Search > Results

You searched for: BR2025GX (EV-TRACK ID)

Showing 1 - 2 of 2

Experiment number
  • If needed, multiple experiments were identified in a single publication based on differing sample types, separation protocols and/or vesicle types of interest.
Species
  • Species of origin of the EVs.
Separation protocol
  • Gives a short, non-chronological overview of the different steps of the separation protocol.
    • (d)(U)C = (differential) (ultra)centrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
    • IAF = immuno-affinity capture
Experiment number
  • Experiments differ in Sample condition
Experiment number
  • Experiments differ in Sample condition
Details EV-TRACK ID Experiment nr. Species Sample type Separation protocol First author Year EV-METRIC
BR2025GX 1/2 Mus musculus Blood plasma DG
(d)(U)C
Zheng, Xi 2020 77%

Study summary

Full title
All authors
Xi Zheng, Kailun Xu, Biting Zhou, Ting Chen, Yanqin Huang, Qilong Li, Fei Wen, Weiting Ge, Jian Wang, Shaojun Yu, Lifeng Sun, Liang Zhu, Wei Liu, Huanhuan Gao, Liang Yue, Xue Cai, Qiushi Zhang, Guan Ruan, Tiansheng Zhu, Zhicheng Wu, Yi Zhu, Yingkuan Shao, Tiannan Guo, and Shu Zheng
Journal
J Extracell Vesicles
Abstract
Background: Early screening for colorectal cancer (CRC) is essential to improve its prognosis. Liqui (show more...)Background: Early screening for colorectal cancer (CRC) is essential to improve its prognosis. Liquid biopsies are increasingly being considered for diagnosing cancer due to low invasiveness and high reproducibility. In addition, circulating extracellular vesicles (crEVs, extracellular vesicles isolated from plasma) expressing tumour-specific proteins are potential biomarkers for various cancers. Here, we present a data-independent acquisition (DIA)-mass spectrometry (MS)-based diagnostic method for liquid biopsies. Methods: Extracellular vesicles (EVs) were isolated from culture supernatants of human CRC cell lines, and plasma of patients with CRC at different tumour stages, by overnight ultracentrifugation coupled with sucrose density gradient centrifugation. Tumour-specific EV proteins were prioritized using Tandem Mass Tag (TMT)-based shotgun proteomics and phosphoproteomics. The results were verified in a second independent cohort and a mouse tumour-bearing model using Western blotting (WB). The candidate biomarkers were further validated in a third cohort by DIA-MS. Finally, the DIA-MS methodology was accelerated to permit high-throughput detection of EV biomarkers in another independent cohort of patients with CRC and healthy controls. Results: High levels of total and phosphorylated fibronectin 1 (FN1) in crEVs, haptoglobin (HP), S100A9 and fibrinogen α chain (FGA) were significantly associated with cancer progression. FGA was the most dominant biomarker candidate. Analysis of the human CRC cell lines and the mouse model indicated that FGA+ crEVs were likely released by CRC cells. Furthermore, fast DIA-MS and parallel reaction monitoring (PRM)-MS both confirmed that FGA+ crEVs could distinguish colon adenoma with an area of curve (AUC) in the receiver operating characteristic (ROC) curve of 0.949 and patients with CRC (AUC of ROC is 1.000) from healthy individuals. The performance outperformed conventional tumour biomarkers. The DIA-MS quantification of FGA+ crEVs among three groups agreed with that from PRM-MS. Conclusion: DIA-MS detection of FGA+ crEVs is a potential rapid and non-invasive screening tool to identify early stage CRC. (hide)
