Summary of Study ST000528
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 PR000388. The data can be accessed directly via it's Project DOI: 10.21228/M8WP4C 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 | ST000528 |
| Study Title | Regulation of Metabolism by LSR |
| Study Type | LC-MS lipidomics |
| Study Summary | Our aim is to identify the LSR-driven metabolomics profile of breast cancer cells in lean and obesogenic environments. Breast cancer cell models with high or undetectable levels of LSR, including drug resistance models, were cultured in lean and obesogenic environments and comprehensive metabolomics profiling, including lipidomics-focused sub-analyses were performed. The metabolomics analyses using both approaches will help us determine if LSR enhances aggressive breast cancer phenotypes via modulation of cellular bioenergetic metabolism, ultimately contributing to poor patient outcome. |
| 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 | 2016-12-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-02-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000388 |
| Project DOI: | doi: 10.21228/M8WP4C |
| Project Title: | Regulation of Metabolism by LSR |
| Project Type: | LC-MS Lipidomics |
| Project Summary: | Breast cancer is a global crisis, accounting for nearly one quarter of all cancers in women. In the U.S., African-American (AA) women suffer disproportionately from breast cancer mortality compared to other racial/ethnic groups. Both social (socioeconomic factors, diet, obesity) and biological hypotheses (gene polymorphisms, gene expression profiling) have been advanced to explain these discrepancies, but the differences remain poorly understood. Multiple aspects of tumor aggressiveness have been identified in the AA population, including a high proportion of basal-like tumors. Basal-like tumors are clinically the most aggressive, characterized by enhanced cancer stem cell-like features. Currently, no effective molecular therapies exist for these highly aggressive cancers and patient survival is poor. Escalating this disparity is the disease promoting effects of obesity and metabolic syndrome, which are significantly higher in AA women. Obesity and its associated inflammation have been attributed to poor patient outcomes, resistance to chemotherapeutics, and/or cancer risk. A meta-analysis of 43 studies of obesity and breast cancer revealed that obese patients were 33% more likely than non-obese patients to die of breast cancer. Yet apart from correlative studies, no reports have combined these factors with cancer disparities to ascertain their molecular interactions and physiology on breast tumorigenesis. We tested the integration these factors, with focus on a specific molecule, Lipolysis Stimulated Lipoprotein Receptor (LSR), in the promotion of aggressive cancer behaviors. LSR is a cell surface molecule that regulates post-prandial lipid uptake in the liver, is sensitive to high fat diets, and is regulated by metabolic cues, including leptin. By testing each of these factors as well as their dynamic interactions on breast cancer tumorigenesis, we will gain valuable insight into biological mechanisms that influence cancer risk/disparities, response to therapy, and ultimately patient outcome. We recently reported LSR is overexpressed in breast tumors, directs aggressive breast cancer cell behaviors including proliferation and migration, and enhances cancer stem cell-like and chemotherapeutic resistance features in breast cancer cells. |
| Institute: | North Carolina Central University |
| Department: | Department of Biology |
| Last Name: | Fleming |
| First Name: | Jodie |
| Address: | 1801 Fayetteville Street, Durham, NC 27707 |
| Email: | Jodie.Fleming@nccu.edu |
| Phone: | 9195416861 |
Subject:
| Subject ID: | SU000550 |
| Subject Type: | Cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
Subject type: Cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Cell Line |
|---|---|---|
| SA027764 | POS_Lip_S_37_LSRH-L4 | Hs578t+ |
| SA027765 | POS_Lip_S_40_LSRH-L10 | Hs578t+ |
| SA027766 | POS_Lip_S_39_LSRH-L8 | Hs578t+ |
| SA027767 | POS_Lip_S_38_LSRH-L6 | Hs578t+ |
