Analysis of recurrently protected genomic regions in urine cell-free DNA
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PROVIDER: PRJNA671389 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of recurrently protected genomic regions in urine cell-free DNA
| PRJNA671390 | ENA
Project description:Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented. Whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we characterized fragmentation patterns in urine cfDNA using whole-genome sequencing. Size distribution of urine cfDNA fragments showed multiple strong peaks between 40 and 120 base pairs (bp) with a modal size of 81- and sharp 10-bp periodicity, suggesting transient protection from complete degradation. These properties were robust to preanalytical perturbations, such as at-home collection and delay in processing. Genome-wide sequencing coverage of urine cfDNA fragments revealed recurrently protected regions (RPRs) conserved across individuals, with partial overlap with nucleosome positioning maps inferred from plasma cfDNA. The ends of cfDNA fragments clustered upstream and downstream of RPRs, and nucleotide frequencies of fragment ends indicated enzymatic digestion of urine cfDNA. Compared to plasma, fragmentation patterns in urine cfDNA showed greater correlation with gene expression and chromatin accessibility in epithelial cells of the urinary tract. We determined that tumor-derived urine cfDNA exhibits a higher frequency of aberrant fragments that end within RPRs. By comparing the fraction of aberrant fragments and nucleotide frequencies of fragment ends, we identified urine samples from cancer patients with an area under the curve of 0.89. Our results revealed nonrandom genomic positioning of urine cfDNA fragments and suggested that analysis of fragmentation patterns across recurrently protected genomic loci may serve as a cancer diagnostic.
| S-EPMC9258975 | biostudies-literature
Project description:Methylation status of free DNA from urine from patients with urothelial tumor and healthy control patients were analysed
2018-09-22 | GSE120288 | GEO
Project description:Human neural stem cells (NSCs) hold great promise in reparative therapy for neural diseases and injuries. However, the isolation of NSCs from either fetal or adult tissue and their application remain difficult due to ethical and immune-rejection concerns. One promising solution is to generate patient specific induced pluripotent stem cells (iPSCs) and subsequently differentiate them into NSCs. Alternatively, induced neurons (iN) can be generated directly from fibroblasts by retroviral delivery of neural specific transcription factors or miroRNAs. The later two approaches remain inefficient and with safety concerns. Here, we describe a process to generate, from epithelial-like cells present in human urine, integration free and engraftable NSCs (UiNSC) efficiently. Using an episomal system to deliver reprogramming factors and microRNAs into human urine cells and subsequently culture them in a chemically defined medium supplemented with a cocktail of small molecules, we generated UiNSCs capable of proliferation and without the transgenes upon prolonged expansion. These transgene free UiNSCs express typical neural stem cell markers and are able to differentiate into all neuronal subtypes and glial cells in vitro and more importantly could engraft and differentiate in vivo upon transplantation into the brain of new born rat. Thus, our work provides an efficient and highly practical platform to generate patient specific NSCs for regenerative medicine. This is a general expression microarray design (NimbleGen platform). It includes 6 samples.
2012-12-01 | E-GEOD-36395 | biostudies-arrayexpress
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.
2016-01-28 | GSE72183 | GEO
Project description:Human neural stem cells (NSCs) hold great promise in reparative therapy for neural diseases and injuries. However, the isolation of NSCs from either fetal or adult tissue and their application remain difficult due to ethical and immune-rejection concerns. One promising solution is to generate patient specific induced pluripotent stem cells (iPSCs) and subsequently differentiate them into NSCs. Alternatively, induced neurons (iN) can be generated directly from fibroblasts by retroviral delivery of neural specific transcription factors or miroRNAs. The later two approaches remain inefficient and with safety concerns. Here, we describe a process to generate, from epithelial-like cells present in human urine, integration free and engraftable NSCs (UiNSC) efficiently. Using an episomal system to deliver reprogramming factors and microRNAs into human urine cells and subsequently culture them in a chemically defined medium supplemented with a cocktail of small molecules, we generated UiNSCs capable of proliferation and without the transgenes upon prolonged expansion. These transgene free UiNSCs express typical neural stem cell markers and are able to differentiate into all neuronal subtypes and glial cells in vitro and more importantly could engraft and differentiate in vivo upon transplantation into the brain of new born rat. Thus, our work provides an efficient and highly practical platform to generate patient specific NSCs for regenerative medicine.
2012-12-01 | GSE36395 | GEO
Project description:Feeder-free mRNA reprogramming of urine-derived cells: combining a faithful reprogramming method with a readily accessible cell type
| PRJEB25626 | ENA
Project description:We performed genome-wide 5hmC Methylated DNA Capture (5hMethylCap-seq) on one pooled RCC tissue sample (n=3) and the corresponding matched normal kidney tissue (NAT) (n=3), and we also performed 5hMethylCap-seq on one pooled urine sample obtained from RCC patients (n=52) along with another pooled urine sample obtained from control patients without malignancy (n=65). Global 5hmC levels were dramatically reduced in RCC tissues compared to matched normal adjacent kidney tissues, and although we detected low levels of 5hmC in urine samples, we also observed reduction of 5hmC in urine samples compared to tissue samples. Through assessing histone marked regions we found that 5hmC levels were enriched in H3K9me3 marked repressive genomic regions of normal adjacent kidney compared to RCC tissue tissues. Given the lower 5hmC signal in other genomic regions in cancer tissues, this upregulated 5hmC levels in H3K9me3 marked regions were also clearly identified comparing urine samples from RCC patients to control patients without RCC. We used Caki1 and Caki2 RCC cells to established stable cells with low H3K9me3 expression by knocking down the SUV39H1 gene. We found that low global H3K9me3 causes major upregulation of 5hmC at H3K9me3 marked regions and minor downregulation of 5hmC at genebody regions without change global 5mC and 5hmC levels.
2019-12-31 | GSE118922 | GEO