EV-METRIC
77% (98th percentile of all experiments on the same sample type)
 Reported
 Not reported
 Not applicable
EV-enriched proteins
Protein analysis: analysis of three or more EV-enriched proteins
non EV-enriched protein
Protein analysis: assessment of a non-EV-enriched protein
qualitative and quantitative analysis
Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected.
electron microscopy images
Particle analysis: inclusion of a widefield and close-up electron microscopy image
density gradient
Separation method: density gradient, at least as validation of results attributed to EVs
EV density
Separation method: reporting of obtained EV density
ultracentrifugation specifics
Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps
antibody specifics
Protein analysis: antibody clone/reference number and dilution
lysate preparation
Protein analysis: lysis buffer composition
Study data
Sample type
Blood plasma
Sample origin
Healthy, adenoma, colorectal cancer
Focus vesicles
exosome
Separation protocol
Separation protocol
  • Gives a short, non-chronological overview of the
    different steps of the separation protocol.
    • dUC = (Differential) (ultra)centrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
    • IAF = immuno-affinity capture
DG
(d)(U)C
Adj. k-factor
88.86 (pelleting) / 43.64 (washing)
Protein markers
EV: TSG101/ HSP70/ CD63
non-EV: None
Proteomics
yes
Show all info
Study aim
Biomarker, Identification of content (omics approaches)
Sample
Species
Mus musculus
Sample Type
Blood plasma
Separation Method
(Differential) (ultra)centrifugation
dUC: centrifugation steps
Equal to or above 150,000 g
Pelleting performed
Yes
Pelleting: time(min)
1200
Pelleting: rotor type
MLS-50
Pelleting: speed (g)
160000
Pelleting: adjusted k-factor
88.86
Wash: time (min)
1200
Wash: Rotor Type
MLA-130
Wash: speed (g)
160000
Wash: adjusted k-factor
43.64
Density gradient
Density medium
142.1
Type
Discontinuous
Number of initial discontinuous layers
5
Lowest density fraction
0.25M
Highest density fraction
2M
Sample volume (mL)
0.5
Orientation
Top-down (sample migrates downwards)
Rotor type
SW 40 Ti
Speed (g)
100000
Duration (min)
150
Fraction volume (mL)
1
Fraction processing
Centrifugation
Pelleting: volume per fraction
1
Pelleting: duration (min)
150
Pelleting: rotor type
MLS-50
Pelleting: speed (g)
100000
Pelleting: adjusted k-factor
142.1
Pelleting-wash: volume per pellet (mL)
1
Pelleting-wash: duration (min)
150
Pelleting-wash: rotor type
142.1
Pelleting-wash: speed (g)
MLS-50
Pelleting-wash: adjusted k-factor
142.1
Characterization: Protein analysis
Protein Concentration Method
BCA
Western Blot
Antibody details provided?
Yes
Lysis buffer provided?
Yes
Detected EV-associated proteins
CD63, HSP70, TSG101
Proteomics database
No
Characterization: Lipid analysis
No
Characterization: Particle analysis
TRPS
Report type
Size range/distribution
EM
EM-type
Transmission-EM
Image type
Wide-field
BR2025GX 2/2 Homo sapiens Blood plasma DG
(d)(U)C
Zheng, Xi 2020 77%

