Summary of Study ST003356

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002086. The data can be accessed directly via it's Project DOI: 10.21228/M8025G This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003356
Study TitleNoninvasive multiomic measurement of cell type repertoires in human urine
Study SummaryBackground: Early detection of the cell type changes underlying several genitourinary tract diseases largely remains an unmet clinical need, whereas existing assays, if available, lack the cellular resolution afforded by an invasive biopsy. While messenger RNA in urine could reflect dynamic signal that facilitates early detection, current measurements primarily detect single genes and thus do not capture the full spectrum of cell type specific contributions. Methods: We isolated and sequenced the cellular and cell-free RNA from urine samples (n = 6 healthy controls and n = 12 kidney stones) alongside the metabolome. We analyzed the resulting urine transcriptomes and metabolomes by comparing the bulk gene expression, deconvolving the noninvasively measurable cell type contributions, and comparing to the plasma cell-free transcriptome. Results: We primarily observed signal originating from genitourinary tract cell types in addition to cell types from high-turnover solid tissues beyond the genitourinary tract. Integration of urinary transcriptomic and metabolomic measurements identified various metabolic pathways involved in amino acid metabolism overlap with metabolic subsystems associated with proximal tubule function. Conclusions: Noninvasive whole transcriptome measurements of human urine reflect signal from hard-to-biopsy tissues exhibiting low representation in the blood at cell type resolution.
Institute
CZ Biohub
Last NameDeFelice
First NameBrian
Address1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA
Emailbcdefelice@ucdavis.edu
Phone5303564485
Submit Date2024-07-29
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-08-15
Release Version1
Brian DeFelice Brian DeFelice
https://dx.doi.org/10.21228/M8025G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Collection:

Collection ID:CO003470
Collection Summary:Clean catch urine specimens were collected from kidney stone patients (n = 12) and healthy controls without known kidney disease (n = 6) with Stanford Institutional Review Board approval. Voided specimens were stored at +4°C until processing; samples were processed within 6 hours of collection. Whole urine was aliquoted for metabolomic analysis. The remaining sample was spun at 4°C and 3000g for 30 min. Cellular RNA samples were prepared as previously described (40): 0.1% v/v betamercaptoethanol (Millipore) and 1 mL Trizol (Ambion) were added to the pellet following centrifugation and frozen at -80°C. Spot creatinine was measured using an aliquot of frozen urine (Biotechne). Standard urine dipstick (Fisherbrand) was additionally measured.
Sample Type:Urine
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