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.
| Study ID | ST003356 |
| Study Title | Noninvasive multiomic measurement of cell type repertoires in human urine |
| Study 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 = 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 Name | DeFelice |
| First Name | Brian |
| Address | 1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA |
| bcdefelice@ucdavis.edu | |
| Phone | 5303564485 |
| Submit Date | 2024-07-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-15 |
| Release Version | 1 |
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 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Disease |
|---|---|---|---|
| SA365750 | SEVO001_BK_2_Neg_QE1_HILIC_031 | Blank | method blank |
| SA365751 | SEVO001_BK_3_Pos_QE1_HILIC_054 | Blank | method blank |
| SA365752 | SEVO001_BK_2_Pos_QE1_HILIC_030 | Blank | method blank |
| SA365753 | SEVO001_BK_1_Pos_QE1_HILIC_006 | Blank | method blank |
| SA365754 | SEVO001_BK_1_Neg_QE1_HILIC_007 | Blank | method blank |
| SA365755 | SEVO001_BK_3_Neg_QE1_HILIC_055 | Blank | method blank |
| SA365760 | SEVO001_Neg_N2_QE1_HILIC_043 | Urine | healthy control |
| SA365761 | SEVO001_Pos_N6_QE1_HILIC_020 | Urine | healthy control |
| SA365762 | SEVO001_Pos_N5_QE1_HILIC_046 | Urine | healthy control |
| SA365763 | SEVO001_Pos_N4_QE1_HILIC_048 | Urine | healthy control |
| SA365764 | SEVO001_Pos_N3_QE1_HILIC_034 | Urine | healthy control |
| SA365765 | SEVO001_Pos_N2_QE1_HILIC_042 | Urine | healthy control |
| SA365766 | SEVO001_Pos_N1_QE1_HILIC_052 | Urine | healthy control |
| SA365767 | SEVO001_Neg_N1_QE1_HILIC_053 | Urine | healthy control |
| SA365768 | SEVO001_Neg_N3_QE1_HILIC_035 | Urine | healthy control |
| SA365769 | SEVO001_Neg_N4_QE1_HILIC_049 | Urine | healthy control |
| SA365770 | SEVO001_Neg_N5_QE1_HILIC_047 | Urine | healthy control |
| SA365771 | SEVO001_Neg_N6_QE1_HILIC_021 | Urine | healthy control |
| SA365772 | SEVO001_Pos_1761_QE1_HILIC_050 | Urine | kidney stone |
| SA365773 | SEVO001_Pos_1756_QE1_HILIC_040 | Urine | kidney stone |
| SA365774 | SEVO001_Pos_1757_QE1_HILIC_018 | Urine | kidney stone |
| SA365775 | SEVO001_Neg_1748_QE1_HILIC_039 | Urine | kidney stone |
| SA365776 | SEVO001_Neg_1746_QE1_HILIC_013 | Urine | kidney stone |
| SA365777 | SEVO001_Pos_221_QE1_HILIC_016 | Urine | kidney stone |
| SA365778 | SEVO001_Pos_1754supt_QE1_HILIC_044 | Urine | kidney stone |
| SA365779 | SEVO001_Neg_1742_QE1_HILIC_029 | Urine | kidney stone |
| SA365780 | SEVO001_Pos_1755_QE1_HILIC_014 | Urine | kidney stone |
| SA365781 | SEVO001_Pos_1749_QE1_HILIC_010 | Urine | kidney stone |
| SA365782 | SEVO001_Neg_1749_QE1_HILIC_011 | Urine | kidney stone |
| SA365783 | SEVO001_Neg_1747_QE1_HILIC_037 | Urine | kidney stone |
| SA365784 | SEVO001_Neg_1754supt_QE1_HILIC_045 | Urine | kidney stone |
| SA365785 | SEVO001_Neg_1755_QE1_HILIC_015 | Urine | kidney stone |
| SA365786 | SEVO001_Neg_1756_QE1_HILIC_041 | Urine | kidney stone |
| SA365787 | SEVO001_Pos_1748_QE1_HILIC_038 | Urine | kidney stone |
| SA365788 | SEVO001_Neg_1761_QE1_HILIC_051 | Urine | kidney stone |
| SA365789 | SEVO001_Neg_1757_QE1_HILIC_019 | Urine | kidney stone |
| SA365790 | SEVO001_Neg_221_QE1_HILIC_017 | Urine | kidney stone |
| SA365791 | SEVO001_Pos_1741_QE1_HILIC_026 | Urine | kidney stone |
| SA365792 | SEVO001_Pos_1742_QE1_HILIC_028 | Urine | kidney stone |
| SA365793 | SEVO001_Neg_1741_QE1_HILIC_027 | Urine | kidney stone |
| SA365794 | SEVO001_Pos_1747_QE1_HILIC_036 | Urine | kidney stone |
| SA365795 | SEVO001_Pos_1746_QE1_HILIC_012 | Urine | kidney stone |
| SA365756 | SEVO001_Neg_128_QE1_HILIC_023 | Urine | NA |
| SA365757 | SEVO001_Neg_1762_QE1_HILIC_025 | Urine | NA |
| SA365758 | SEVO001_Pos_1762_QE1_HILIC_024 | Urine | NA |
| SA365759 | SEVO001_Pos_128_QE1_HILIC_022 | Urine | NA |
| SA365796 | SEVO001_QC_3_Neg_QE1_HILIC_057 | Urine | pooled control |
| SA365797 | SEVO001_QC_1_Pos_QE1_HILIC_008 | Urine | pooled control |
| SA365798 | SEVO001_QC_2_Pos_QE1_HILIC_032 | Urine | pooled control |
| SA365799 | SEVO001_QC_3_Pos_QE1_HILIC_056 | Urine | pooled control |
| SA365800 | SEVO001_QC_2_Neg_QE1_HILIC_033 | Urine | pooled control |
| SA365801 | SEVO001_QC_1_Neg_QE1_HILIC_009 | Urine | 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 |
Combined analysis:
| Analysis ID | AN005497 | AN005498 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
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 |
