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

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002086
Project DOI:doi: 10.21228/M8025G
Project Title:Noninvasive multiomic measurement of cell type repertoires in human urine
Project Summary:Background: 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 = 6healthy 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 Name:DeFelice
First Name:Brian
Address:1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA
Email:briancdefelice@gmail.com , bcdefelice@formerstudents.ucdavis.edu
Phone:5303564485
Publications:https://www.biorxiv.org/content/10.1101/2023.10.20.563226v1.abstract

Subject:

Subject ID:SU003477
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Disease
SA365750SEVO001_BK_2_Neg_QE1_HILIC_031Blank method blank
SA365751SEVO001_BK_3_Pos_QE1_HILIC_054Blank method blank
SA365752SEVO001_BK_2_Pos_QE1_HILIC_030Blank method blank
SA365753SEVO001_BK_1_Pos_QE1_HILIC_006Blank method blank
SA365754SEVO001_BK_1_Neg_QE1_HILIC_007Blank method blank
SA365755SEVO001_BK_3_Neg_QE1_HILIC_055Blank method blank
SA365760SEVO001_Neg_N2_QE1_HILIC_043Urine healthy control
SA365761SEVO001_Pos_N6_QE1_HILIC_020Urine healthy control
SA365762SEVO001_Pos_N5_QE1_HILIC_046Urine healthy control
SA365763SEVO001_Pos_N4_QE1_HILIC_048Urine healthy control
SA365764SEVO001_Pos_N3_QE1_HILIC_034Urine healthy control
SA365765SEVO001_Pos_N2_QE1_HILIC_042Urine healthy control
SA365766SEVO001_Pos_N1_QE1_HILIC_052Urine healthy control
SA365767SEVO001_Neg_N1_QE1_HILIC_053Urine healthy control
SA365768SEVO001_Neg_N3_QE1_HILIC_035Urine healthy control
SA365769SEVO001_Neg_N4_QE1_HILIC_049Urine healthy control
SA365770SEVO001_Neg_N5_QE1_HILIC_047Urine healthy control
SA365771SEVO001_Neg_N6_QE1_HILIC_021Urine healthy control
SA365772SEVO001_Pos_1761_QE1_HILIC_050Urine kidney stone
SA365773SEVO001_Pos_1756_QE1_HILIC_040Urine kidney stone
SA365774SEVO001_Pos_1757_QE1_HILIC_018Urine kidney stone
SA365775SEVO001_Neg_1748_QE1_HILIC_039Urine kidney stone
SA365776SEVO001_Neg_1746_QE1_HILIC_013Urine kidney stone
SA365777SEVO001_Pos_221_QE1_HILIC_016Urine kidney stone
SA365778SEVO001_Pos_1754supt_QE1_HILIC_044Urine kidney stone
SA365779SEVO001_Neg_1742_QE1_HILIC_029Urine kidney stone
SA365780SEVO001_Pos_1755_QE1_HILIC_014Urine kidney stone
SA365781SEVO001_Pos_1749_QE1_HILIC_010Urine kidney stone
SA365782SEVO001_Neg_1749_QE1_HILIC_011Urine kidney stone
SA365783SEVO001_Neg_1747_QE1_HILIC_037Urine kidney stone
SA365784SEVO001_Neg_1754supt_QE1_HILIC_045Urine kidney stone
SA365785SEVO001_Neg_1755_QE1_HILIC_015Urine kidney stone
SA365786SEVO001_Neg_1756_QE1_HILIC_041Urine kidney stone
SA365787SEVO001_Pos_1748_QE1_HILIC_038Urine kidney stone
SA365788SEVO001_Neg_1761_QE1_HILIC_051Urine kidney stone
SA365789SEVO001_Neg_1757_QE1_HILIC_019Urine kidney stone
SA365790SEVO001_Neg_221_QE1_HILIC_017Urine kidney stone
SA365791SEVO001_Pos_1741_QE1_HILIC_026Urine kidney stone
SA365792SEVO001_Pos_1742_QE1_HILIC_028Urine kidney stone
SA365793SEVO001_Neg_1741_QE1_HILIC_027Urine kidney stone
SA365794SEVO001_Pos_1747_QE1_HILIC_036Urine kidney stone
SA365795SEVO001_Pos_1746_QE1_HILIC_012Urine kidney stone
SA365756SEVO001_Neg_128_QE1_HILIC_023Urine NA
SA365757SEVO001_Neg_1762_QE1_HILIC_025Urine NA
SA365758SEVO001_Pos_1762_QE1_HILIC_024Urine NA
SA365759SEVO001_Pos_128_QE1_HILIC_022Urine NA
SA365796SEVO001_QC_3_Neg_QE1_HILIC_057Urine pooled control
SA365797SEVO001_QC_1_Pos_QE1_HILIC_008Urine pooled control
SA365798SEVO001_QC_2_Pos_QE1_HILIC_032Urine pooled control
SA365799SEVO001_QC_3_Pos_QE1_HILIC_056Urine pooled control
SA365800SEVO001_QC_2_Neg_QE1_HILIC_033Urine pooled control
SA365801SEVO001_QC_1_Neg_QE1_HILIC_009Urine pooled control
Showing results 1 to 52 of 52

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

Treatment:

Treatment ID:TR003486
Treatment Summary:Patients were clinically diagnosed

Sample Preparation:

Sampleprep ID:SP003484
Sampleprep Summary:Urine specimens were thawed on wet ice, 100 µL aliquots were extracted with addition of 80 uL of chilled extraction solvent containing stable deuterated internal standards (Supplementary Table 3) at -20ºC (1:1 ACN:MEOH with 1% Water) followed by an additional 320 uL of 1:1 ACN:MEOH at -20ºC. Specimens were hand shaken to mix, then chilled at -20ºC for one hour. Next, specimens were vortexed for 10 seconds and centrifuged at -9ºC for 5 minutes at 14000 RCF. The supernatant was then transferred to a fresh tube for drying in a centrivap at room temperature. Residues were then reconstituted in 100uL of 3:2 ACN:H2O containing 60ng/mL CUDA (1-cyclohexyl-urido-3-dodecanoic acid). Specimens were then vortexed, centrifuged for 10 seconds at 14,000 RCF, from which the supernatant was sealed in glass autosampler inserts, 2ul were injected

Chromatography:

Chromatography ID:CH004180
Chromatography Summary:a Waters Acquity UPLC BEH Amide column (150 mm length × 2.1 mm id; 1.7 μm particle size) with an additional Waters Acquity VanGuard BEH Amide pre-column (5 mm × 2.1 mm id; 1.7 μm particle size) maintained at 45°C and coupled to an Thermo Vanquish UPLC. Mobile phases were prepared with 10 mM ammonium formate and 0.125% formic acid and 100% LC-MS grade water for mobile phase (A) or (B) 95:5 v/v acetonitrile:water. Gradient elution:100% (B) at 0–2 min to 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until 16.75 min with a column flow of 0.4 mL/min.
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45C
Flow Gradient:Gradient elution was performed from 100% (B) at 0–2 min to 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until 16.75 min with a column flow of
Flow Rate:0.4 mL/min
Solvent A:100% water; 10mM ammonium formate; 0.125% formic acid
Solvent B:95% acetonitrile/5% water; 10mM ammonium formate; 0.125% formic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN005497
Analysis Type:MS
Chromatography ID:CH004180
Num Factors:5
Num Metabolites:383
Rt Units:Minutes
Units:Peak height
  
Analysis ID:AN005498
Analysis Type:MS
Chromatography ID:CH004180
Num Factors:5
Num Metabolites:375
Rt Units:Minutes
Units:Peak height
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