| SA027768 | POS_Lip_S_36_LSRH-L2 | Hs578t+ |
| SA027759 | POS_Lip_S_31_HS2 | Hs578t parental |
| SA027760 | POS_Lip_S_33_HS#2 | Hs578t parental |
| SA027761 | POS_Lip_S_35_HS#2 | Hs578t parental |
| SA027762 | POS_Lip_S_32_HS | Hs578t parental |
| SA027763 | POS_Lip_S_34_HS#2 | Hs578t parental |
| SA027769 | POS_Lip_S_27_MCF7-CRISPR | MCF7 CRISPR |
| SA027770 | POS_Lip_S_26_MCF7-CRISPR | MCF7 CRISPR |
| SA027771 | POS_Lip_S_28_MCF7-CRISPR | MCF7 CRISPR |
| SA027772 | POS_Lip_S_29-2_MCF7-CRISPR | MCF7 CRISPR |
| SA027773 | POS_Lip_S_30_MCF7-CRISPR | MCF7 CRISPR |
| SA027774 | POS_Lip_S_23_MCF7 | MCF7 parental |
| SA027775 | POS_Lip_S_25_MCF7 | MCF7 parental |
| SA027776 | POS_Lip_S_22_MCF7-2 | MCF7 parental |
| SA027777 | POS_Lip_S_21_MCF7-1 | MCF7 parental |
| SA027778 | POS_Lip_S_24_MCF7 | MCF7 parental |
| SA027779 | POS_Lip_P_30_JFtotPool3 | Study Pool |
| SA027780 | POS_Lip_P_29_JFtotPool2 | Study Pool |
| SA027781 | POS_Lip_P_31_JFtotPool4 | Study Pool |
| SA027782 | POS_Lip_P_32_JFtotPool5 | Study Pool |
| SA027783 | POS_Lip_P_33_JFtotPool6 | Study Pool |
| SA027784 | POS_Lip_EQ_P28_JFtotPool1-6 | Study Pool |
| Showing results 1 to 26 of 26 |
Collection:
| Collection ID: | CO000544 |
| Collection Summary: | 20 breast cancer cell pellets from four cell lines [MCF7 parental (LSR+), MCF7 Crisper (LSR-), Hs578t parental (LSR-) and Hs578t (LSR++)], with five replicate samples for each cell line were stored at -80˚ until sample preparation. |
| Sample Type: | Cell pellets |
| Storage Conditions: | -80˚C |
Treatment:
| Treatment ID: | TR000564 |
| Treatment Summary: | The cells were cultured under obesogenic media conditions. |
Sample Preparation:
| Sampleprep ID: | SP000557 |
| Sampleprep Summary: | Cell pellets were resuspended in volume of ice cold Lipid Extractions Solvent (50 µg/mL) based on biomass. Contents were transferred to new, pre-labeled 2.0 mL LoBind tube with 10-15 ceramic beads, and homogenized using 2 pulses at 2,000 rpm for 30 sec on a MagNA Lyser. Volume of HPLC-grade water (with 0.02 mg/mL Tryptophan-d5 in water) was added based on biomass. Samples were allowed to sit at room temperature for 10 minutes, then centrifuged at 16,000 rcf for 10 min at 10˚C. For lipidomics, transferred the maximum clean volume of the lower lipid-rich DCM layer to a new, pre-labeled LoBind tube and a 375 µL aliquot was then transferred to a new 1.5 mL, LoBind tube for analysis. An additional 125 µL aliquot of each study sample was transferred to a 7.0 mL glass vial to make a QC pool, which was vortexed for 30 sec and aliquoted into 5 Total Pool samples (375 µL each), and the remaining was used for 1 Equilibrium sample (column conditioning). Samples were frozen at -80˚C for 60 mins and lyophilized to dryness. Samples were reconstituted in ACN/IPA/H2O (65:30:5 v/v/v), vortexed at 4,000 rpm for 2 mins and centrifuged at 16,000 rcf for 4 min. 225 µL of the supernatant was transferred to pre-labeled autosampler vials and 10 µL was injected into OrbiTrap Velos. |
Combined analysis:
| Analysis ID | AN000806 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap |
| Ion Mode | POSITIVE |
| Units | m/z |
Chromatography:
| Chromatography ID: | CH000581 |
| Chromatography Summary: | Lipidomics |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 6000-7500psi |
| Column Temperature: | 50 °C |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 60% water/40% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Analytical Time: | 30 min |
| Weak Wash Solvent Name: | 60:40 water/ACN |
| Strong Wash Solvent Name: | 90:10 IPA/ACN |
| Target Sample Temperature: | 8 °C |
| Sample Loop Size: | 20 µL |
| Randomization Order: | Yes |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000713 |
| Analysis ID: | AN000806 |
| Instrument Name: | Thermo Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 250 °C |
| Collision Energy: | 35 eV |
| Fragmentation Method: | CID |
| Ionization: | ES+ |
| Mass Accuracy: | 10 ppm |
| Source Temperature: | 400 °C |
| Spray Voltage: | 4.0 kV |
| Dataformat: | Profile |
| Resolution Setting: | 30,000 |
| Scan Range Moverz: | 120-2000 m/z |
| Scanning Range: | Normal |
