Summary of Study ST004002
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002507. The data can be accessed directly via it's Project DOI: 10.21228/M8KN8R This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST004002 |
| Study Title | A deep, quantitative lipid atlas of extracellular vesicles across multiple cell lines |
| Study Summary | Extracellular vesicles (EVs) are defined as subcellular particles surrounded by a lipid bilayer membrane and incorporating various additional biomolecules derived from their donor cell, such as proteins and nucleic acid species. In many disease contexts circulating EVs have received increasing scientific attention due to their potential diagnostic and prognostic value. Additionally, EVs have been ascribed a range of biological functions, ranging from cellular waste disposal to sophisticated, intercellular communication. Consequently, EVs involved in pathological processes may represent therapeutic targets, whereas EV-based therapeutics are being developed for targeted delivery of molecular cargoes in vivo. Detailed knowledge of the molecular make-up of natural EVs derived from diverse tissue and cellular origins is crucial to identify biomarkers, dissect EV functions, and optimize EV engineering for therapeutic purposes. Although the lipid composition of biological membranes has a significant impact on their biophysical and -chemical properties and may affect signaling and interactions at the molecular and cellular level, relatively little is known about the lipid composition of EV membranes. Here, we applied high resolution mass spectrometry to deeply and quantitatively characterize the lipidome of EVs isolated from a panel of malignant and non-malignant cell lines, providing a comprehensive data resource for biomarker research and EV engineering efforts. Furthermore, subset comparisons indicate striking differences between lipid profiles of EVs isolated from cells of different tissue origin, suggesting distinct membrane characteristics that could affect EV biodistribution and function in vivo. |
| Institute | European Molecular Biology Laboratory |
| Department | EMBL Heidelberg |
| Last Name | Drotleff |
| First Name | Bernhard |
| Address | Meyerhofstr. 1, Heidelberg, BW, 69117, Germany |
| bernhard.drotleff@embl.de | |
| Phone | none |
| Submit Date | 2025-04-15 |
| Publications | in preparation |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-07-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002507 |
| Project DOI: | doi: 10.21228/M8KN8R |
| Project Title: | A deep, quantitative lipid atlas of extracellular vesicles across multiple cell lines |
| Project Summary: | Extracellular vesicles (EVs) are defined as subcellular particles surrounded by a lipid bilayer membrane and incorporating various additional biomolecules derived from their donor cell, such as proteins and nucleic acid species. In many disease contexts circulating EVs have received increasing scientific attention due to their potential diagnostic and prognostic value. Additionally, EVs have been ascribed a range of biological functions, ranging from cellular waste disposal to sophisticated, intercellular communication. Consequently, EVs involved in pathological processes may represent therapeutic targets, whereas EV-based therapeutics are being developed for targeted delivery of molecular cargoes in vivo. Detailed knowledge of the molecular make-up of natural EVs derived from diverse tissue and cellular origins is crucial to identify biomarkers, dissect EV functions, and optimize EV engineering for therapeutic purposes. Although the lipid composition of biological membranes has a significant impact on their biophysical and -chemical properties and may affect signaling and interactions at the molecular and cellular level, relatively little is known about the lipid composition of EV membranes. Here, we applied high resolution mass spectrometry to deeply and quantitatively characterize the lipidome of EVs isolated from a panel of malignant and non-malignant cell lines, providing a comprehensive data resource for biomarker research and EV engineering efforts. Furthermore, subset comparisons indicate striking differences between lipid profiles of EVs isolated from cells of different tissue origin, suggesting distinct membrane characteristics that could affect EV biodistribution and function in vivo. |
| Institute: | European Molecular Biology Laboratory |
| Department: | EMBL Heidelberg |
| Last Name: | Drotleff |
| First Name: | Bernhard |
