Summary of Study ST002231

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 PR001421. The data can be accessed directly via it's Project DOI: 10.21228/M81X41 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	ST002231
Study Title	Metabolomics Analysis of HOG-EV and HOG-R132H Cells with and without BAY 2402234 Treatment
Study Type	Metabolomics Analysis
Study Summary	HOG cells were plated in 6-well plates (0.5 × 10^6 cells per well). 24 hours later, HOG-EV or HOG-R132H cells were treated for 24 hours with 10 nM BAY 2402234 or DMSO. Cells were then harvested for LC-MS analysis.
Institute	UT Southwestern Medical Center
Department	Children's Research Institute
Laboratory	McBrayer Laboratory
Last Name	McBrayer
First Name	Samuel
Address	6000 Harry Hines Boulevard, NL10.110K, Dallas, TX 75235, USA
Email	samuel.mcbrayer@utsouthwestern.edu
Phone	(214)-648-3730
Submit Date	2022-07-14
Num Groups	4
Total Subjects	1
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-07-28
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001421
Project DOI:	doi: 10.21228/M81X41
Project Title:	De Novo Pyrimidine Synthesis is a Targetable Vulnerability in IDH Mutant Glioma
Project Type:	LC-MS Quantitative Analysis
Project Summary:	Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they appear less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1 mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH mutant gliomas. Mechanistically, this reflects an obligate dependence of glioma cells on the de novo pyrimidine synthesis pathway and mutant IDH’s ability to sensitize to DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.
Institute:	UT Southwestern Medical Center
Department:	Children's Research Institute
Laboratory:	McBrayer Laboratory
Last Name:	McBrayer
First Name:	Samuel
Address:	6000 Harry Hines Boulevard, NL11.110K, Dallas, Texas, 75235, USA
Email:	samuel.mcbrayer@utsouthwestern.edu
Phone:	(214)-648-3730

Subject:

Subject ID:	SU002317
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Genotype Strain:	HOG
Gender:	Male
Cell Strain Details:	Human oligodendroglioma cell line
Cell Counts:	500,000

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Genotype	Treatment
SA212572	ML-11_Negative	HOG EV	BAY2402234
SA212573	ML-11_Positive	HOG EV	BAY2402234
SA212574	ML-12_Positive	HOG EV	BAY2402234
SA212575	ML-20_Positive	HOG EV	BAY2402234
SA212576	ML-20_Negative	HOG EV	BAY2402234
SA212577	ML-19_Negative	HOG EV	BAY2402234
SA212578	ML-19_Positive	HOG EV	BAY2402234
SA212579	ML-12_Negative	HOG EV	BAY2402234
SA212580	ML-27_Negative	HOG EV	BAY2402234
SA212581	ML-28_Negative	HOG EV	BAY2402234
SA212582	ML-28_Positive	HOG EV	BAY2402234
SA212583	ML-27_Positive	HOG EV	BAY2402234
SA212584	ML-03_Negative	HOG EV	BAY2402234
SA212585	ML-04_Positive	HOG EV	BAY2402234
SA212586	ML-04_Negative	HOG EV	BAY2402234
SA212587	ML-03_Positive	HOG EV	BAY2402234
SA212588	ML-17_Positive	HOG EV	DMSO
SA212589	ML-18_Negative	HOG EV	DMSO
SA212590	ML-26_Negative	HOG EV	DMSO
SA212591	ML-26_Positive	HOG EV	DMSO
SA212592	ML-25_Positive	HOG EV	DMSO
SA212593	ML-25_Negative	HOG EV	DMSO
SA212594	ML-18_Positive	HOG EV	DMSO
SA212595	ML-17_Negative	HOG EV	DMSO
SA212596	ML-10_Positive	HOG EV	DMSO
SA212597	ML-02_Positive	HOG EV	DMSO
SA212598	ML-10_Negative	HOG EV	DMSO
SA212599	ML-09_Positive	HOG EV	DMSO
SA212600	ML-09_Negative	HOG EV	DMSO
SA212601	ML-01_Positive	HOG EV	DMSO
SA212602	ML-02_Negative	HOG EV	DMSO
SA212603	ML-01_Negative	HOG EV	DMSO
SA212604	ML-07_Negative	HOG R132H	BAY2402234
SA212605	ML-24_Negative	HOG R132H	BAY2402234
SA212606	ML-24_Positive	HOG R132H	BAY2402234
SA212607	ML-32_Positive	HOG R132H	BAY2402234
SA212608	ML-31_Negative	HOG R132H	BAY2402234
SA212609	ML-31_Positive	HOG R132H	BAY2402234
SA212610	ML-32_Negative	HOG R132H	BAY2402234
SA212611	ML-23_Negative	HOG R132H	BAY2402234
SA212612	ML-23_Positive	HOG R132H	BAY2402234
SA212613	ML-16_Positive	HOG R132H	BAY2402234
SA212614	ML-08_Positive	HOG R132H	BAY2402234
SA212615	ML-16_Negative	HOG R132H	BAY2402234
SA212616	ML-07_Positive	HOG R132H	BAY2402234
SA212617	ML-08_Negative	HOG R132H	BAY2402234
SA212618	ML-15_Positive	HOG R132H	BAY2402234
SA212619	ML-15_Negative	HOG R132H	BAY2402234
SA212620	ML-29_Negative	HOG R132H	DMSO
SA212621	ML-14_Negative	HOG R132H	DMSO
SA212622	ML-29_Positive	HOG R132H	DMSO
SA212623	ML-30_Positive	HOG R132H	DMSO
SA212624	ML-14_Positive	HOG R132H	DMSO
SA212625	ML-30_Negative	HOG R132H	DMSO
SA212626	ML-05_Negative	HOG R132H	DMSO
SA212627	ML-21_Negative	HOG R132H	DMSO
SA212628	ML-22_Positive	HOG R132H	DMSO
SA212629	ML-22_Negative	HOG R132H	DMSO
SA212630	ML-13_Negative	HOG R132H	DMSO
SA212631	ML-06_Positive	HOG R132H	DMSO
SA212632	ML-13_Positive	HOG R132H	DMSO
SA212633	ML-05_Positive	HOG R132H	DMSO
SA212634	ML-06_Negative	HOG R132H	DMSO
SA212635	ML-21_Positive	HOG R132H	DMSO
SA212636	Blank	N/A	N/A
SA212637	ML-33_Negative	Pooled Sample	N/A
SA212638	ML-33_Positive	Pooled Sample	N/A

