Summary of Study ST003484
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 PR002140. The data can be accessed directly via it's Project DOI: 10.21228/M80R74 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 | ST003484 |
| Study Title | Metabolism of TNBC cell line MDA-MB-453 is altered by cytokines, TDO2 inhibition, or suspension growth conditions - cellular steady state metabolome and in vitro tracing with 13C11 tryptophan |
| Study Summary | TNBC cell line MDA-MB-453 was cultured in 13C11 tryptophan and experimental treatments were as follows: a) cytokine treatment (TNFα+IL1β); b) treated with TDO2/IDO1 dual inhibitor AT-0174 for 24 or 48 hours with an without labeled tryptophan; c) cultured in 13C11 tryptophan and suspension condition. |
| Institute | University of Colorado Anschutz Medical Campus |
| Last Name | Haines |
| First Name | Julie |
| Address | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| julie.haines@cuanschutz.edu | |
| Phone | 3037243339 |
| Submit Date | 2024-09-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-10-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002140 |
| Project DOI: | doi: 10.21228/M80R74 |
| Project Title: | Blocking tryptophan catabolism reduces triple-negative breast cancer invasive capacity |
| Project Summary: | Anchorage-independent triple-negative breast cancer (TNBC) cells exhibit elevated levels of the tryptophan (TRP) catabolizing enzyme tryptophan 2,3-dioxygenase 2 (TDO2) compared to the same cells grown in two-dimensional culture. Tracing of 13C11-TRP demonstrated that anchorage-independent culture and/or inflammatory cytokines that activate nuclear factor kappa-light-chain-enhancer of activated B (NFκB) increase TRP catabolism and production of downstream catabolites such as kynurenine (KYN), which activate the aryl hydrocarbon receptor (AhR). TDO2 expression is heterogeneous within TNBC cell lines. To determine the function of TDO2, both pharmacologic inhibition and genetic manipulation were conducted. TDO2 knockdown revealed a compensatory increase in indoleamine 2,3-dioxygenase 1 (IDO1), a non-homologous TRP catabolizing enzyme, indicating that dual inhibition of these two enzymes is necessary to reliably block TRP catabolism. Thus, we tested a newly developed TDO2/IDO1 dual inhibitor, AT-0174, and found that it effectively inhibits TNBC TRP catabolism. Furthermore, AT-0174 treatment or AhR inhibitor significantly decreased TNBC anchorage-independent survival, invasive capacity, and expression of mesenchymal genes and protein, while exogenous KYN increased invasion through AhR-mediated ZEB1 expression. Thus, dual inhibition of TDO2/IDO1 may prove efficacious against TNBC progression. |
| Institute: | University of Colorado Anschutz Medical Campus |
| Laboratory: | Lab of Angelo D'Alessandro in collaboration with lab of Jennifer Richer |
| Last Name: | Haines |
| First Name: | Julie |
| Address: | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| Email: | julie.haines@cuanschutz.edu |
| Phone: | 3037243339 |
Subject:
| Subject ID: | SU003612 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Gender: | Female |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Growth condition | time (h) | treatment | Sample source |
|---|---|---|---|---|---|
| SA383874 | MA0-2 | Attached | 0 | none | Breast cancer cells |
| SA383875 | MA0-1 | Attached | 0 | none | Breast cancer cells |
| SA383876 | MA0-3 | Attached | 0 | none | Breast cancer cells |
| SA383877 | MA610-24-3 | Attached | 24 | 10µM 68c091 | Breast cancer cells |
| SA383878 | MA610-24-2 | Attached | 24 | 10µM 68c091 | Breast cancer cells |
| SA383879 | MA610-24-1 | Attached | 24 | 10µM 68c091 | Breast cancer cells |
| SA383880 | MAA10-24-2 | Attached | 24 | 10µM AT0174 | Breast cancer cells |
| SA383881 | MAA10-24-3 | Attached | 24 | 10µM AT0174 | Breast cancer cells |
| SA383882 | MAA10-24-1 | Attached | 24 | 10µM AT0174 | Breast cancer cells |
| SA383883 | MAA1-24-2 | Attached | 24 | 1µM AT0174 | Breast cancer cells |
| SA383884 | MAA1-24-1 | Attached | 24 | 1µM AT0174 | Breast cancer cells |
