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

ABSTRACT: 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 extracellular vesicles. We developed a SWATH-MS workflow with a curated spectral library of 1,145 targets. Application of the workflow across nine replicates of three sample types (exosome-like vesicles (ELVs), microvesicles (MVs) and urine proteins (UPs)) resulted in the quantitation of 888 proteins at FDR <1%. The median-coefficient of variation of the 888 proteins in the ELV sample was 7.7%, indicating excellent reproducibility. Data analysis showed common exosome markers, (i.e. CD9, CD63, ALIX, TSG101 and HSP70) were enriched in urinary ELVs as compared to MVs and UPs. The use of a multiplex biomarker screening assay focused on ELVs was investigated, and perspectives in future applications are discussed.

SUBMITTER: Chutipongtanate S

PROVIDER: S-EPMC6177456 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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

Chutipongtanate Somchai S Greis Kenneth D KD

Scientific reports 20181009 1

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 extracellular vesicles. We developed a SWATH-MS workflow with a curated spectral library of 1,145 targets. Application of the workflow across nine replicates of three sample types (exosome-like vesicles (ELVs), microvesicles (MVs) and urine proteins (UPs)) resulted in the quantitation of 88 ...[more]

PMID: 30301925

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

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2018-10-11 | PXD008891 | Pride

Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study.

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

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Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease.

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Isolation and characterization of urinary extracellular vesicles: implications for biomarker discovery.

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Proteomic analysis of urinary extracellular vesicles from high Gleason score prostate cancer.

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

2016-09-01 | GSE72922 | GEO

MiR-21-5p in urinary extracellular vesicles is a novel biomarker of urothelial carcinoma.

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| S-EPMC5421878 | biostudies-literature

Proteomic analysis of urinary and tissue-exudative extracellular vesicles to discover novel bladder cancer biomarkers.

Project description:Proteomic analysis of urinary extracellular vesicles (EVs) is a powerful approach to discover potential bladder cancer (BCa) biomarkers, however urine contains numerous EVs derived from the kidney and normal urothelial epithelium, which can obfuscate information related to BCa cell-derived EVs. In this study, we combined proteomic analysis of urinary EVs and tissue-exudative EVs (Te-EVs), which were isolated from culture medium of freshly resected viable BCa tissues. Urinary EVs were isolated from urine samples of 11 individuals (7 BCa patients and 4 healthy individuals), and Te-EVs were isolated from 7 BCa tissues. We performed tandem mass tag (TMT)-labeling liquid chromatography (LC-MS/MS) analysis for both urinary EVs and Te-EVs and identified 1960 proteins in urinary EVs and 1538 proteins in Te-EVs. Most of the proteins identified in Te-EVs were also present in urinary EVs (82.4%), with 55 of these proteins showing upregulated levels in the urine of BCa patients (fold change > 2.0; P < .1). Among them, we selected 22 membrane proteins as BCa biomarker candidates for validation using selected reaction monitoring/multiple reaction monitoring (SRM/MRM) analysis on urine samples from 70 individuals (40 BCa patients and 30 healthy individuals). Six urinary EV proteins (heat-shock protein 90, syndecan-1, myristoylated alanine-rich C-kinase substrate (MARCKS), MARCKS-related protein, tight junction protein ZO-2, and complement decay-accelerating factor) were quantified using SRM/MRM analysis and validated as significantly upregulated in BCa patients (P < .05). In conclusion, the novel strategy that combined proteomic analysis of urinary EVs and Te-EVs enabled selective detection of urinary BCa biomarkers.

| S-EPMC8088963 | biostudies-literature

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