Summary of Study ST000220
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 PR000050. The data can be accessed directly via it's Project DOI: 10.21228/M8RG6T This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000220 |
| Study Title | Small cell lung cancer metabolome (part II) |
| Study Type | Comparison of normal, lung adenocarcinoma and SCLC tissue metabolomes |
| Study Summary | In addition to the generation and analysis of metabolomics data on cell lines, samples of normal lung tissue, adenocarcinoma lung tissue and small cell lung carcinoma tissue (seven samples/group) were processed and evaluated metabolite profile differences under the scope of the pilot and feasibility study. These data can be correlated to the metabolite profiles defined in the SCLC and NSCLC cell lines and integrated with the ABPP-determined metabolic kinases to identify distinct metabolic signatures or biomarkers (?oncometabolites?) that distinguish small cell lung cancer from non-small cell lung cancer. |
| Institute | University of North Carolina |
| Department | Systems and Translational Sciences |
| Laboratory | Sumner Lab |
| Last Name | Sumner |
| First Name | Susan |
| Address | Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081 |
| susan_sumner @unc.edu | |
| Phone | 704-250-5066 |
| Submit Date | 2015-06-26 |
| Num Groups | 3 |
| Total Subjects | 21 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Waters) |
| Uploaded File Size | 58 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-07-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000050 |
| Project DOI: | doi: 10.21228/M8RG6T |
| Project Title: | Small cell lung cancer metabolome |
| Project Type: | Metabolomic profiling comparison between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), to define novel biomarkers for therapy, diagnostics and early detection. |
| Project Summary: | The goal of this pilot project is to comprehensively evaluate metabolic underpinnings of small cell lung cancer (SCLC) and couple with proteome level measurements of global kinase and other enzyme level expression data to provide insight into the upstream signaling networks that may be driving the pathogenesis of SCLC. Alterations in cancer metabolism are increasingly realized as an emerging area of research and potentially offers new therapeutic strategies. As part of ongoing studies, we are employing a chemical biology platform, activity-based protein profiling (ABPP), to study the SCLC proteome. ABPP uses chemical probes that are directed against the active sites of enzymes to interrogate the functional state of enzymes in biological samples. We used ATP based probes to study differences in kinase and other ATP binding proteins between SCLC and non-small cell lung cancer (NSCLC). We used well curated lung cancer cell lines that facilitate functional analysis of key proteins and pathways. Interestingly, our preliminary data strongly implicates hyperactivated metabolic pathways in SCLC when compared to NSCLC cell lines. A strong signal of upregulated metabolic kinases and other proteins involved in glycolysis, pyruvate metabolism, and purine metabolism have been identified through this approach. However, whether the alterations in the protein levels identified through this proteomic based approach corresponds to altered levels of metabolites through metabolic pathways remains unclear. This new opportunity will allow us to profile SCLC for alterations in metabolism that can be compared to NSCLC. We will conduct metabolomics studies on our SCLC cell lines. Relationships between the underlying alterations in metabolic kinases and other signaling molecules and mechanisms promoting the aggressive phenotype of these SCLC tumors remain unclear. We will collaborate with the NIH Eastern Regional Comprehensive Metabolomics Resource Core at RTI International (RTI RCMRC) to enable metabolomic profiling and analysis of our existing cell lines and tumor tissues. |
| Institute: | H. Lee Moffitt Cancer Center |
| Department: | NCI-designated comprehensive cancer center |
| Last Name: | Haura |
| First Name: | Eric B. |
| Address: | 12902 Magnolia Drive, MRC 3 East |
| Email: | eric.haura@moffitt.org |
| Phone: | 813-745-6827 |
Subject:
| Subject ID: | SU000239 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Biosource Or Supplier: | Moffitt Cancer Center Tissue Core |
