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.

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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.

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Study IDST003484
Study TitleMetabolism 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 SummaryTNBC 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 NameHaines
First NameJulie
Address12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Emailjulie.haines@cuanschutz.edu
Phone3037243339
Submit Date2024-09-16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-10-03
Release Version1
Julie Haines Julie Haines
https://dx.doi.org/10.21228/M80R74
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
Species Group:Mammals

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
SA383874MA0-2Attached 0 none Breast cancer cells
SA383875MA0-1Attached 0 none Breast cancer cells
SA383876MA0-3Attached 0 none Breast cancer cells
SA383877MA610-24-3Attached 24 10µM 68c091 Breast cancer cells
SA383878MA610-24-2Attached 24 10µM 68c091 Breast cancer cells
SA383879MA610-24-1Attached 24 10µM 68c091 Breast cancer cells
SA383880MAA10-24-2Attached 24 10µM AT0174 Breast cancer cells
SA383881MAA10-24-3Attached 24 10µM AT0174 Breast cancer cells
SA383882MAA10-24-1Attached 24 10µM AT0174 Breast cancer cells
SA383883MAA1-24-2Attached 24 1µM AT0174 Breast cancer cells
SA383884MAA1-24-1Attached 24 1µM AT0174 Breast cancer cells
SA383885MAA1-24-3Attached 24 1µM AT0174 Breast cancer cells
SA383886MAD-24-1Attached 24 DMSO Breast cancer cells
SA383887MAD-24-3Attached 24 DMSO Breast cancer cells
SA383888MAD-24-2Attached 24 DMSO Breast cancer cells
SA383889MAT-24-1Attached 24 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383890MAT-24-2Attached 24 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383891MAT-24-3Attached 24 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383892MAV-24-1Attached 24 Vehicle Breast cancer cells
SA383893MAV-24-2Attached 24 Vehicle Breast cancer cells
SA383894MAV-24-3Attached 24 Vehicle Breast cancer cells
SA383895MA610-48-1Attached 48 10µM 68c091 Breast cancer cells
SA383896MA610-48-2Attached 48 10µM 68c091 Breast cancer cells
SA383897MA610-48-3Attached 48 10µM 68c091 Breast cancer cells
SA383898MAA10-48-2Attached 48 10µM AT0174 Breast cancer cells
SA383899MAA10-48-1Attached 48 10µM AT0174 Breast cancer cells
SA383900MAA10-48-3Attached 48 10µM AT0174 Breast cancer cells
SA383901MAA1-48-2Attached 48 1µM AT0174 Breast cancer cells
SA383902MAA1-48-1Attached 48 1µM AT0174 Breast cancer cells
SA383903MAA1-48-3Attached 48 1µM AT0174 Breast cancer cells
SA383904MAD-48-3Attached 48 DMSO Breast cancer cells
SA383905MAD-48-2Attached 48 DMSO Breast cancer cells
SA383906MAD-48-1Attached 48 DMSO Breast cancer cells
SA383907MAT-48-1Attached 48 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383908MAT-48-2Attached 48 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383909MAT-48-3Attached 48 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383913MA48-3Attached 48 none Breast cancer cells
SA383914MA48-1Attached 48 none Breast cancer cells
SA383915MA48-2Attached 48 none Breast cancer cells
SA383910MAV-48-1Attached 48 Vehicle Breast cancer cells
SA383911MAV-48-2Attached 48 Vehicle Breast cancer cells
SA383912MAV-48-3Attached 48 Vehicle Breast cancer cells
SA383916MA72-3Attached 72 none Breast cancer cells
SA383917MA72-2Attached 72 none Breast cancer cells
SA383918MA72-1Attached 72 none Breast cancer cells
SA383919MS0-3Suspension 0 none Breast cancer cells
SA383920MS0-1Suspension 0 none Breast cancer cells
SA383921MS0-2Suspension 0 none Breast cancer cells
SA383922MS610-24-1Suspension 24 10µM 68c091 Breast cancer cells
SA383923MS610-24-2Suspension 24 10µM 68c091 Breast cancer cells
SA383924MS610-24-3Suspension 24 10µM 68c091 Breast cancer cells
SA383925MSA10-24-2Suspension 24 10µM AT0174 Breast cancer cells
SA383926MSA10-24-3Suspension 24 10µM AT0174 Breast cancer cells
SA383927MSA10-24-1Suspension 24 10µM AT0174 Breast cancer cells
SA383928MSA1-24-2Suspension 24 1µM AT0174 Breast cancer cells
SA383929MSA1-24-3Suspension 24 1µM AT0174 Breast cancer cells
SA383930MSA1-24-1Suspension 24 1µM AT0174 Breast cancer cells
SA383931MSD-24-3Suspension 24 DMSO Breast cancer cells
SA383932MSD-24-1Suspension 24 DMSO Breast cancer cells
SA383933MSD-24-2Suspension 24 DMSO Breast cancer cells
SA383934MST-24-3Suspension 24 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383935MST-24-1Suspension 24 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383936MST-24-2Suspension 24 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383937MSV-24-2Suspension 24 Vehicle Breast cancer cells
SA383938MSV-24-3Suspension 24 Vehicle Breast cancer cells
SA383939MSV-24-1Suspension 24 Vehicle Breast cancer cells
SA383940MS610-48-2Suspension 48 10µM 68c091 Breast cancer cells
SA383941MS610-48-1Suspension 48 10µM 68c091 Breast cancer cells
SA383942MS610-48-3Suspension 48 10µM 68c091 Breast cancer cells
SA383943MSA10-48-3Suspension 48 10µM AT0174 Breast cancer cells
SA383944MSA10-48-1Suspension 48 10µM AT0174 Breast cancer cells
SA383945MSA10-48-2Suspension 48 10µM AT0174 Breast cancer cells
SA383946MSA1-48-3Suspension 48 1µM AT0174 Breast cancer cells
SA383947MSA1-48-2Suspension 48 1µM AT0174 Breast cancer cells
SA383948MSA1-48-1Suspension 48 1µM AT0174 Breast cancer cells
SA383949MSD-48-3Suspension 48 DMSO Breast cancer cells
SA383950MSD-48-2Suspension 48 DMSO Breast cancer cells
SA383951MSD-48-1Suspension 48 DMSO Breast cancer cells
SA383952MST-48-2Suspension 48 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383953MST-48-3Suspension 48 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383954MST-48-1Suspension 48 NFkB cocktail 10 ng/ml IL1b + 10 ng/ml TNFa Breast cancer cells
SA383958MS48-1Suspension 48 none Breast cancer cells
SA383959MS48-2Suspension 48 none Breast cancer cells
SA383960MS48-3Suspension 48 none Breast cancer cells
SA383955MSV-48-3Suspension 48 Vehicle Breast cancer cells
SA383956MSV-48-2Suspension 48 Vehicle Breast cancer cells
SA383957MSV-48-1Suspension 48 Vehicle Breast cancer cells
SA383961MS72-1Suspension 72 none Breast cancer cells
SA383962MS72-2Suspension 72 none Breast cancer cells
SA383963MS72-3Suspension 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
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