| SA383885 | MAA1-24-3 | Attached | 24 | 1µM AT0174 | Breast cancer cells |
| SA383886 | MAD-24-1 | Attached | 24 | DMSO | Breast cancer cells |
| SA383887 | MAD-24-3 | Attached | 24 | DMSO | Breast cancer cells |
| SA383888 | MAD-24-2 | Attached | 24 | DMSO | Breast cancer cells |
| SA383889 | MAT-24-1 | Attached | 24 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383890 | MAT-24-2 | Attached | 24 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383891 | MAT-24-3 | Attached | 24 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383892 | MAV-24-1 | Attached | 24 | Vehicle | Breast cancer cells |
| SA383893 | MAV-24-2 | Attached | 24 | Vehicle | Breast cancer cells |
| SA383894 | MAV-24-3 | Attached | 24 | Vehicle | Breast cancer cells |
| SA383895 | MA610-48-1 | Attached | 48 | 10µM 68c091 | Breast cancer cells |
| SA383896 | MA610-48-2 | Attached | 48 | 10µM 68c091 | Breast cancer cells |
| SA383897 | MA610-48-3 | Attached | 48 | 10µM 68c091 | Breast cancer cells |
| SA383898 | MAA10-48-2 | Attached | 48 | 10µM AT0174 | Breast cancer cells |
| SA383899 | MAA10-48-1 | Attached | 48 | 10µM AT0174 | Breast cancer cells |
| SA383900 | MAA10-48-3 | Attached | 48 | 10µM AT0174 | Breast cancer cells |
| SA383901 | MAA1-48-2 | Attached | 48 | 1µM AT0174 | Breast cancer cells |
| SA383902 | MAA1-48-1 | Attached | 48 | 1µM AT0174 | Breast cancer cells |
| SA383903 | MAA1-48-3 | Attached | 48 | 1µM AT0174 | Breast cancer cells |
| SA383904 | MAD-48-3 | Attached | 48 | DMSO | Breast cancer cells |
| SA383905 | MAD-48-2 | Attached | 48 | DMSO | Breast cancer cells |
| SA383906 | MAD-48-1 | Attached | 48 | DMSO | Breast cancer cells |
| SA383907 | MAT-48-1 | Attached | 48 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383908 | MAT-48-2 | Attached | 48 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383909 | MAT-48-3 | Attached | 48 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383913 | MA48-3 | Attached | 48 | none | Breast cancer cells |
| SA383914 | MA48-1 | Attached | 48 | none | Breast cancer cells |
| SA383915 | MA48-2 | Attached | 48 | none | Breast cancer cells |
| SA383910 | MAV-48-1 | Attached | 48 | Vehicle | Breast cancer cells |
| SA383911 | MAV-48-2 | Attached | 48 | Vehicle | Breast cancer cells |
| SA383912 | MAV-48-3 | Attached | 48 | Vehicle | Breast cancer cells |
| SA383916 | MA72-3 | Attached | 72 | none | Breast cancer cells |
| SA383917 | MA72-2 | Attached | 72 | none | Breast cancer cells |
| SA383918 | MA72-1 | Attached | 72 | none | Breast cancer cells |
| SA383919 | MS0-3 | Suspension | 0 | none | Breast cancer cells |
| SA383920 | MS0-1 | Suspension | 0 | none | Breast cancer cells |
| SA383921 | MS0-2 | Suspension | 0 | none | Breast cancer cells |
| SA383922 | MS610-24-1 | Suspension | 24 | 10µM 68c091 | Breast cancer cells |
| SA383923 | MS610-24-2 | Suspension | 24 | 10µM 68c091 | Breast cancer cells |
| SA383924 | MS610-24-3 | Suspension | 24 | 10µM 68c091 | Breast cancer cells |
| SA383925 | MSA10-24-2 | Suspension | 24 | 10µM AT0174 | Breast cancer cells |
| SA383926 | MSA10-24-3 | Suspension | 24 | 10µM AT0174 | Breast cancer cells |
| SA383927 | MSA10-24-1 | Suspension | 24 | 10µM AT0174 | Breast cancer cells |
| SA383928 | MSA1-24-2 | Suspension | 24 | 1µM AT0174 | Breast cancer cells |
| SA383929 | MSA1-24-3 | Suspension | 24 | 1µM AT0174 | Breast cancer cells |
| SA383930 | MSA1-24-1 | Suspension | 24 | 1µM AT0174 | Breast cancer cells |
| SA383931 | MSD-24-3 | Suspension | 24 | DMSO | Breast cancer cells |
| SA383932 | MSD-24-1 | Suspension | 24 | DMSO | Breast cancer cells |
| SA383933 | MSD-24-2 | Suspension | 24 | DMSO | Breast cancer cells |
| SA383934 | MST-24-3 | Suspension | 24 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383935 | MST-24-1 | Suspension | 24 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383936 | MST-24-2 | Suspension | 24 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383937 | MSV-24-2 | Suspension | 24 | Vehicle | Breast cancer cells |
| SA383938 | MSV-24-3 | Suspension | 24 | Vehicle | Breast cancer cells |
| SA383939 | MSV-24-1 | Suspension | 24 | Vehicle | Breast cancer cells |