Study summary

Full title
All authors
Xi Zheng, Kailun Xu, Biting Zhou, Ting Chen, Yanqin Huang, Qilong Li, Fei Wen, Weiting Ge, Jian Wang, Shaojun Yu, Lifeng Sun, Liang Zhu, Wei Liu, Huanhuan Gao, Liang Yue, Xue Cai, Qiushi Zhang, Guan Ruan, Tiansheng Zhu, Zhicheng Wu, Yi Zhu, Yingkuan Shao, Tiannan Guo, and Shu Zheng
Journal
J Extracell Vesicles
Abstract
Background: Early screening for colorectal cancer (CRC) is essential to improve its prognosis. Liqui (show more...)Background: Early screening for colorectal cancer (CRC) is essential to improve its prognosis. Liquid biopsies are increasingly being considered for diagnosing cancer due to low invasiveness and high reproducibility. In addition, circulating extracellular vesicles (crEVs, extracellular vesicles isolated from plasma) expressing tumour-specific proteins are potential biomarkers for various cancers. Here, we present a data-independent acquisition (DIA)-mass spectrometry (MS)-based diagnostic method for liquid biopsies. Methods: Extracellular vesicles (EVs) were isolated from culture supernatants of human CRC cell lines, and plasma of patients with CRC at different tumour stages, by overnight ultracentrifugation coupled with sucrose density gradient centrifugation. Tumour-specific EV proteins were prioritized using Tandem Mass Tag (TMT)-based shotgun proteomics and phosphoproteomics. The results were verified in a second independent cohort and a mouse tumour-bearing model using Western blotting (WB). The candidate biomarkers were further validated in a third cohort by DIA-MS. Finally, the DIA-MS methodology was accelerated to permit high-throughput detection of EV biomarkers in another independent cohort of patients with CRC and healthy controls. Results: High levels of total and phosphorylated fibronectin 1 (FN1) in crEVs, haptoglobin (HP), S100A9 and fibrinogen α chain (FGA) were significantly associated with cancer progression. FGA was the most dominant biomarker candidate. Analysis of the human CRC cell lines and the mouse model indicated that FGA+ crEVs were likely released by CRC cells. Furthermore, fast DIA-MS and parallel reaction monitoring (PRM)-MS both confirmed that FGA+ crEVs could distinguish colon adenoma with an area of curve (AUC) in the receiver operating characteristic (ROC) curve of 0.949 and patients with CRC (AUC of ROC is 1.000) from healthy individuals. The performance outperformed conventional tumour biomarkers. The DIA-MS quantification of FGA+ crEVs among three groups agreed with that from PRM-MS. Conclusion: DIA-MS detection of FGA+ crEVs is a potential rapid and non-invasive screening tool to identify early stage CRC. (hide)
EV-METRIC
77% (98th percentile of all experiments on the same sample type)
 Reported
 Not reported
 Not applicable
EV-enriched proteins
Protein analysis: analysis of three or more EV-enriched proteins
non EV-enriched protein
Protein analysis: assessment of a non-EV-enriched protein
qualitative and quantitative analysis
Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected.
electron microscopy images
Particle analysis: inclusion of a widefield and close-up electron microscopy image
density gradient
Separation method: density gradient, at least as validation of results attributed to EVs
EV density
Separation method: reporting of obtained EV density
ultracentrifugation specifics
Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps
antibody specifics
Protein analysis: antibody clone/reference number and dilution
lysate preparation
Protein analysis: lysis buffer composition
Study data
Sample type
Blood plasma
Sample origin
Healthy, adenoma, colorectal cancer
Focus vesicles
exosome
Separation protocol
Separation protocol
  • Gives a short, non-chronological overview of the
    different steps of the separation protocol.
    • dUC = (Differential) (ultra)centrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
    • IAF = immuno-affinity capture
DG
(d)(U)C
Adj. k-factor
88.86 (pelleting) / 43.64 (washing)
Protein markers
EV: TSG101/ HSP70/ CD63
non-EV: None
Proteomics
yes
Show all info
Study aim
Biomarker, Identification of content (omics approaches)
Sample
Species
Homo sapiens
Sample Type
Blood plasma
Separation Method
(Differential) (ultra)centrifugation
dUC: centrifugation steps
Equal to or above 150,000 g
Pelleting performed
Yes
Pelleting: time(min)
1200
Pelleting: rotor type
MLS-50
Pelleting: speed (g)
160000
Pelleting: adjusted k-factor
88.86
Wash: time (min)
1200
Wash: Rotor Type
MLA-130
Wash: speed (g)
160000
Wash: adjusted k-factor
43.64
Density gradient
Density medium
142.1
Type
Discontinuous
Number of initial discontinuous layers
5
Lowest density fraction
0.25M
Highest density fraction
2M
Sample volume (mL)
0.5
Orientation
Top-down (sample migrates downwards)
Rotor type
SW 40 Ti
Speed (g)
100000
Duration (min)
150
Fraction volume (mL)
1
Fraction processing
Centrifugation
Pelleting: volume per fraction
1
Pelleting: duration (min)
150
Pelleting: rotor type
MLS-50
Pelleting: speed (g)
100000
Pelleting: adjusted k-factor
142.1
Pelleting-wash: volume per pellet (mL)
1
Pelleting-wash: duration (min)
150
Pelleting-wash: rotor type
142.1
Pelleting-wash: speed (g)
MLS-50
Pelleting-wash: adjusted k-factor
142.1
Characterization: Protein analysis
Protein Concentration Method
BCA
Western Blot
Antibody details provided?
Yes
Lysis buffer provided?
Yes
Detected EV-associated proteins
CD63, HSP70, TSG101
Proteomics database
No
Characterization: Lipid analysis
No
Characterization: Particle analysis
TRPS
Report type
Size range/distribution
EM
EM-type
Transmission-EM
Image type
Wide-field
1 - 2 of 2
  • CM = Commercial method
  • dUC = differential ultracentrifugation
  • DG = density gradient
  • UF = ultrafiltration
  • SEC = size-exclusion chromatography
EV-TRACK ID
BR2025GX
species
Mus musculus
Homo sapiens
sample type
Blood plasma
Blood plasma
condition
Healthy
adenoma
colorectal cancer
Healthy
adenoma
colorectal cancer
separation protocol
DG
(d)(U)C
DG
(d)(U)C
Exp. nr.
1
2
EV-METRIC %
77
77