Project description:Non-invasive cellular models for genetic growth disorders affecting cartilage and bone remain rare, hampering mechanistic studies and the development of personalized therapies. Here, we present urine-derived stem cells (USCs), as a robust in vitro system for human chondrogenesis. Single-cell RNA sequencing of undifferentiated USCs revealed distinct clusters, of which a subset had high stem cell character. After differentiation, USCs underwent osteogenic and chondrogenic lineage with positive marker expression, confirmed by bulk-RNA-Seq. Single cell transcriptomic comparisons with healthy cartilage revealed a healthy cartilage mimicking, chondrocyte-like subcluster. Pseudotime analysis revealed multiple chondrogenic trajectories.
Project description:Non-invasive cellular models for genetic growth disorders affecting cartilage and bone remain rare, hampering mechanistic studies and the development of personalized therapies. Here, we present urine-derived stem cells (USCs), as a robust in vitro system for human chondrogenesis. Single-cell RNA sequencing of undifferentiated USCs revealed distinct clusters, of which a subset had high stem cell character. After differentiation, USCs underwent osteogenic and chondrogenic lineage with positive marker expression, confirmed by bulk-RNA-Seq. Single cell transcriptomic comparisons with healthy cartilage revealed a healthy cartilage mimicking, chondrocyte-like subcluster. Pseudotime analysis revealed multiple chondrogenic trajectories.
Project description:Background: Urine is a potential source of biomarkers for diseases of the kidneys and urinary tract. RNA, including microRNA, is present in the urine enclosed in detached cells or in extracellular vesicles (EVs) or bound and protected by extracellular proteins. Detection of cell- and disease-specific microRNA in urine may aid early diagnosis of organ-specific pathology. In this study, we applied barcoded deep sequencing to profile microRNAs in urine of healthy volunteers, and characterized the effects of sex, urine fraction (cells vs. EVs) and repeated voids by the same individuals. Results: Compared to urine-cell-derived small RNA libraries, urine-EV-derived libraries were relatively enriched with miRNA, and accordingly had lesser content of other small RNA such as rRNA, tRNA and sn/snoRNA. Unsupervised clustering of specimens in relation to miRNA expression levels showed prominent bundling by specimen type (urine cells or EVs) and by sex, as well as a tendency of repeated (first and second void) samples to neighbor closely. Likewise, miRNA profile correlations between void repeats, as well as fraction counterparts (cells and EVs from the same specimen) were distinctly higher than correlations between miRNA profiles overall. Differential miRNA expression by sex was similar in cells and EVs. Conclusions: miRNA profiling of both urine EVs and sediment cells can convey biologically important differences between individuals. However, to be useful as urine biomarkers, careful consideration is needed for biofluid fractionation and sex-specific analysis, while the time of voiding appears to be less important.
Project description:Urine proteomics has been applied to uncover age-related differences in host immune response. About 65 human subjects aged between 65-85 were recruitted to the project, including one group of 33 subjects that have not suffered from any major diseases and the other group of 32 subjects that have history of heart disease, diabetes, cancer, asthma or have at least one hospitalization in last 10 years.
Project description:Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.
Project description:Examination of E. coli transcripts present in bacteria in urine samples from 8 patients attending a urology clinic with symptoms of cystitis, as compared to transcripts present in the same E. coli strains during mid-exponential growth in filter-sterilized human urine in vitro. A 48 array study using total RNA recovered from eight clinical E. coli isolates immediately following collection from women and following culture in pooled human urine ex vivo. Each array measures the expression of the 5,379 ORFs in the CFT073 genome, using an average of 14 60-mer probes per ORF. Arrays were performed in triplicate: biological replicates of the in vitro-cultured samples and technical replicates of the in vivo samples.