Summary of Study ST001025

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 PR000684. The data can be accessed directly via it's Project DOI: 10.21228/M8868G This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST001025
Study Title	TCA Isotopmer metabolomics of H3K27M Cells grown in regular media, glutamine enriched regular media, and glucose encriched regular media (Part-III)
Study Summary	TCA Isotopmer metabolomics of H3K27M Cells grown in regular media, glutamine enriched regular media, and glucose encriched regular media. TCA isotopomers traced for 0, 12, or 24 hours were measured.
Institute	Mayo Clinic
Last Name	Daniels
First Name	David
Address	200 First Street SW Rochester, MN 55905
Email	daniels.david@mayo.edu
Phone	507-284-2511
Submit Date	2018-07-18
Analysis Type Detail	GC-MS
Release Date	2020-07-15
Release Version	1

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Project:

Project ID:	PR000684
Project DOI:	doi: 10.21228/M8868G
Project Title:	Mayo Pilot and Feasibility: H3K27M cells and glutamine metabolomics quatitation studies
Project Summary:	In children, tumors affecting the brain and nervous system result in more cancer-related deaths than any other type of tumor. It is thus critical to identify new approaches for therapy. Among pediatric patients, one of the most devastating brain tumor types is Diffuse Intrinsic Pontine Gliomas (DIPG). Our understanding of this deadly disease has recently been advanced by important discoveries, including the discovery that the majority of DIPG tumors harbor the histone H3K27M mutation. This mutation results in global hypomethylation of H3K27 residues and is the pathological hallmark for this disease. Glutamine (Gln) addiction has been reported in many cancers including malignant adult gliomas. Glutamine likely promotes cancer cell proliferation and survival likely through generation of the TCA cycle intermediate alpha-ketoglutarate (α-KG). Importantly, α-KG is a critical co-factor for histone lysine demethylases including JMJD3, the enzyme responsible for removing the methyl groups from H3K27me3. Our preliminary data shows H3K27M tumor cells require Gln for survival, and if Gln is removed from the culture media, cells can be rescued by the addition of α-KG. Furthermore, Gln deprivation leads to an increase in H3K27 trimethylation similar to direct inhibition of JMJD3. It is for these reasons we hypothesize that H3K27M tumors are dependent on Gln derived α-KG both for feeding the TCA cycle and for further decreasing H3K27 trimethylation. Inhibition of Gln metabolism will likely uncover novel therapeutic targets for this deadly disease. In Aim 1 we will study Gln and glucose metabolism in H3K27M tumor cells and compare this to Wild Type (WT) tumors and Embryonic Stem Cells (ESCs). In Aim 2 we will validate the therapeutic validity of inhibiting Gln metabolism in H3K27M tumors.
Institute:	Mayo Clinic
Last Name:	Daniels
First Name:	David
Address:	200 First Street SW Rochester, MN 55905
Email:	daniels.david@mayo.edu
Phone:	507-284-2511

Subject:

Subject ID:	SU001064
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Sample type	Grouping
SA064356	ms6602-43	Cells	IV 12h GLC
SA064357	ms6602-44	Cells	IV 12h GLC
SA064358	ms6602-45	Cells	IV 12h GLC
SA064359	ms6602-19	Cells	IV 12h GLN
SA064360	ms6602-20	Cells	IV 12h GLN
SA064361	ms6602-21	Cells	IV 12h GLN
SA064362	ms6602-57	Cells	IV 24h GLC
SA064363	ms6602-56	Cells	IV 24h GLC
SA064364	ms6602-55	Cells	IV 24h GLC
SA064365	ms6602-31	Cells	IV 24h GLN
SA064366	ms6602-33	Cells	IV 24h GLN
SA064367	ms6602-32	Cells	IV 24h GLN
SA064368	ms6602-8	Cells	IV Basal
SA064369	ms6602-9	Cells	IV Basal
SA064370	ms6602-7	Cells	IV Basal
SA064371	ms6602-101	Cells	XVII 12h GLC
SA064372	ms6602-100	Cells	XVII 12h GLC
SA064373	ms6602-102	Cells	XVII 12h GLC
SA064374	ms6602-76	Cells	XVII 12h GLN
SA064375	ms6602-78	Cells	XVII 12h GLN
SA064376	ms6602-77	Cells	XVII 12h GLN
SA064377	ms6602-112	Cells	XVII 24h GLC
SA064378	ms6602-113	Cells	XVII 24h GLC
SA064379	ms6602-114	Cells	XVII 24h GLC
SA064380	ms6602-88	Cells	XVII 24h GLN
SA064381	ms6602-90	Cells	XVII 24h GLN
SA064382	ms6602-89	Cells	XVII 24h GLN
SA064383	ms6602-66	Cells	XVII Basal
SA064384	ms6602-65	Cells	XVII Basal
SA064385	ms6602-64	Cells	XVII Basal
SA064386	ms6602-39	Media	IV 12h GLC
SA064387	ms6602-40	Media	IV 12h GLC
SA064388	ms6602-41	Media	IV 12h GLC
SA064389	ms6602-37	Media	IV 12h GLC
SA064390	ms6602-42	Media	IV 12h GLC
SA064391	ms6602-38	Media	IV 12h GLC
SA064392	ms6602-35	Media	IV 12h GLC
SA064393	ms6602-34	Media	IV 12h GLC
SA064394	ms6602-36	Media	IV 12h GLC
SA064395	ms6602-10	Media	IV 12h GLN
SA064396	ms6602-11	Media	IV 12h GLN
SA064397	ms6602-15	Media	IV 12h GLN
SA064398	ms6602-18	Media	IV 12h GLN
SA064399	ms6602-12	Media	IV 12h GLN
SA064400	ms6602-16	Media	IV 12h GLN
SA064401	ms6602-14	Media	IV 12h GLN
SA064402	ms6602-13	Media	IV 12h GLN
SA064403	ms6602-17	Media	IV 12h GLN
SA064404	ms6602-53	Media	IV 24h GLC
SA064405	ms6602-52	Media	IV 24h GLC
SA064406	ms6602-54	Media	IV 24h GLC
SA064407	ms6602-46	Media	IV 24h GLC
SA064408	ms6602-48	Media	IV 24h GLC
SA064409	ms6602-47	Media	IV 24h GLC
SA064410	ms6602-51	Media	IV 24h GLC
SA064411	ms6602-50	Media	IV 24h GLC
SA064412	ms6602-49	Media	IV 24h GLC
SA064413	ms6602-25	Media	IV 24h GLN
SA064414	ms6602-24	Media	IV 24h GLN
SA064415	ms6602-30	Media	IV 24h GLN
SA064416	ms6602-27	Media	IV 24h GLN
SA064417	ms6602-28	Media	IV 24h GLN
SA064418	ms6602-29	Media	IV 24h GLN
SA064419	ms6602-23	Media	IV 24h GLN
SA064420	ms6602-26	Media	IV 24h GLN
SA064421	ms6602-22	Media	IV 24h GLN
SA064422	ms6602-2	Media	IV Basal
SA064423	ms6602-1	Media	IV Basal
SA064424	ms6602-5	Media	IV Basal
SA064425	ms6602-3	Media	IV Basal
SA064426	ms6602-6	Media	IV Basal
SA064427	ms6602-4	Media	IV Basal
SA064428	ms6602-91	Media	XVII 12h GLC
SA064429	ms6602-92	Media	XVII 12h GLC
SA064430	ms6602-94	Media	XVII 12h GLC
SA064431	ms6602-98	Media	XVII 12h GLC
SA064432	ms6602-99	Media	XVII 12h GLC
SA064433	ms6602-97	Media	XVII 12h GLC
SA064434	ms6602-96	Media	XVII 12h GLC
SA064435	ms6602-95	Media	XVII 12h GLC
SA064436	ms6602-93	Media	XVII 12h GLC
SA064437	ms6602-67	Media	XVII 12h GLN
SA064438	ms6602-73	Media	XVII 12h GLN
SA064439	ms6602-74	Media	XVII 12h GLN
SA064440	ms6602-71	Media	XVII 12h GLN
SA064441	ms6602-70	Media	XVII 12h GLN
SA064442	ms6602-68	Media	XVII 12h GLN
SA064443	ms6602-69	Media	XVII 12h GLN
SA064444	ms6602-75	Media	XVII 12h GLN
SA064445	ms6602-72	Media	XVII 12h GLN
SA064446	ms6602-104	Media	XVII 24h GLC
SA064447	ms6602-103	Media	XVII 24h GLC
SA064448	ms6602-110	Media	XVII 24h GLC
SA064449	ms6602-105	Media	XVII 24h GLC
SA064450	ms6602-106	Media	XVII 24h GLC
SA064451	ms6602-109	Media	XVII 24h GLC
SA064452	ms6602-108	Media	XVII 24h GLC
SA064453	ms6602-107	Media	XVII 24h GLC
SA064454	ms6602-111	Media	XVII 24h GLC
SA064455	ms6602-85	Media	XVII 24h GLN

