Summary of Study ST003893

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 PR002436. The data can be accessed directly via it's Project DOI: 10.21228/M8RN89 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	ST003893
Study Title	Respiration defects limit serine synthesis required for lung cancer growth and survival - NSCLC rewires glycolytic metabolism to synthesize more serine from glucose (Tumors)
Study Type	In vivo Isotope Tracing
Study Summary	This study investigates the impact of mtDNA mutation burden induced by the PolGD256A mutation in Non-Small cell lung cancer (NSCLC). Using in vivo, we characterized the metabolic profile of NSCLC harboring this mutation compared to controls after submit the animals to 12 weeks of special diet and 2h30 of [U-13C]D-Glucose infusion. Here we found that mitochondria impairment causes more use of glucose to synthesize serine in NSCLC tumors but not in other tissues (lungs, liver, plasma, and muscle. Due the lack of carbons from glucose to TCA (Tricarboxylic acid cycle) the PGKP cells have an energetic imbalance. WT: Wild Type animals KP: NSCLC conditional animals PolG: Animals with PolG mutation PGKP: NSCLC conditional animals with PolG mutation
Institute	Rutgers University
Department	Rutgers Cancer Institute
Laboratory	Eileen White
Last Name	Lopes
First Name	Eduardo
Address	195 Little Albany Street
Email	edu.llopes@gmail.com
Phone	732-235-5795
Submit Date	2025-03-20
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2025-05-06
Release Version	1

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Project:

Project ID:	PR002436
Project DOI:	doi: 10.21228/M8RN89
Project Title:	Respiration defects limit serine synthesis required for lung cancer growth and survival
Project Type:	Pool Size Metabolomic in vivo
Project Summary:	Mitochondrial function supports energy and anabolic metabolism. Pathogenic mitochondrial DNA (mtDNA) mutations impair these processes, causing mitochondrial diseases. Their role in human cancers is less clear; while some cancers harbor high mtDNA mutation burden, others do not. Here we show that a proofreading mutant of DNA polymerase gamma (PolGD256A) increases the mtDNA mutation burden in non-small-cell lung cancer (NSCLC). This mutation promotes the accumulation of defective mitochondria, reduces tumor cell proliferation and viability, and improves cancer survival. In NSCLC, pathogenic mtDNA mutations enhance glycolysis and create a glucose dependency to support mitochondrial energy, but at the expense of a lower NAD⁺/NADH ratio that hinders de novo serine synthesis. Thus, mitochondrial function in NSCLC is essential for maintaining adequate serine synthesis, which in turn supports the anabolic metabolism and redox homeostasis required for tumor growth, explaining why these cancers preserve functional mtDNA.
Institute:	Rutgers University
Department:	Rutgers Cancer Institute
Laboratory:	Eileen White
Last Name:	Cararo Lopes
First Name:	Eduardo
Address:	195 Little Albany Street
Email:	edu.llopes@gmail.com
Phone:	732-235-5795
Funding Source:	NIH
Publications:	Respiration defects limit serine synthesis required for lung cancer growth and survival

Subject:

Subject ID:	SU004028
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Gender:	Male and female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Diet
SA427649	AAK_4900_TuII_C_PGKP_Control	Control
SA427650	KP_5020_Tu_C_KP_Control	Control
SA427651	KP_5020_TuII_C_KP_Control	Control
SA427652	KP_5021_Tu_C_KP_Control	Control
SA427653	KP_5021_TuII_C_KP_Control	Control
SA427654	AAK_5005_TuII_C_PGKP_Control	Control
SA427655	KP_5022_Tu_C_KP_Control	Control
SA427656	AAK_5004_TuII_C_PGKP_Control	Control
SA427657	AAK_5004_Tu_C__PGKP_Control	Control
SA427658	AAK_4942_TuII_C_PGKP_Control	Control
SA427659	AAK_4942_Tu_C_PGKP_Control	Control
SA427660	AAK_4900_Tu_C_PGKP_Control	Control
SA427661	AAK_4898_TuII_C_PGKP_Control	Control
SA427662	AAK_4898_Tu_C_PGKP_Control	Control
SA427663	AAK_4896_TuII_C_PGKP_Control	Control
SA427664	AAK_4896_Tu_C_PGKP_Control	Control
SA427665	KP_5022_TuII_C_KP_Control	Control
SA427666	KP_5155_Tu_C_KP_Control	Control
SA427667	KP_5155_TuII_C_KP_Control	Control
SA427668	KP_5156_Tu_C_KP_Control	Control
SA427669	KP_5156_Tu_CII_KP_Control	Control
SA427670	KP_3425_Tu_woSG_KP_Ser/Gly free	Ser/Gly free
SA427671	KP_5167_Tu_woSG_KP_Ser/Gly free	Ser/Gly free
SA427672	KP_5169_Tu_woSG_KP_Ser/Gly free	Ser/Gly free
SA427673	KP_5169_TuII_woSG_KP_Ser/Gly free	Ser/Gly free
SA427674	KP_3430_TuII_woSG_KP_Ser/Gly free	Ser/Gly free
SA427675	KP_3430_Tu_woSG_KP_Ser/Gly free	Ser/Gly free
SA427676	KP_3425_TuII_woSG_KP_Ser/Gly free	Ser/Gly free
SA427677	AAK_4830_Tu_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427678	KP_3371_TuII_woSG_KP_Ser/Gly free	Ser/Gly free
SA427679	AAK_4840_Tu_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427680	AAK_4835_Tu_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427681	AAK_4835_TuII_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427682	AAK_4837_Tu_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427683	AAK_4837_TuII_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427684	AAK_4838_Tu_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427685	AAK_4838_TuII_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427686	AAK_4840_TuII_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427687	KP_3371_Tu_woSG_KP_Ser/Gly free	Ser/Gly free
SA427688	AAK_5005_Tu_C_PGKP_Ser/Gly free	Ser/Gly free
SA427689	AAK_5013_Tu_C_PGKP_Ser/Gly free	Ser/Gly free
SA427690	AAK_5013_TuII_C_PGKP_Ser/Gly free	Ser/Gly free
SA427691	AAK_4830_TuII_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427692	AAK_5359_TuII_woSG_PGKP_Ser/Gly free	Ser/Gly free
SA427693	KP_3327_Tu_woSG_KP_Ser/Gly free	Ser/Gly free
SA427694	KP_3327_TuII_woSG_KP_Ser/Gly free	Ser/Gly free
SA427695	AAK_5359_Tu_woSG_PGKP_Ser/Gly free	Ser/Gly free