| Address: | Meyerhofstr. 1, Heidelberg, BW, 69117, Germany |
| Email: | bernhard.drotleff@embl.de |
| Phone: | none |
| Publications: | in preparation |
| Contributors: | Alperen Acari, Pragati Lodha, Selin Özhan, Shruthi Hemanna, Jochen Rieck, Bernhard Drotleff, Lothar C. Dieterich |
Subject:
| Subject ID: | SU004140 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Cell line | Species | Disease |
|---|---|---|---|---|---|
| SA461384 | Blank_PBS+IS | Blank | Blank | - | - |
| SA461385 | Blank_PBS+IS_end | Blank | Blank | - | - |
| SA461386 | Blank_Medium | Blank | Blank | - | - |
| SA461387 | Blank_Medium_end | Blank | Blank | - | - |
| SA461388 | A_R2_L | Cell EVs | B16 | Mouse | Melanoma |
| SA461389 | A_R1_L | Cell EVs | B16 | Mouse | Melanoma |
| SA461390 | A_R4_L | Cell EVs | B16 | Mouse | Melanoma |
| SA461391 | A_R3_L | Cell EVs | B16 | Mouse | Melanoma |
| SA461392 | B_R2_L | Cell EVs | E0771 | Human | Breast cancer |
| SA461393 | B_R4_L | Cell EVs | E0771 | Human | Breast cancer |
| SA461394 | B_R1_L | Cell EVs | E0771 | Human | Breast cancer |
| SA461395 | B_R3_L | Cell EVs | E0771 | Human | Breast cancer |
| SA461396 | C_R1_L | Cell EVs | HEK293T | Human | Embryonic kidney cells |
| SA461397 | C_R2_L | Cell EVs | HEK293T | Human | Embryonic kidney cells |
| SA461398 | C_R3_L | Cell EVs | HEK293T | Human | Embryonic kidney cells |
| SA461399 | C_R4_L | Cell EVs | HEK293T | Human | Embryonic kidney cells |
| SA461400 | D_R4_L | Cell EVs | MB49-luc2 | Mouse | Bladder cancer |
| SA461401 | D_R2_L | Cell EVs | MB49-luc2 | Mouse | Bladder cancer |
| SA461402 | D_R1_L | Cell EVs | MB49-luc2 | Mouse | Bladder cancer |
| SA461403 | D_R3_L | Cell EVs | MB49-luc2 | Mouse | Bladder cancer |
| SA461404 | E_R1_L | Cell EVs | MC38 | Mouse | Colorectal cancer |
| SA461405 | E_R2_L | Cell EVs | MC38 | Mouse | Colorectal cancer |
| SA461406 | E_R3_L | Cell EVs | MC38 | Mouse | Colorectal cancer |
| SA461407 | E_R4_L | Cell EVs | MC38 | Mouse | Colorectal cancer |
| SA461408 | F_R4_L | Cell EVs | Melan-A | Mouse | Non-malignant melanocyte |
| SA461409 | F_R2_L | Cell EVs | Melan-A | Mouse | Non-malignant melanocyte |
| SA461410 | F_R3_L | Cell EVs | Melan-A | Mouse | Non-malignant melanocyte |
| SA461411 | F_R1_L | Cell EVs | Melan-A | Mouse | Non-malignant melanocyte |
| SA461412 | G_R1_L | Cell EVs | Sk-Mel28 | Human | Melanoma |
| SA461413 | G_R2_L | Cell EVs | Sk-Mel28 | Human | Melanoma |
| SA461414 | G_R4_L | Cell EVs | Sk-Mel28 | Human | Melanoma |
| SA461415 | G_R3_L | Cell EVs | Sk-Mel28 | Human | Melanoma |
| SA461416 | H_R2_L | Cell EVs | Yumm1.7 | Mouse | Melanoma |
| SA461417 | H_R3_L | Cell EVs | Yumm1.7 | Mouse | Melanoma |
| SA461418 | H_R4_L | Cell EVs | Yumm1.7 | Mouse | Melanoma |
| SA461419 | H_R1_L | Cell EVs | Yumm1.7 | Mouse | Melanoma |
| SA461420 | I_R4_L | Cell EVs | Yummer | Mouse | Melanoma |
| SA461421 | I_R3_L | Cell EVs | Yummer | Mouse | Melanoma |
| SA461422 | I_R2_L | Cell EVs | Yummer | Mouse | Melanoma |
| SA461423 | I_R1_L | Cell EVs | Yummer | Mouse | Melanoma |
| SA461424 | QC03 | pooled QC | pooled QC | - | - |
| SA461425 | QC05 | pooled QC | pooled QC | - | - |
| SA461426 | QC06 | pooled QC | pooled QC | - | - |
| SA461427 | QC07 | pooled QC | pooled QC | - | - |
| SA461428 | QC08 | pooled QC | pooled QC | - | - |
| SA461429 | QC09 | pooled QC | pooled QC | - | - |
| SA461430 | QC10 | pooled QC | pooled QC | - | - |
| SA461431 | QC11 | pooled QC | pooled QC | - | - |
| SA461432 | QC12_end | pooled QC | pooled QC | - | - |
| SA461433 | QC04 | pooled QC | pooled QC | - | - |
| Showing results 1 to 50 of 50 |
Collection:
| Collection ID: | CO004133 |
| Collection Summary: | We selected a total of 9 cell lines of non-malignant and malignant origin, representing a range of tissue origins. These included the murine melanoma cell lines B16-F10, YUMM1.7 and the closely related YUMMER1.7, the non-malignant melanocyte cell line Melan-A, colorectal carcinoma cells MC38, the luminal B-type breast cancer cell line E0771 and the bladder cancer cell line MB49 (all C57Bl/6 syngeneic). In addition, we included the human melanoma cell line SK-Mel-28 and HEK293T human embryonic kidney cells. Cell lines: B16-F10 (ATCC), E0771 (kindly provided by Dr. Mahak Singhal, Medical Faculty Mannheim, Heidelberg University), HEK293T, MB49-luc2, MC38 (all provided by Prof. Michael Detmar, Swiss Federal Institute of Technology Zurich), and SK-Mel-28 (kindly provided by Prof. Dr. Rüdiger Rudolf, Mannheim University of Applied