Summary of Study ST002991
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 PR001862. The data can be accessed directly via it's Project DOI: 10.21228/M81M8F 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 | ST002991 |
| Study Title | Metabolomics studies on human colorectal cancer cell lines |
| Study Summary | Although targeting oxidative phosphorylation (OXPHOS) for cancer treatment is currently impeded due to dose-limiting toxicities, there remain opportunities through combinations that provide therapeutic benefits at doses attainable in patients. On the other hand, while glycolysis-deficient cancers are generally vulnerable to OXPHOS inhibition in preclinical models, the full extent of phenotypical and mechanistic consequences of inhibiting OXPHOS in cancers capable of glycolysis is not yet well understood. We aimed to clarify the response and underlying mechanisms of colorectal cancer (CRC) that commonly exhibit the glycolytic phenotype to OXPHOS inhibition and to identify potential approaches to render such cells more sensitive to OXPHOS inhibitors. The responses of glycolysis-competent CRC cells to targeting OXPHOS were tested using targeted meatbolomics. |
| Institute | The University of Newcastle |
| Last Name | Zhao |
| First Name | Xiaohong |
| Address | University Drive, Callaghan, NSW, 2308, Australia |
| xiaohong.zhao@newcastle.edu.au | |
| Phone | 61 0466219528 |
| Submit Date | 2023-11-27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-01-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001862 |
| Project DOI: | doi: 10.21228/M81M8F |
| Project Title: | DNA replication stress underpins the vulnerability to oxidative phosphorylation inhibition in colorectal cancer |
| Project Summary: | Although targeting oxidative phosphorylation (OXPHOS) for cancer treatment is currently impeded due to dose-limiting toxicities, there remain opportunities through combinations that provide therapeutic benefits at doses attainable in patients. On the other hand, while glycolysis-deficient cancers are generally vulnerable to OXPHOS inhibition in preclinical models, the full extent of phenotypical and mechanistic consequences of inhibiting OXPHOS in cancers capable of glycolysis is not yet well understood. We aimed to clarify the response and underlying mechanisms of colorectal cancer (CRC) that commonly exhibit the glycolytic phenotype to OXPHOS inhibition and to identify potential approaches to render such cells more sensitive to OXPHOS inhibitors. |
| Institute: | The University of Newcastle |
| Last Name: | Zhao |
| First Name: | Xiaohong |
| Address: | University Drive, Callaghan, NSW, 2308, Australia |
| Email: | xiaohong.zhao@newcastle.edu.au |
| Phone: | 61 0466219528 |
Subject:
| Subject ID: | SU003104 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA325792 | LJ_038 | 100 nM IACS-010759 |
| SA325793 | LJ_026 | 100 nM IACS-010759 |
| SA325794 | LJ_037 | 100 nM IACS-010759 |
| SA325795 | LJ_041 | 100 nM IACS-010759 |
| SA325796 | LJ_027 | 100 nM IACS-010759 |
| SA325797 | LJ_029 | 100 nM IACS-010759 |
| SA325798 | LJ_031 | 100 nM IACS-010759+10 mM Aspartate |
| SA325799 | LJ_048 | 100 nM IACS-010759+10 mM Aspartate |
| SA325800 | LJ_032 | 100 nM IACS-010759+10 mM Aspartate |
| SA325801 | LJ_034 | 100 nM IACS-010759+10 mM Aspartate |
| SA325802 | LJ_046 | 100 nM IACS-010759+10 mM Aspartate |
| SA325803 | LJ_045 | 100 nM IACS-010759+10 mM Aspartate |
| SA325786 | LJ_023 | 10 mM Aspartate |
| SA325787 | LJ_024 | 10 mM Aspartate |
| SA325788 | LJ_010 | 10 mM Aspartate |
| SA325789 | LJ_008 | 10 mM Aspartate |
| SA325790 | LJ_009 | 10 mM Aspartate |
| SA325791 | LJ_020 | 10 mM Aspartate |
| SA325804 | LJ_014 | Control |
| SA325805 | LJ_002 | Control |
| SA325806 | LJ_006 | Control |
| SA325807 | LJ_001 | Control |
| SA325808 | LJ_015 | Control |
| SA325809 | LJ_018 | Control |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003097 |
| Collection Summary: | 1. Metabolic Arrest 1.1 Remove culture from incubator 1.2 Aspirate media from wells using vacuum sipper 1.3 Dispense about 1mL of 37oC MilliQ water to the cell surface 1.4 Briefly ‘rock’ the plate for 2 secs 1.5 Aspirate the water off the cells 1.6 Wait 3 more secs then add ~ enough LN2 to cover surface of well/plate 1.7 Briefly store on dry ice, and transfer to a -80oC freezer if not extracting immediately. 1.8 Extract/assay within 7 days 1.9 Time to complete steps 1.3 – 1.5 should be minimised to prevent changes in metabolic state due to cells being stressed 2. Metabolic Extraction 2.1 Transfer plates from the -80 deg C freezer to a 4 deg C cold room 2.2 Add 500μL of ice cold 9:1 MeOH:CHCl3, v/v (+ internal standards, allow to incubate for 10 minutes 2.3 Scrape/suspend with a cell lifter 2.4 Transfer to 1.5mL microcentrifuge tubes, Vortex for 30s 2.5 Thermomix at 950rpm for 5 mins 2.6 Centrifuge at 15,000rpm for 5 mins |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003113 |
| Treatment Summary: | After seeding cells in 6-well plates for 24 hours, Colo205 and LIM1215 cells were treated with Vehicle control DMSO, 100 nM IACS-010759, 10 mM Aspartate, 100 nM IACS-010759 combined with 10 mM Aspartate, for 24 hours. |
Sample Preparation:
| Sampleprep ID: | SP003110 |
| Sampleprep Summary: | Add 500uL of ice cold 1:9 chloroform:methanol (+ internal standards) and scrape/suspend with a cell lifter Transfer to 1.5 mL microcentrifuge tubes Vortex for 30s Thermomix at 950rpm for 5 mins Centrifuge at 15,000rpm for 5 mins |
Combined analysis:
| Analysis ID | AN004911 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 1200 |
| Column | Merck Millipore SeQuant ZIC-pHILIC column (150 mm × 4.6 mm, 5 μm) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6545 QTOF |
| Ion Mode | NEGATIVE |
| Units | peak intensity |
Chromatography:
| Chromatography ID: | CH003706 |
| Instrument Name: | Agilent 1200 |
| Column Name: | Merck Millipore SeQuant ZIC-pHILIC column (150 mm × 4.6 mm, 5 μm) |
| Column Temperature: | 30 ◦C |
| Flow Gradient: | time (t) =0 min, 80% B; t =0.5 min, 80% B; t =15.5 min, 50% B; t =17.5 min, 30% B; t =18.5 min, 5% B, t =21.0 min, 5% B; t =23 min, 80% B, t =33 min, 80% B. |
| Flow Rate: | 300 μL/min |
| Solvent A: | 20 mM (NH4)2CO3, pH 9.0, Sigma-Aldrich |
| Solvent B: | 100% acetonitrile, Hypergrade for LCMS LiChrosolv, Merck |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004654 |
| Analysis ID: | AN004911 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Peak intensity data was analyzed using MetaboAnalyst. Briefly, data was normalized using median, log2FC, and p-value was generated using one-factor statistical analysis. |
| Ion Mode: | NEGATIVE |