Showing results 1 to 47 of 47

Showing results 1 to 47 of 47

Collection:

Collection ID:	CO004021
Collection Summary:	Extraction of polar metabolites from solid tissues: 20 to 30 mg of tissues were weighed and added to a 2 mL round-tipped microtube with a – 80° C cold Yttria Grinding Ball per tube. The tissues were pulverized in CryoMill (Retsch) following alternating three cycles at 5 Hz for 2 min with three cycles at 25 Hz for 2 min. Buffer was added to each 2 mL microtube (sample weight x 40)/2 volume of the buffer) 40:40:20 buffer with 0.5% formic acid, samples were vigorously vortexed and incubated on ice for 10 minutes, vortexed, and incubated for an additional 10 min. After the samples were centrifuged for 10 min at 16,000g at 4° C, the supernatant A was collected and saved, and the pellets were submitted to re-extraction following the same procedure to generate supernatant B. Supernatant A and B were mixed and transferred to a clean 1.5 mL microtube with the appropriated volume of 15% NH4CO3. The samples were stored in a -80° C freezer until analysis by LC-MS. Extraction of polar metabolites from plasma:To extract polar metabolites from mouse plasma 40 µL of cold methanol was added to a 15 µL of mouse plasma in a 1.5 mL microtube. This mixture was vortexed for 10 seconds and incubated for 20 minutes in a -20° C freezer. Samples were centrifuged for 10 min at 16,000g at 4° C. Next, supernatant A was collected in a new tube, and the pellet was saved for re-extraction. For re-extraction, the pellet was resuspended in 200 µL of 40:40:20 buffer, vortexed, and allowed to sit on ice for 10 min. The samples were centrifuged for 10 min at 16,000 g at 4° C. Supernatant B was collected and mixed with supernatant A. This mixture was further processed to remove phospholipids using 1 mL Phenomenex (Phenomenex Inc.) tubes according to the manufacturer's instruction and stored at -80° C until analysis by LC-MS.
Sample Type:	Tumors
Volumeoramount Collected:	1mL of organic phase of metabolites extraction
Storage Conditions:	-80℃
Collection Vials:	1.5 mL Eppendorf tubes
Storage Vials:	1.5 mL Eppendorf tubes

Treatment:

Treatment ID:	TR004037
Treatment Summary:	Tumor were collected from animals with NSCLC. The animals were weighed one week before NSCLC induction. In the same period, special diets (control amino acid food and ser/gly free diet) were provided and kept until the end of the experiment (12 weeks). After this period the animals were subjected to [U13C]-Glucose infusion for 2h30. Therefore the animals were euthanized and have their tissues collected. Muscle (gastrocnemius), liver, plasma, lung or tumors.

Treatment ID:

TR004037

Treatment Summary:

Tumor were collected from animals with NSCLC. The animals were weighed one week before NSCLC induction. In the same period, special diets (control amino acid food and ser/gly free diet) were provided and kept until the end of the experiment (12 weeks). After this period the animals were subjected to [U13C]-Glucose infusion for 2h30. Therefore the animals were euthanized and have their tissues collected. Muscle (gastrocnemius), liver, plasma, lung or tumors.

