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MStern Blot - Urinary Biomarker Study

ABSTRACT: This large-scale study focused on the discovery on urinary biomarker for ovarian cyst.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Hanno Steen, PhD

PROVIDER: MSV000080874 | MassIVE | Sat Apr 01 04:25:00 BST 2017

SECONDARY ACCESSION(S): PXD002549

REPOSITORIES: MassIVE

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Publications

MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates.

Berger Sebastian T ST Ahmed Saima S Muntel Jan J Cuevas Polo Nerea N Bachur Richard R Kentsis Alex A Steen Judith J Steen Hanno H

Molecular & cellular proteomics : MCP 20150729 10

We describe a 96-well plate compatible membrane-based proteomic sample processing method, which enables the complete processing of 96 samples (or multiples thereof) within a single workday. This method uses a large-pore hydrophobic PVDF membrane that efficiently adsorbs proteins, resulting in fast liquid transfer through the membrane and significantly reduced sample processing times. Low liquid transfer speeds have prevented the useful 96-well plate implementation of FASP as a widely used membra ...[more]

PMID: 26223766

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MStern Blot - Urinary Biomarker Study

Project description:This large-scale study focused on the discovery on urinary biomarker for ovarian cyst.

2015-07-30 | PXD002549 | Pride

A novel urinary microRNA biomarker panel for detecting gastric cancer

Project description:Purpose: Gastric cancer (GC) is one of the most common causes of cancer deaths worldwide; however, reliable and non-invasive screening methods for GC are not established. Therefore, we conducted this study to develop a biomarker for GC detection, consisting of urinary microRNAs (miRNAs). Experimental Design: We matched 306 participants by age and sex (153 pairs consisting of patients with GC and healthy controls [HCs]), then randomly divided them across three groups: (1) the discovery cohort (4 pairs); (2) the training cohort (95 pairs); (3) the validation cohort (54 pairs). Moreover, 64 participants (32 pairs) with serum samples were also enrolled in the serum cohort. Result: There were 22 urinary miRNAs with significantly aberrant expressions between the two groups in the discovery cohort. Upon multivariate analysis of the training cohort, urinary expression levels of miR-6807-5p and miR-6856-5p were significantly independent biomarkers for diagnosis of GC, in addition to Helicobacter pylori (H. pylori) status. A diagnostic panel that combined the aberrant miRNAs and H. pylori status distinguished between HC and GC samples with an area under the curve (AUC) = 0.736. In the validation cohort, urinary miR-6807-5p and miR-6856-5p showed significantly higher expression levels in the GC group, and the combination biomarker panel of miR-6807-5p, miR-6856-5p, and H. pylori status also showed excellent performance (AUC = 0.885). In addition, serum levels of miR-6807-5p and miR-6856-5p were significantly higher in the GC group. Conclusion: This novel biomarker panel enables early and non-invasive detection of GC.

2019-12-22 | GSE128720 | GEO

Urinary Exosome as a Potential Biomarker of Exercise-Induced Fatigue in Young Adult Males

Project description:Exercise could stimulate the release of exosomes into the circulation, transferring signals between the cells. Exosomes are also found in urine, which is an emerging biomarker of several diseases. However, the characteristics of urinary exosomes and their contents after exercise remain poorly understood. We used microarrays to identify the alteration of gene expression in urinary exosomes after exercise bout.

2022-01-09 | GSE193186 | GEO

Detection of urinary microRNAs from epithelial ovarian cancer patients as biomarker

Project description:The Urine RNA from 5 ovarian cancer and 5 healthy control were analyzed with the Human miRNA Microarray and then validated with a quantitative reverse-transcription PCR assay with 29 individual samples, 20 benign gynecological disease and 26 age/sex-matched healthy control. This study determines the clinical value of urine miRNAs as biomarker for epithelial ovarian cancer. Results: The miRNA microarray results demonstrate that the original 38 were identified that were significantly differentially expression in epithelial ovarian cancer compared with healthy control (P<0.01). A total of 1 miRNA was up-regulated in ovarian cancer, while 37 miRNA were down-regulated. the urine RNA from 5 ovarian cancer and 5 healthy women were analysised with Human mirRNA microarry

2015-06-17 | E-GEOD-58517 | biostudies-arrayexpress

Detection of urinary microRNAs from epithelial ovarian cancer patients as biomarker

2015-06-17 | GSE58517 | GEO

A novel urinary microRNA biomarker panel for detecting gastric cancer

Project description:A novel urinary microRNA biomarker panel for detecting gastric cancer

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Multiplex Biomarker Screening Assay for Urinary Extracellular Vesicles Study: A Targeted Label-Free Proteomic Approach

Project description:The recent advance in targeted label-free proteomics, SWATH-MS, can provide consistent protein detection and reproducible protein quantitation, which is a considerable advantage for biomarker study of urinary exosome-enriched extracellular vesicles (EVs). We developed a SWATH-MS workflow with a curated spectral library of 1,073 targets. Application of the workflow across nine replicates of three sample types (EVs, microvesicles (MVs) and urine proteins (UP)) resulting in the quantitation of 842 proteins. The median-coefficient of variation of the 842 proteins in the EV sample was 7.6%, indicating excellent reproducibility. Data analysis showed common EV markers, (i.e. CD9, CD63, ALIX, TSG101 and HSP70) were enriched in urinary EVs as compared to MV and UP samples. Further development and applicationof this SWATH-MS workflow to a variety of kidney diseases may allow for new and robust avenues for biomarker identification and validation for clinical use.

2018-10-11 | PXD008891 | Pride

Urinary Extracellular Vesicles RNA Profile in Clear Cell Renal Cell Carcinoma as Biomarker

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

Urinary exosome miR-30c-5p as a biomarker of clear cell renal cell carcinoma that inhibits progression by targeting HSPA5

Project description:Exosome-derived miRNAs are regarded as biomarkers for the diagnosis and prognosis of many human cancers. However, its function in clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, differentially expressed miRNAs from urinal exosomes were identified using next-generation sequencing (NGS) and verified using urine samples of ccRCC patients and healthy donors. Then the exosomes were analyzed in early-stage ccRCC patients, healthy individuals and patients suffering with other urinary system cancers. Afterwards, the target gene of the miRNA was detected. Its biological function was investigated in vitro and in vivo. The results showed that miR-30c-5p could be stably amplified. Its expression pattern was significantly different only between ccRCC patients and healthy control individuals, but not compared with that of other urinary system cancers, which indicated its ccRCC specificity. Additionally, the overexpression of miR-30c-5p inhibited ccRCC progression in vitro and in vivo. Heat shock Protein 5 (HSPA5) was found to be a direct target gene of miR-30c-5p. HSPA5 depletion caused by miR-30c-5p inhibition reversed the promoting effect of ccRCC growth. In conclusion, urinary exosomal miR-30c-5p acts as a potential diagnostic biomarker of early-stage ccRCC, and might modulate the expression of HSPA5, which is correlated with the progression of ccRCC.

2019-04-03 | GSE129255 | GEO

Urinary exosome microRNA signatures as a non-invasive prognostic biomarker for prostate cancer

Project description:Urinary exosome microRNA signatures as a non-invasive prognostic biomarker for prostate cancer

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