ArticleClinical chemistry2024
Deconvolution of Human Urine across the Transcriptome and Metabolome.
Article in Clinical chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Exploratory study on blood and urine transcriptomes for identifying miRNA biomarkers in pediatric febrile bacterial and viral infections.Scientific reports · 2026Article
- Application of PathoChip to urine-derived nucleic acids for broad microbial profiling in men with suspected prostate cancer: setup of a methodological workflow and pilot feasibility study.The journal of liquid biopsy · 2026Article
- exoRBase 3.0: an updated resource for extracellular RNAs from human biofluids.Nucleic acids research · 2026Article
- Development and validation of a routine urinalysis-based risk stratification model for IgA nephropathy in a multicenter real-world hospital population.Frontiers in nephrology · 2026Article
- Cell type inference in cell-free nucleic acid liquid biopsy.Nature biotechnology · 2025Review
- Transcriptomic profiling of shed cells enables spatial mapping of cellular turnover in human organs.Molecular systems biology · 2025Article
- Urine Cell-Free RNA vs Plasma Cell-Free RNA for Monitoring of Kidney Injury and Immune Complications.Clinical chemistry · 2025Article
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Abstract
backgroundEarly detection of the cell type changes underlying several genitourinary tract diseases largely remains an unmet clinical need, where existing assays, if available, lack the cellular resolution afforded by an invasive biopsy. While messenger RNA in urine could reflect the dynamic signal that facilitates early detection, current measurements primarily detect single genes and thus do not reflect the entire transcriptome and the underlying contributions of cell type-specific RNA.
methodsWe isolated and sequenced the cell-free RNA (cfRNA) and sediment RNA from human urine samples (n = 6 healthy controls and n = 12 kidney stone patients) and measured the urine metabolome. We analyzed the resulting urine transcriptomes by deconvolving the noninvasively measurable cell type contributions and comparing to plasma cfRNA and the measured urine metabolome.
resultsUrine transcriptome cell type deconvolution primarily yielded relative fractional contributions from genitourinary tract cell types in addition to cell types from high-turnover solid tissues beyond the genitourinary tract. Comparison to plasma cfRNA yielded enrichment of metabolic pathways and a distinct cell type spectrum. Integration of urine transcriptomic and metabolomic measurements yielded enrichment for metabolic pathways involved in amino acid metabolism and overlapped with metabolic subsystems associated with proximal tubule function.
conclusionsNoninvasive whole transcriptome measurements of human urine cfRNA and sediment RNA reflects signal from hard-to-biopsy tissues exhibiting low representation in blood plasma cfRNA liquid biopsy at cell type resolution and are enriched in signal from metabolic pathways measurable in the urine metabolome.
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