Urine Cell-Free RNA versus Plasma Cell-Free RNA for Monitoring of Immune and Urinary Tract Complications
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PROVIDER: PRJNA1084833 | ENA |
REPOSITORIES: ENA
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Project description:While it is well known that cell-free RNA (cfRNA) can be isolated from urine, the diagnostic potential of this urine cfRNA, especially in comparison to plasma cfRNA, remains underexplored. Here, we directly compared the utility of urine cfRNA and plasma cfRNA for the monitoring of systemic and urinary tract related complications. We analyzed 272 matched plasma and urine cfRNA isolates obtained from three cohorts of patients: Hematopoietic Stem Cell Transplant (HSCT) recipients, patients with acute kidney injury (AKI), and healthy volunteers. The data highlight the unique cellular origins and properties of urinary and plasma RNA. Most importantly, we find that although plasma cfRNA is a superior analyte for monitoring immune and systemic complications, urinary cfRNA is more sensitive to complications of the urinary tract, including cell-type specific injury in the kidney. These findings highlight the potential of urine cfRNA as a novel analyte in diagnostic medicine.
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Project description:To identify urinary RNA from prospective urine as non-invasive biomarkers for kidney transplant patients
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Project description:To identify urinary RNA from biopsy associated urine as non-invasive biomarkers for kidney transplant patients
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Project description:Urinary extracellular vesicle (EV)-derived microRNAs (miRNAs) have emerged as promising noninvasive biomarkers for disease prediction. However, fluctuations in urine concentration throughout the day may influence miRNA abundance and profiles, potentially limiting their clinical utility. To ensure the broader applicability of urinary miRNAs in disease prediction, it is essential that their profiles remain stable regardless of collection time. In this study, we systematically examined factors influencing urinary miRNA abundance and assessed the stability of miRNA profiles. We collected serial urine samples from healthy individuals over three days, and performed small RNA sequencing to analyze urinary miRNA profiles in relation to various urine concentration parameters. Total miRNA counts were negatively correlated with urine volume and positively correlated with urine concentration indicators, including specific gravity and creatinine levels. miRNA profiles remained stable across different times and days when samples with low miRNA counts were excluded. These findings indicate that urine dilution—primarily due to fluid intake—is a major cause of variation in urinary miRNA abundance. Our results highlight the importance of collecting adequately concentrated samples and provide foundational insights for developing standardized urine collection protocols to enhance the reliability of urinary miRNAs as biomarkers.
2025-07-31 | GSE297465 | GEO
Project description:Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic formalin-fixed paraffin embedded (FFPE) tumour DNAs for 23 well-characterised UBC patients.
2015-12-31 | E-MTAB-3841 | biostudies-arrayexpress
Project description:Urine passes through the entire kidney and urinary tract system starting from the glomerulus and ending to the urethra. Cells in the kidney and urinary tract could be exfoliated from the epithelium into the urine, while leukocyte could infiltrate from the local tissue into the urine, which makes the urine a useful subject for clinical evaluation of relevant diseases. We performed scRNA-seq on voided urine samples. 50–100 mL middle stream urine samples were collected from 12 Chinese healthy adults and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells. We presented the first single-cell atlas of adult human urine and identified multiple previously unrecognized cell types. Based on our scRNA-seq analysis data, a SOX9+ cell population was identified in adult human urine which we speculated to have progenitor potential.
2021-01-25 | GSE165396 | GEO
Project description:Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically even impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that Sendai virus transduction of reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to generate primate iPSCs non-invasively from urinary samples.
2020-08-31 | GSE155889 | GEO
Project description:BACKGROUND: Long-term complications of type 2 diabetes (T2D), such as macrovascular and microvascular events, are the major causes for T2D-related disability and mortality. A clinically convenient, non-invasive approach for monitoring the development of these complications would improve the overall life quality of patients with T2D and help reduce healthcare burden through preventive interventions. METHODS: A selective chemical labeling strategy for 5-hydroxymethylcytosines (5hmC-Seal) was used to profile genome-wide 5hmCs, an emerging class of epigenetic markers implicated in complex diseases including diabetes, in circulating cell-free DNA (cfDNA) from a collection of Chinese patients (n = 62). Differentially modified 5hmC markers between patients with T2D with and without macrovascular/microvascular complications were analyzed under a case-control design. RESULTS: Statistically significant changes in 5hmC markers were associated with T2D-related macrovascular/microvascular complications, involving genes and pathways relevant to vascular biology and diabetes, including insulin resistance and inflammation. A 16-gene 5hmC marker panel accurately distinguished patients with vascular complications from those without (testing set: AUC = 0.85, 95%CI, 0.73-0.96), outperforming conventional clinical variables such as urinary albumin. In addition, a separate 13-gene 5hmC marker panel could distinguish patients with single complications from those with multiple complications (testing set: AUC = 0.84, 95%CI, 0.68-0.99), showing superiority over conventional clinical variables. CONCLUSIONS: The 5hmC markers in cfDNA reflected the epigenetic changes in patients with T2D who developed macrovascular/microvascular complications. The 5hmC-Seal assay has the potential to be a clinically convenient, non-invasive approach that can be applied in the clinic to monitor the presence and severity of diabetic vascular complications.
2020-01-31 | GSE125929 | GEO
Project description:Urinary tract-associated lymphoid structures (UTLASs), tertiary lymphoid tissues, are formed in renal pelvis (RP) of humans and mice with chronic kidney disease. We found that UTALS development was accelerated by urine leakage from RP lumen to the parenchyma following dysfunction of transitional epithelium covering UTLASs. Thus, UTALS-forming cells were stimulated by urine including urinary bio active substances.
2024-04-15 | GSE207999 | GEO
Project description:Background: Renal cell carcinoma (RCC) accounts for about 2% of all cancers. Renal biopsy is the gold standard among the diagnostic tools, but it is invasive and not suitable for all patients. Therefore, new reliable and non-invasive biomarkers for ccRCC detection are required. Secretion of extracellular vesicles (EVs), containing RNA molecules that can be transferred between cells, seems to be a general characteristic of malignant transformation. Consistently, cancer-derived EVs are enriched in the blood, urine and various malignant effusions of cancer patients. Therefore, urinary samples can be a non-invasive approach for discovering diagnostic biomarkers. Methods: We enrolled 33 clear-cell RCC (ccRCC) patients and 22 healthy subjects (HS), age and sex-matched, for urine collection and extracellular vesicles isolation by differential centrifugation. Transcriptional profiles of urinary EVs from 12 patients with ccRCC and 11 HS were generated using the Illumina HumanHT-12 v4 BeadChip oligonucleotide arrays. Microarray analysis led to the identification of RNA that were then validated using RT-qPCR. Results: We showed for the first time that urinary exosomal shuttle RNA (esRNA) was significantly different in ccRCC patients compared to HS and we identified three EVs esRNA involved in the tumor biology that are potentially suitable as non-invasive biomarkers. GSTA1, CEBPA and PCBD1 RNA levels decreased in urinary EVs of patients compared to HS. After 1 month post-operation, the levels of RNA increased to reach the normal level. Conclusions: This study suggests, for the first time, the potential use of the RNA content of urinary EVs to provide a non-invasive first step to diagnose the ccRCC. Total RNA obtained from urinary extracellular vesicles isolated from ccRCC patients and healthy subjects.
2016-09-01 | E-GEOD-72922 | biostudies-arrayexpress