RNA sequencing of RNA obtained from urinary extracellular vesicles
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30403 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3006060.fastq.gz | Fastqsanger.gz | |||
| ERR3006070.fastq.gz | Fastqsanger.gz | |||
| ERR3006080.fastq.gz | Fastqsanger.gz | |||
| ERR3006061.fastq.gz | Fastqsanger.gz | |||
| ERR3006071.fastq.gz | Fastqsanger.gz |
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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.
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Project description:By comparing urinary microRNA expression in representative cases of pancreatic and gastric cancer with that in healthy individuals, we were able to extract candidate biomarkers.
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Project description:Urinary extracellular vesicles (uEV) are a precious new source of biomarkers reflecting the physiological state of the upstream parent cells and organ systems. However, urinary Tamm-Horsfall Protein (THP; uromodulin) interferes heavily with all vesicle isolation attempts, precipitates with normal urinary proteins thus representing an unwanted “contaminant” in urinary assays. Here we developed a simple method to manage THP efficiently. Accordingly, uEV were isolated by hydrostatic filtration dialysis (HFD) and treated with a solution of urea to release most uEV. Presence of uEV was then confirmed by transmission electron microscopy, Western blot and proteomic profiling in MS, all showing that urea treatment did not affect integrity of uEV.
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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.
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