Summary of project PR002086
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
| 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 |
Summary of all studies in project PR002086
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST003356 | Noninvasive multiomic measurement of cell type repertoires in human urine | Homo sapiens | CZ Biohub | MS | 2024-08-15 | 1 | 52 | Uploaded data (1.2G)* |