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Collection:

Collection ID:	CO001058
Collection Summary:	DIPG IV and DIPG XVII cell lines are collected in this experiment. Susupension cells are harvested using centrifugation at 1200 rpm for 5 min. 1 mL of the supernatant media werr collected in an eppendorf tube and snapped frozen. The cell pellets were broken up into single cell suspension and counted. 1 million cells were taken from the stock and washed 1 x with PBS using table top centrifuge with 10 sec quick spin. The resulting cell pellet was snap frozen. Both the frozen media and cell pellet are stored in -80 C prior transfer.
Sample Type:	Glioma cells

Treatment:

Treatment ID:	TR001078
Treatment Summary:	TCA isotopomer in H3K27M cell lines traced for 0, 12, or 24 hours. Cells grow in regular media without isotopes Cells grow in regular media enriched with 35% U-13C-glutamine Cells grow in regular media enriched with 35% U-13C-glucose Study Design Factors IV Basal - DIPG IV Regular Media No Tracers IV 12h GLN - DIPG IV Gultamine enriched media 12 hour Tracers IV 24h GLN - DIPG IV Gultamine enriched media 24 hour Tracers IV 12h GLC - DIPG IV Glucose enriched media 12 hour Tracers IV 24h GLC - DIPG IV Glucose enriched media 24 hour Tracers XVII Basal - DIPG XVII Regular Media No Tracers XVII 12h GLN - DIPG XVII Gultamine enriched media 12 hour Tracers XVII 24h GLN - DIPG XVII Gultamine enriched media 24 hour Tracers XVII 12h GLC - DIPG XVII Glucose enriched media 12 hour Tracers XVII 24h GLC - DIPG XVII Glucose enriched media 24 hour Tracers

Treatment ID:

TR001078

Treatment Summary:

TCA isotopomer in H3K27M cell lines traced for 0, 12, or 24 hours. Cells grow in regular media without isotopes Cells grow in regular media enriched with 35% U-13C-glutamine Cells grow in regular media enriched with 35% U-13C-glucose Study Design Factors IV Basal - DIPG IV Regular Media No Tracers IV 12h GLN - DIPG IV Gultamine enriched media 12 hour Tracers IV 24h GLN - DIPG IV Gultamine enriched media 24 hour Tracers IV 12h GLC - DIPG IV Glucose enriched media 12 hour Tracers IV 24h GLC - DIPG IV Glucose enriched media 24 hour Tracers XVII Basal - DIPG XVII Regular Media No Tracers XVII 12h GLN - DIPG XVII Gultamine enriched media 12 hour Tracers XVII 24h GLN - DIPG XVII Gultamine enriched media 24 hour Tracers XVII 12h GLC - DIPG XVII Glucose enriched media 12 hour Tracers XVII 24h GLC - DIPG XVII Glucose enriched media 24 hour Tracers

Sample Preparation:

Sampleprep ID:	SP001071
Sampleprep Summary:	TCA Isotopomers in glioma cell lines traced for 0, 12, 24 hours

Combined analysis:

Analysis ID	AN001682
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890B
Column	Agilent HP5-MS (30m × 0.25mm, 0.25 um)
MS Type	EI
MS instrument type	Single quadrupole
MS instrument name	Agilent 5977A
Ion Mode	POSITIVE
Units	Enrichment

Chromatography:

Chromatography ID:	CH001183
Instrument Name:	Agilent 7890B
Column Name:	Agilent HP5-MS (30m × 0.25mm, 0.25 um)
Chromatography Type:	GC

MS:

MS ID:	MS001557
Analysis ID:	AN001682
Instrument Name:	Agilent 5977A
Instrument Type:	Single quadrupole
MS Type:	EI
Ion Mode:	POSITIVE