh_terms: D002874:Chromosome Mapping; D055354:Exosomes / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012313:RNA / Q000737:chemistry / Q000235:genetics* / Q000652:urine; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000652:urine; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics* / Q000652:urine; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D059467:Transcriptome; D014566:Urogenital System / Q000378:metabolism
chemical_list: D012335:RNA, Ribosomal; D022661:RNA, Untranslated; D012313:RNA