Sample Preparation:

Sampleprep ID:	SP004034
Sampleprep Summary:	For Tumor: 20 to 30 mg of tissues were weighed and added to a 2 mL round-tipped microtube with a – 80° C cold Yttria Grinding Ball per tube. The tissues were pulverized in CryoMill (Retsch) following alternating three cycles at 5 Hz for 2 min with three cycles at 25 Hz for 2 min. Buffer was added to each 2 mL microtube (sample weight x 40)/2 volume of the buffer) 40:40:20 buffer with 0.5% formic acid, samples were vigorously vortexed and incubated on ice for 10 minutes, vortexed, and incubated for an additional 10 min. After the samples were centrifuged for 10 min at 16,000g at 4° C, the supernatant A was collected and saved, and the pellets were submitted to re-extraction following the same procedure to generate supernatant B. Supernatant A and B were mixed and transferred to a clean 1.5 mL microtube with the appropriated volume of 15% NH4CO3. The samples were stored in a -80° C freezer until analysis by LC-MS. For Plasma: To extract polar metabolites from mouse plasma 40 µL of cold methanol was added to a 15 µL of mouse plasma in a 1.5 mL microtube. This mixture was vortexed for 10 seconds and incubated for 20 minutes in a -20° C freezer. Samples were centrifuged for 10 min at 16,000g at 4° C. Next, supernatant A was collected in a new tube, and the pellet was saved for re-extraction. For re-extraction, the pellet was resuspended in 200 µL of 40:40:20 buffer, vortexed, and allowed to sit on ice for 10 min. The samples were centrifuged for 10 min at 16,000 g at 4° C. Supernatant B was collected and mixed with supernatant A. This mixture was further processed to remove phospholipids using 1 mL Phenomenex (Phenomenex Inc.) tubes according to the manufacturer's instruction and stored at -80° C until analysis by LC-MS.

Sampleprep ID:

SP004034

Sampleprep Summary:

For Tumor: 20 to 30 mg of tissues were weighed and added to a 2 mL round-tipped microtube with a – 80° C cold Yttria Grinding Ball per tube. The tissues were pulverized in CryoMill (Retsch) following alternating three cycles at 5 Hz for 2 min with three cycles at 25 Hz for 2 min. Buffer was added to each 2 mL microtube (sample weight x 40)/2 volume of the buffer) 40:40:20 buffer with 0.5% formic acid, samples were vigorously vortexed and incubated on ice for 10 minutes, vortexed, and incubated for an additional 10 min. After the samples were centrifuged for 10 min at 16,000g at 4° C, the supernatant A was collected and saved, and the pellets were submitted to re-extraction following the same procedure to generate supernatant B. Supernatant A and B were mixed and transferred to a clean 1.5 mL microtube with the appropriated volume of 15% NH4CO3. The samples were stored in a -80° C freezer until analysis by LC-MS. For Plasma: To extract polar metabolites from mouse plasma 40 µL of cold methanol was added to a 15 µL of mouse plasma in a 1.5 mL microtube. This mixture was vortexed for 10 seconds and incubated for 20 minutes in a -20° C freezer. Samples were centrifuged for 10 min at 16,000g at 4° C. Next, supernatant A was collected in a new tube, and the pellet was saved for re-extraction. For re-extraction, the pellet was resuspended in 200 µL of 40:40:20 buffer, vortexed, and allowed to sit on ice for 10 min. The samples were centrifuged for 10 min at 16,000 g at 4° C. Supernatant B was collected and mixed with supernatant A. This mixture was further processed to remove phospholipids using 1 mL Phenomenex (Phenomenex Inc.) tubes according to the manufacturer's instruction and stored at -80° C until analysis by LC-MS.

Chromatography:

Chromatography ID:	CH004848
Chromatography Summary:	Tumor
Methods Filename:	Chromatography_method.pdf
Instrument Name:	Thermo Vanquish
Column Name:	XBridge BEH Amide (150 × 2.1mm, 2.5um)
Column Temperature:	25 °C
Flow Gradient:	0 min, 100% B; 3 min, 100% B; 3.2 min, 90% B; 6.2 min, 90% B; 6.5 min, 80% B; 10.5 min, 80% B; 10.7 min, 70% B; 13.5 min, 70% B; 13.7 min, 45% B; 16 min, 45% B; 16.5 min, 100% B; and 22 min, 100% B
Flow Rate:	300 μL/min
Solvent A:	95% water/5% acetonitrile; 20mM acetic acid; 40mM ammonium hydroxide (pH 9.4)
Solvent B:	20% H2O, 80% acetonitrile with 20 mM acetic acid20% water/80% acetonitrile; 20mM acetic acid, 40mM ammonium hydroxide (pH 9.4), 40 mM ammonium hydroxide, (pH 9.4)
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006395
Analysis Type:	MS
Chromatography ID:	CH004848
Num Factors:	2
Num Metabolites:	300
Units:	ion count

Analysis ID:	AN006396
Analysis Type:	MS
Chromatography ID:	CH004848
Num Factors:	2
Num Metabolites:	567
Units:	ion count