title: Processing of voided urine for prostate cancer RNA biomarker analysis.
abstract: BACKGROUND
  Voided urine samples have been shown to contain cells released from prostate tumors. Could good quality RNA from cells in urine be obtained from every donor for multimarker analysis? In addition, could urine donation be as simple as possible, a practical consideration for a lab test, without involving a prostate massage (as indicated for PCA3 testing), which precludes frequent collection; needing it done at a specific time of day (e.g., first or second urine); and requiring prompt processing of samples in clinics with limited molecular biology capability?
  
  
  METHODS
  Collected urine samples were pelleted, and the RNA isolated was processed for cDNA synthesis and in vitro transcription to generate amplified sense aRNA. The resultant aRNA was rigorously analyzed for possible introduced changes. DMSO was used as a cell preservative for frozen storage of urine samples.
  
  
  RESULTS
  Good quality aRNA was obtained for over 100 samples collected at two different institutions. The process of RNA amplification removed co-isolated DNA in some samples, which did not affect RNA amplification. Amplification did not amplify genes that were absent and produce other expression alterations. The sense aRNA could be used to generate urinary transcriptomes specific to individual patients. No chaotropic agents for RNA preservation were added to the urine samples so that the supernatant could be used for analysis of secreted protein biomarkers. The time of donation was not important since patients were seen during the entire day. DMSO was an effective cell preservative for freezing urine.
  
  
  CONCLUSIONS
  Urinary RNA can be readily isolated and amplified for prostate cancer biomarker analysis. Individual patients had unique set of transcripts derived from their tumor.
authors: Department of Urology, University of Washington, Seattle, Washington.|Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
authors: Sue-Ing
authors: SI
authors: Quek
authors: Department of Urology, University of Washington, Seattle, Washington.|Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
authors: Olivia M
authors: OM
authors: Wong
authors: Department of Urology, University of Washington, Seattle, Washington.|Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
authors: Adeline
authors: A
authors: Chen
authors: Department of Urology, University of Washington, Seattle, Washington.|Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
authors: Gisely T
authors: GT
authors: Borges
authors: Department of Urology, University of Washington, Seattle, Washington.
authors: William J
authors: WJ
authors: Ellis
authors: Department of Computation and Mathematics, University of São Paulo at Riberão Preto, Brazil.
authors: Diego M
authors: DM
authors: Salvanha
authors: Department of Computation and Mathematics, University of São Paulo at Riberão Preto, Brazil.
authors: Ricardo Z N
authors: RZ
authors: Vêncio
authors: Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas.
authors: Brandi
authors: B
authors: Weaver
authors: Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas.
authors: Yasmin M
authors: YM
authors: Ench
authors: Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas.
authors: Robin J
authors: RJ
authors: Leach
authors: Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas.
authors: Ian M
authors: IM
authors: Thompson
authors: Department of Urology, University of Washington, Seattle, Washington.|Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
authors: Alvin Y
authors: AY
authors: Liu
mesh_terms: D014408:Biomarkers, Tumor / Q000652:urine*; D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000175:diagnosis* / Q000652:urine*; D012313:RNA / Q000652:urine*
chemical_list: D014408:Biomarkers, Tumor; D012313:RNA
keywords: DMSO cell preservative; RNA amplification; RNA digital counts; urinary transcriptomes; urine RNA