| Species Group: | Human |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Histology Type Conformed - CAP |
|---|---|---|
| SA010716 | SF-100109-231142 | Adenocarcinoma, NOS |
| SA010717 | SF-100109-244079 | Adenocarcinoma, NOS |
| SA010718 | SF-100109-227718 | Adenocarcinoma, NOS |
| SA010719 | SF-120831-00062 | Adenocarcinoma, NOS |
| SA010720 | SF-100109-255622 | Adenocarcinoma, NOS |
| SA010721 | SF-100109-239012 | Adenocarcinoma, NOS |
| SA010722 | SF-100109-259700 | Adenocarcinoma, NOS |
| SA010736 | SF-110121-00073 | Combined small cell carcinoma |
| SA010723 | SF-100109-114720 | Normal |
| SA010724 | SF-100109-121711 | Normal |
| SA010725 | SF-100109-130034 | Normal |
| SA010726 | SF-100109-124896 | Normal |
| SA010727 | SF-100109-199550 | Normal |
| SA010728 | SF-100109-169058 | Normal |
| SA010729 | SF-100109-124904 | Normal |
| SA010734 | SF-100109-146730 | Small cell carcinoma |
| SA010730 | SF-100109-199546 | Small cell carcinoma, NOS |
| SA010731 | SF-100109-225118 | Small cell carcinoma, NOS |
| SA010732 | SF-100109-252159 | Small cell carcinoma, NOS |
| SA010733 | SF-110908-00016 | Small cell carcinoma, NOS |
| SA010735 | SF-100109-142930 | Small cell carcinoma, NOS |
| Showing results 1 to 21 of 21 |
Collection:
| Collection ID: | CO000227 |
| Collection Summary: | - |
| Sample Type: | tissue |
| Collection Method: | Snap frozen |
Treatment:
| Treatment ID: | TR000247 |
Sample Preparation:
| Sampleprep ID: | SP000241 |
| Sampleprep Summary: | Pulverized tissue samples were incubated in 50:50 Acetonitrile:Water for 1 hr, vortexed and centrifuged. Supernatants were transferred to new tubes along with isotopocially labled internal standard and samples were lyophilized to dryness. Dried samples were resuspended in 95:5 Water:Methanol and an aliquot was transferred to autosampler vials forbroad spectrum metabolomics data analysis acquisition. |
| Processing Method: | Pulverization of frozen tissue (performed at Moffitt and supplied to RTI) |
| Extraction Method: | 50:50 Acetonitrile:Water |
| Extract Storage: | -80 C |
| Sample Resuspension: | 95:5 Water:Methanol |
| Sample Spiking: | L-Tryptophan-d5 |
| Organ: | Lung |
Combined analysis:
| Analysis ID | AN000325 | AN000326 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Waters Synapt-G2-Si | Waters Synapt-G2-Si |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Normalized abundance | Normalized abundance |
Chromatography:
| Chromatography ID: | CH000245 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| Column Pressure: | 6000-10000 |
| Column Temperature: | 50 C |
| Flow Gradient: | Time(min) Flow Rate %A %B Curve; 1. Initial 0.400 100.0 0.0; 2. 1.00 0.400 100.0 0.0 6;3. 16.00 0.400 0.0 100.0 6; 4. 20.00 0.400 0.0 100.0 6; 5. 22.00 0.400 100.0 0.0 6 |
| Flow Rate: | 0.4 mL/min |
| Injection Temperature: | 8 C |
| Internal Standard: | L-Tryptophan-d5 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Analytical Time: | 22 min |
| Weak Wash Solvent Name: | 5%MeOH |
| Weak Wash Volume: | 1000 uL |
| Strong Wash Solvent Name: | 80%MeOH |
| Strong Wash Volume: | 1000 uL |
| Target Sample Temperature: | 8 C |
| Sample Loop Size: | 10 uL |
| Sample Syringe Size: | 100 uL |
| Randomization Order: | Yes |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000274 |
| Analysis ID: | AN000325 |
| Instrument Name: | Waters Synapt-G2-Si |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 110 C |
| Capillary Voltage: | 1.0 kV |
| Collision Energy: | 4 |
| Fragmentation Method: | CID |
| Helium Flow: | 180 |
| Ionization: | ES+ |
| Mass Accuracy: | 5 ppm |
| Source Temperature: | 110 C |
| Dataformat: | Continuum |
| Desolvation Gas Flow: | 400 L/Hr |
| Desolvation Temperature: | 400 C |
| Resolution Setting: | 18000 |
| Scan Range Moverz: | 50-1000 m/s |
| Scanning Cycle: | 1 s |
| Tube Lens Voltage: | 75 |
| MS ID: | MS000275 |
| Analysis ID: | AN000326 |
| Instrument Name: | Waters Synapt-G2-Si |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 110 C |
| Capillary Voltage: | 1.0 kV |
| Collision Energy: | 4 |
| Fragmentation Method: | CID |
| Helium Flow: | 180 |
| Ionization: | ES- |
| Mass Accuracy: | 5 ppm |
| Source Temperature: | 110 C |
| Dataformat: | Continuum |
| Desolvation Gas Flow: | 400 L/Hr |
| Desolvation Temperature: | 400 C |
| Resolution Setting: | 18000 |
| Scan Range Moverz: | 50-1000 m/z |
| Scanning Cycle: | 1 s |
| Tube Lens Voltage: | 74 |
