Summary of Study ST001755
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 PR001125. The data can be accessed directly via it's Project DOI: 10.21228/M88X12 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 | ST001755 |
| Study Title | A reductionist approach using primary and metastatic cell-derived extracellular vesicles reveals hub proteins associated with oral cancer prognosis |
| Study Summary | Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher the role of EV cargo in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of extracellular vesicles (EVs) derived from human primary tumor (SCC-9) cells and matched lymph node metastases (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 64 lipids differentially abundant between LN1- and SCC-9-derived EVs. A multi-omics integration identified 11 ‘hub proteins’ significantly decreased at the metastatic site compared to primary tumor-derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases, and found that low abundance of seven hub proteins in metastatic EVs is correlated with reduced survival and tumor aggressiveness in cancer patients. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis, and which may potentially serve as prognostic markers in OSCC. |
| Institute | National Center for Research in Energy and Materials |
| Department | Brazilian Biosciences National Laboratory - LNBio |
| Laboratory | Mass Spectrometry Laboratory |
| Last Name | Busso Lopes |
| First Name | Ariane |
| Address | R. Giuseppe Máximo Scolfaro, 10000 |
| ariane.lopes@lnbio.cnpem.br | |
| Phone | +55 19 3512-1276 |
| Submit Date | 2021-04-26 |
| Num Groups | 2 |
| Total Subjects | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-05-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001125 |
| Project DOI: | doi: 10.21228/M88X12 |
| Project Title: | A reductionist approach using primary and metastatic cell-derived extracellular vesicles reveals hub proteins associated with oral cancer prognosis |
| Project Summary: | Metabolomics analysis of cancer-derived extracellular vesicles. |
| Institute: | National Center for Research in Energy and Materials - CNPEM |
| Department: | Brazilian Biosciences National Laboratory - LNBio |
| Laboratory: | Mass Spectrometry Laboratory |
| Last Name: | Busso Lopes |
| First Name: | Ariane |
| Address: | R. Giuseppe Máximo Scolfaro, 10000, Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil |
| Email: | ariane.lopes@lnbio.cnpem.br |
| Phone: | +55 19 3512-1276 |
Subject:
| Subject ID: | SU001832 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | SCC-9 and LN1 |
| Cell Strain Details: | Primary tumor (SCC-9) and metastatic (LN1) oral cancer cell lines |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA163992 | LN1_3-EV intensity | Metastatic EV |
| SA163993 | LN1_4-EV intensity | Metastatic EV |
| SA163994 | LN1_5-EV intensity | Metastatic EV |
| SA163995 | LN1_2-EV intensity | Metastatic EV |
| SA163996 | LN1_1-EV intensity | Metastatic EV |
| SA163997 | SCC-9_2-EV intensity | Primary tumor EV |
| SA163998 | SCC-9_3-EV intensity | Primary tumor EV |
| SA163999 | SCC-9_4-EV intensity | Primary tumor EV |
| SA164000 | SCC-9_5-EV intensity | Primary tumor EV |
| SA164001 | SCC-9_1-EV intensity | Primary tumor EV |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO001825 |
| Collection Summary: | EVs were isolated from SCC-9 and LN1 cell cultures through differential centrifugation. Cells were cultured until 80% cell confluence in 150 mm diameter plates, washed three times with phosphate buffered saline (PBS) and further cultivated for 48 h in media without FBS, at 37°C and 5% CO2. After serum deprivation treatment, the conditioned media (200 mL) was collected and centrifuged at 200 x g for 5 min, 2,000 x g for 15 min, 3,500 x g for 30 min and 10,000 x g for 90 min. The cleared supernatant was further ultracentrifuged at 100,000 x g for 90 min at 4°C and vesicle-containing pellets were washed with PBS by ultracentrifugation for 1.5 h at the same speed. The samples were stored at -80°C until further use. |
| Sample Type: | Keratinocytes |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001845 |
| Treatment Summary: | EVs were not submitted to any treatment prior to metabolites extraction. |
Sample Preparation:
| Sampleprep ID: | SP001838 |
| Sampleprep Summary: | SCC-9 and LN1-derived EVs (5x10e10 particles; 5 biological replicates for each group) were submitted to metabolite extraction using the MTBE method. Derivatization of metabolites was performed as outlined previously (Lisec et al., Nat Protoc. 2015;10(9):1457). |
Combined analysis:
| Analysis ID | AN002859 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Agilent DB-35MS (30m x 0,32mm x 0,25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus HT TOF |
| Ion Mode | POSITIVE |
| Units | intensity log2 |
Chromatography:
| Chromatography ID: | CH002117 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Agilent DB-35MS (30m x 0,32mm x 0,25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002652 |
| Analysis ID: | AN002859 |
| Instrument Name: | Leco Pegasus HT TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | GC-TOF-MS data were obtained using a PAL-Combi XT autosampler (PAL System, Switzerland, http://www.palsystem.com/), coupled to an Agilent 7890 A gas chromatograph - Leco Pegasus HT time-of-flight mass spectrometer (LECO, USA) in both split (1:15 and 1:50) and splitless modes (Weckwerth et al., 2004; 101:7809–14). Chromatograms were exported from Leco ChromaTOF software (version 3.25) to R. Peak detection, retention time alignment, and library matching were obtained using the TargetSearch package from Bioconductor (Cuadros-Inostroza et al., BMC Bioinformatics. 2009;10:428). Metabolites were quantified by peak intensity of a selective mass, and metabolite intensities were normalized dividing by the sum of the total ion count followed by log2 transformation. |
| Ion Mode: | POSITIVE |
| Collision Energy: | 70 eV |