MS:
| MS ID: | MS005223 |
| Analysis ID: | AN005497 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS-DIAL 4.60 (http://prime.psc.riken.jp/compms/msdial/main.html) was used for peak picking, annotation, and alignment. We use two different metabolite libraries (‘local’ and ‘global’) to annotate metabolites in our data. The local library contains metabolite information applicable to only the exact chromatographic method used in this study. The global library is chromatographically agnostic, instead relying on the pattern of metabolite fragmentation (MS2) to identify unknown features. Highest confidence annotations (MSI level 1) occur when a metabolite matches both our local and global libraries. Local: Our ‘local’ library is LC-MS/MS method specific and contains over 800 unique metabolites and 400 exposome compounds. The ‘local’ library was created from the analysis of authentic metabolite standards using the same chromatographic conditions used to analyze samples in this study. When the m/z and retention time of a metabolic feature matches that of the local library it is flagged as a potential match and then the MS2 spectra of that metabolite is compared to that in the global library. Global: Metabolites fragment reproducibly when a known energy is applied. Our global library is composed of metabolite MS2 spectra from several repositories which have been combined at the MassBank of North America (MoNA). MSI Level: All annotations are manually verified to ensure spectral similarity. The following numbers correspond with varying levels of confidence based on the data available: • 1: mz-RT and MS2 match • 2: mz-RT and MS2 match – MS2 match is not exact - roughly MSI2 occurs when there is a convoluted experimental MS2 spectra where the experimental spectra has all (or almost all) the peaks from the library spectra, but also contains many more peaks (likely from near RT or mz features allowed through the Quad) • 3: MS2 matches above 85% similarity and with visual conformation • 4: MS2 matches but stereospecific structure cannot be determined o Ie: unsaturated or oxidized lipid chains, peptides containing Leucine or Isoleucine, many flavonoids, sugars, bile acids |
| Ion Mode: | POSITIVE |
| MS ID: | MS005224 |
| Analysis ID: | AN005498 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS-DIAL 4.60 (http://prime.psc.riken.jp/compms/msdial/main.html) was used for peak picking, annotation, and alignment. We use two different metabolite libraries (‘local’ and ‘global’) to annotate metabolites in our data. The local library contains metabolite information applicable to only the exact chromatographic method used in this study. The global library is chromatographically agnostic, instead relying on the pattern of metabolite fragmentation (MS2) to identify unknown features. Highest confidence annotations (MSI level 1) occur when a metabolite matches both our local and global libraries. Local: Our ‘local’ library is LC-MS/MS method specific and contains over 800 unique metabolites and 400 exposome compounds. The ‘local’ library was created from the analysis of authentic metabolite standards using the same chromatographic conditions used to analyze samples in this study. When the m/z and retention time of a metabolic feature matches that of the local library it is flagged as a potential match and then the MS2 spectra of that metabolite is compared to that in the global library. Global: Metabolites fragment reproducibly when a known energy is applied. Our global library is composed of metabolite MS2 spectra from several repositories which have been combined at the MassBank of North America (MoNA). MSI Level: All annotations are manually verified to ensure spectral similarity. The following numbers correspond with varying levels of confidence based on the data available: • 1: mz-RT and MS2 match • 2: mz-RT and MS2 match – MS2 match is not exact - roughly MSI2 occurs when there is a convoluted experimental MS2 spectra where the experimental spectra has all (or almost all) the peaks from the library spectra, but also contains many more peaks (likely from near RT or mz features allowed through the Quad) • 3: MS2 matches above 85% similarity and with visual conformation • 4: MS2 matches but stereospecific structure cannot be determined o Ie: unsaturated or oxidized lipid chains, peptides containing Leucine or Isoleucine, many flavonoids, sugars, bile acids |
| Ion Mode: | NEGATIVE |