Showing results 1 to 67 of 67

Showing results 1 to 67 of 67

Collection:

Collection ID:	CO002310
Collection Summary:	Cells were washed with ice-cold saline and snap frozen in liquid nitrogen.
Sample Type:	Cultured cells

Treatment:

Treatment ID:	TR002329
Treatment Summary:	HOG cells were plated in 6-well plates (0.5 × 10^6 cells per well). 24 hours later, HOG-EV or HOG-R132H cells were treated for 24 hours with 10 nM BAY 2402234 or DMSO.

Sample Preparation:

Sampleprep ID:	SP002323
Sampleprep Summary:	Metabolites were extracted in 80% methanol, vortexed for 20 min at 4°C, and centrifuged (21,100 × g for 10 min at 4°C). Metabolite samples were dried using a CentriVap (Labconco) or SpeedVac (Thermo Fisher) concentrator. Dried metabolites were resuspended in 40-50 µL 80% acetonitrile, vortexed for 20 min at 4°C, and centrifuged (21,100 × g for 10 min at 4°C). 10 µL was injected and analyzed with a Q-Exactive HF-X hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher) coupled to a Vanquish Flex UHPLC system (Thermo Fisher).

Sampleprep ID:

SP002323

Sampleprep Summary:

Metabolites were extracted in 80% methanol, vortexed for 20 min at 4°C, and centrifuged (21,100 × g for 10 min at 4°C). Metabolite samples were dried using a CentriVap (Labconco) or SpeedVac (Thermo Fisher) concentrator. Dried metabolites were resuspended in 40-50 µL 80% acetonitrile, vortexed for 20 min at 4°C, and centrifuged (21,100 × g for 10 min at 4°C). 10 µL was injected and analyzed with a Q-Exactive HF-X hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher) coupled to a Vanquish Flex UHPLC system (Thermo Fisher).

Combined analysis:

Analysis ID	AN003640	AN003641
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Vanquish Flex UHPLC	Vanquish Flex UHPLC
Column	Millipore ZIC-pHILIC	Millipore ZIC-pHILIC
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive HF-X Orbitrap	Thermo Q Exactive HF-X Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	TIC-Corrected Peak Area	TIC-Corrected Peak Area

Chromatography:

Chromatography ID:	CH002695
Chromatography Summary:	Chromatographic resolution of metabolites was achieved using on a Millipore ZIC-pHILIC column using a linear gradient of 10 mM ammonium formate pH 9.8 and acetonitrile.
Instrument Name:	Vanquish Flex UHPLC
Column Name:	Millipore ZIC-pHILIC
Flow Gradient:	linear gradient of 10 mM ammonium formate pH 9.8 and acetonitrile
Solvent A:	100% water; 10 mM ammonium formate pH 9.8
Solvent B:	100% acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS003391
Analysis ID:	AN003640
Instrument Name:	Thermo Q Exactive HF-X Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Spectra were acquired with a resolving power of 60,000 full width at half maximum (FWHM), a scan range set to 80–1,200 m/z, and polarity switching. Data-dependent MS/MS data was acquired on unlabeled pooled samples to confirm metabolite IDs when necessary. Peaks were integrated using El-Maven 0.12.0 software (Elucidata) or TraceFinder 5.1 SP2 software (Thermo Fisher). Total ion counts were quantified using Freestyle 1.7 SP1 software (Thermo Fisher). Peaks were normalized to total ion counts using the R statistical programming language.
Ion Mode:	POSITIVE

MS ID:	MS003392
Analysis ID:	AN003641
Instrument Name:	Thermo Q Exactive HF-X Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Spectra were acquired with a resolving power of 60,000 full width at half maximum (FWHM), a scan range set to 80–1,200 m/z, and polarity switching. Data-dependent MS/MS data was acquired on unlabeled pooled samples to confirm metabolite IDs when necessary. Peaks were integrated using El-Maven 0.12.0 software (Elucidata) or TraceFinder 5.1 SP2 software (Thermo Fisher). Total ion counts were quantified using Freestyle 1.7 SP1 software (Thermo Fisher). Peaks were normalized to total ion counts using the R statistical programming language.
Ion Mode:	NEGATIVE