| SA383940 | MS610-48-2 | Suspension | 48 | 10µM 68c091 | Breast cancer cells |
| SA383941 | MS610-48-1 | Suspension | 48 | 10µM 68c091 | Breast cancer cells |
| SA383942 | MS610-48-3 | Suspension | 48 | 10µM 68c091 | Breast cancer cells |
| SA383943 | MSA10-48-3 | Suspension | 48 | 10µM AT0174 | Breast cancer cells |
| SA383944 | MSA10-48-1 | Suspension | 48 | 10µM AT0174 | Breast cancer cells |
| SA383945 | MSA10-48-2 | Suspension | 48 | 10µM AT0174 | Breast cancer cells |
| SA383946 | MSA1-48-3 | Suspension | 48 | 1µM AT0174 | Breast cancer cells |
| SA383947 | MSA1-48-2 | Suspension | 48 | 1µM AT0174 | Breast cancer cells |
| SA383948 | MSA1-48-1 | Suspension | 48 | 1µM AT0174 | Breast cancer cells |
| SA383949 | MSD-48-3 | Suspension | 48 | DMSO | Breast cancer cells |
| SA383950 | MSD-48-2 | Suspension | 48 | DMSO | Breast cancer cells |
| SA383951 | MSD-48-1 | Suspension | 48 | DMSO | Breast cancer cells |
| SA383952 | MST-48-2 | Suspension | 48 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383953 | MST-48-3 | Suspension | 48 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383954 | MST-48-1 | Suspension | 48 | NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa | Breast cancer cells |
| SA383958 | MS48-1 | Suspension | 48 | none | Breast cancer cells |
| SA383959 | MS48-2 | Suspension | 48 | none | Breast cancer cells |
| SA383960 | MS48-3 | Suspension | 48 | none | Breast cancer cells |
| SA383955 | MSV-48-3 | Suspension | 48 | Vehicle | Breast cancer cells |
| SA383956 | MSV-48-2 | Suspension | 48 | Vehicle | Breast cancer cells |
| SA383957 | MSV-48-1 | Suspension | 48 | Vehicle | Breast cancer cells |
| SA383961 | MS72-1 | Suspension | 72 | none | Breast cancer cells |
| SA383962 | MS72-2 | Suspension | 72 | none | Breast cancer cells |
| SA383963 | MS72-3 | Suspension | 72 | none | Breast cancer cells |
| Showing results 1 to 90 of 90 |
Collection:
| Collection ID: | CO003605 |
| Collection Summary: | The cells were detached using 0.5% trypsin/EDTA and then centrifuged at 1500rpm for 5 mins at 4℃, and the supernatants were discarded. Next, PBS was used to resuspend the cell pellets and centrifuged again at 13000rpm for 15 mins at 4℃. The supernatant then discarded. The cell pellets were frozen at -80℃. |
| Sample Type: | Breast cancer cells |
Treatment:
| Treatment ID: | TR003621 |
| Treatment Summary: | TNBC cell line MDA-MB-453 was first cultured in 13C11 tryptophan for 24 hours and treated with cytokines (10ng/ml TNFα+ 10ng/ml IL1β) for 24 hours and 48 hours. Culture media was not changed during the duration of the experiments. |
Sample Preparation:
| Sampleprep ID: | SP003619 |
| Sampleprep Summary: | Metabolites from frozen pellets were extracted at 2e6 cells per mL using ice cold 5:3:2 methanol:acetonitrile:water (v/v/v) with vigorous vortexing at 4 degrees C followed by centrifugation as described for 10 min at 18,000 g. Aliquots of supernatant (50 uL) were dried using a speedvac then reconstituted in an equivalent volume of 0.1% formic acid. Samples were maintained at 4°C until analysis that same day. |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN005721 | AN005722 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH004340 |
| Chromatography Summary: | Negative C18 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-0.5 min 0% B, 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min 100-0% B, 3-5 min hold at 0% B |
| Flow Rate: | 450 uL/min |
| Sample Injection: | 6 uL |
| Solvent A: | 95% water/5% acetonitrile; 1 mM ammonium acetate |
| Solvent B: | 95% acetonitrile/5% water; 1 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004341 |
| Chromatography Summary: | Positive C18 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-0.5 min 5% B, 0.5-1.1 min 5-95% B, 1.1-2.75 min hold at 95% B, 2.75-3 min 95-5% B, 3-5 min hold at 5% B |
| Flow Rate: | 450 uL/min |
| Sample Injection: | 6 uL |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005444 |
| Analysis ID: | AN005721 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005445 |
| Analysis ID: | AN005722 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | POSITIVE |