Science) cells were cultured in DMEM media supplemented with pyruvate, glutamax, and 10% FBS (all Gibco). The YUMMER1.7 [12] (kindly provided by Prof. Dr. Cornelia Halin, Swiss Federal Institute of Technoloy Zurich) and YUMM1.7 [13] (kindly provided by Prof. Dr. Jonathan Sleeman, Medical Faculty Mannheim, Heidelberg University) cells were cultured in DMEM/F12 media supplemented with 1% non-essential amino acids (NEAA) and 10% FBS. Melan-A cells (kindly provided by Prof. Jonathan Sleeman, Medical Faculty Mannheim, Heidelberg University) were cultured in RPMI media with 200 nM phorbol 12-myristate 13-acetate (PMA) and 10% FBS. EV isolation: For EV production, cells were cultured for 48 hours in DMEM media with 5% exosome-free FBS (Gibco). The supernatant was collected and cleared from dead cells and debris by centrifugation at 700 g for 10 min. Next, the clarified media was concentrated using 100 kDa cutoff centrifugal filter units (Amicon) to a volume of ≤500 μL. Then, EVs were isolated using 70 nm pore-sized resin size exclusion chromatography (SEC) columns (iZON) according to the manufacturer’s instructions. For lipid extraction, 5 x 109 EVs were pelleted by ultracentrifugation at 100.000 g, 4 oC for an hour using an Micro Ultracentrifuge CS 150FNX (Hitachi). |
| Sample Type: | Cell derived Extracellular Vesicles |
Treatment:
| Treatment ID: | TR004149 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP004146 |
| Sampleprep Summary: | Pelleted samples were reconstituted in 250 µL isopropanol/methanol (50:50, v:v; including internal standards). After vortexing for 30 sec, shaking for 30 min at 4 °C, and subsequent centrifugation for 10 min at 15,000g and 4 °C with a 5415R microcentrifuge (Eppendorf, Hamburg, Germany), extract supernatants were transferred to analytical glass vials and placed in the autosampler. |
Chromatography:
| Chromatography ID: | CH005010 |
| Chromatography Summary: | LC-MS/MS analysis was performed on a Vanquish UHPLC system coupled to an Orbitrap Exploris 240 high-resolution mass spectrometer (Thermo Scientific, MA, USA) in positive ESI (electrospray ionization) mode. Chromatographic separation was carried out on an ACQUITY Premier CSH C18 column (Waters; 2.1 mm x 100 mm, 1.7 µm) at a flow rate of 0.3 mL/min. The mobile phase consisted of water:ACN (40:60, v/v; mobile phase phase A) and IPA:ACN (9:1, v/v; mobile phase B), which were modified with a total buffer concentration of 10 mM ammonium formate + 0.1% formic acid. The following gradient (23 min total run time including re-equilibration) was applied (min/%B): 0/15, 2.5/30, 3.2/48, 15/82, 17.5/99, 19.5/99, 20/15, 23/15. Column temperature was maintained at 65°C, the autosampler was set to 4°C and sample injection volume was 5 µL. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | time [min]/%B: 0/15, 2.5/30, 3.2/48, 15/82, 17.5/99, 19.5/99, 20/15, 23/15 |
| Flow Rate: | 0.3mL/min |
| Solvent A: | 40% water/60% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005011 |
| Chromatography Summary: | LC-MS/MS analysis was performed on a Vanquish UHPLC system coupled to an Orbitrap Exploris 240 high-resolution mass spectrometer (Thermo Scientific, MA, USA) in negative ESI (electrospray ionization) mode. Chromatographic separation was carried out on an ACQUITY Premier CSH C18 column (Waters; 2.1 mm x 100 mm, 1.7 µm) at a flow rate of 0.3 mL/min. The mobile phase consisted of water:ACN (40:60, v/v; mobile phase phase A) and IPA:ACN (9:1, v/v; mobile phase B), which were modified with a total buffer concentration of 10 mM ammonium acetate + 0.1% acetic acid. The following gradient (23 min total run time including re-equilibration) was applied (min/%B): 0/15, 2.5/30, 3.2/48, 15/82, 17.5/99, 19.5/99, 20/15, 23/15. Column temperature was maintained at 65°C, the autosampler was set to 4°C and sample injection volume was 7 µL. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | time [min]/%B: 0/15, 2.5/30, 3.2/48, 15/82, 17.5/99, 19.5/99, 20/15, 23/15 |
| Flow Rate: | 0.3mL/min |
| Solvent A: | 40% water/60% acetonitrile; 10 mM ammonium acetate; 0.1% acetic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10 mM ammonium acetate; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006600 |
| Analysis Type: | MS |
| Chromatography ID: | CH005010 |
| Num Factors: | 11 |
| Num Metabolites: | 332 |
| Units: | peak area |
| Analysis ID: | AN006601 |
| Analysis Type: | MS |
| Chromatography ID: | CH005011 |
| Num Factors: | 11 |
| Num Metabolites: | 279 |
| Units: | Peak area |
