Summary of Study ST003886

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	ST003886
Study Title	Respiration defects limit serine synthesis required for lung cancer growth and survival - Effect of Polg mutation in NSCLC TDCLs
Study Summary	This study explores the impact of mtDNA mutation burden induced by the PolG 𝐷 256 𝐴 D256A mutation in NSCLC. Using in vitro models (TDCLs) cultured in either standard RPMI medium or RPMI without serine and glycine, we characterized the [U-¹³C]D-glucose metabolism in NSCLC cells harboring this mutation compared to controls. Here we found that mitochondria impairment cause more use of glucose to synthesize serine. Due the lack of carbons from glucose to TCA (Tricarboxylic acid cycle) the PGKP cells have a energetic imbalance. KP: NSCLC TDCLs generated from conditional animals PGKP: NSCLC TDCLs generated from conditional animals bearing PolG mutation
Institute	Rutgers Cancer Institute
Last Name	Cararo Lopes
First Name	Eduardo
Address	10 LANDING LN, New Brunswick, NJ, 08901, USA
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:	SU004021
Subject Type:	Cultured cells
Subject Species:	Mus musculus
Taxonomy ID:	10090
Gender:	Male and female

Factors:

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

mb_sample_id	local_sample_id	Genotype	Medium
SA427224	KP_+SG_483Cell_1_KP_Control	KP	Control
SA427225	KP_+SG_311Cell_2_KP_Control	KP	Control
SA427226	KP_+SG_483Cell_3_KP_Control	KP	Control
SA427227	KP_+SG_483Cell_2_KP_Control	KP	Control
SA427228	KP_+SG_311Cell_1_KP_Control	KP	Control
SA427229	KP_+SG_313Cell_3_KP_Control	KP	Control
SA427230	KP_+SG_313Cell_2_KP_Control	KP	Control
SA427231	KP_+SG_311Cell_3_KP_Control	KP	Control
SA427232	KP_+SG_313Cell_1_KP_Control	KP	Control
SA427233	KP_-SG_311Cell_1_KP_woSer/Gly	KP	woSer/Gly
SA427234	KP_-SG_311Cell_2_KP_woSer/Gly	KP	woSer/Gly
SA427235	KP_-SG_311Cell_3_KP_woSer/Gly	KP	woSer/Gly
SA427236	KP_-SG_313Cell_1_KP_woSer/Gly	KP	woSer/Gly
SA427237	KP_-SG_313Cell_2_KP_woSer/Gly	KP	woSer/Gly
SA427238	KP_-SG_313Cell_3_KP_woSer/Gly	KP	woSer/Gly
SA427239	KP_-SG_483Cell_2_KP_woSer/Gly	KP	woSer/Gly
SA427240	KP_-SG_483Cell_3_KP_woSer/Gly	KP	woSer/Gly
SA427241	KP_-SG_483Cell_1_KP_woSer/Gly	KP	woSer/Gly
SA427242	PG_+SG_262Cell_3_PGKP_Control	PGKP	Control
SA427243	PG_+SG_693Cell_3_PGKP_Control	PGKP	Control
SA427244	PG_+SG_693Cell_2_PGKP_Control	PGKP	Control
SA427245	PG_+SG_693Cell_1_PGKP_Control	PGKP	Control
SA427246	PG_+SG_263Cell_3_PGKP_Control	PGKP	Control
SA427247	PG_+SG_263Cell_2_PGKP_Control	PGKP	Control
SA427248	PG_+SG_263Cell_1_PGKP_Control	PGKP	Control
SA427249	PG_+SG_262Cell_2_PGKP_Control	PGKP	Control
SA427250	PG_+SG_41Cell_2_PGKP_Control	PGKP	Control
SA427251	PG_+SG_261Cell_3_PGKP_Control	PGKP	Control
SA427252	PG_+SG_41Cell_1_PGKP_Control	PGKP	Control
SA427253	PG_+SG_262Cell_1_PGKP_Control	PGKP	Control
SA427254	PG_+SG_41Cell_3_PGKP_Control	PGKP	Control
SA427255	PG_+SG_261Cell_1_PGKP_Control	PGKP	Control
SA427256	PG_+SG_261Cell_2_PGKP_Control	PGKP	Control
SA427257	PG_-SG_693Cell_3_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427258	PG_-SG_693Cell_2_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427259	PG_-SG_693Cell_1_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427260	PG_-SG_263Cell_3_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427261	PG_-SG_263Cell_2_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427262	PG_-SG_263Cell_1_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427263	PG_-SG_262Cell_2_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427264	PG_-SG_262Cell_3_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427265	PG_-SG_262Cell_1_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427266	PG_-SG_261Cell_3_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427267	PG_-SG_261Cell_1_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427268	PG_-SG_41Cell_3_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427269	PG_-SG_41Cell_2_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427270	PG_-SG_41Cell_1_PGKP_woSer/Gly	PGKP	woSer/Gly
SA427271	PG_-SG_261Cell_2_PGKP_woSer/Gly	PGKP	woSer/Gly

Showing results 1 to 48 of 48

Showing results 1 to 48 of 48

Collection:

Collection ID:	CO004014
Collection Summary:	TDCLs were plated in 6-well plates (Corning) and cultured for 72 hours to reach 60-80% confluence at the time of incubation. Cells were then incubated with 2 g/L of [U-¹³C]D-glucose (Cambridge Isotope Laboratories) for 12 hours before metabolite extraction. For tracing, cells were incubated with 2g/L of [U-13C]D-glucose (Cambridge Isotope Laboratories) for 12h before metabolite extraction. Three wells were used for the metabolite extraction, and the other three were harvested using trypsin 0.25% to measure the wet cell volume using a PCV-packed cell volume tube (TPP).
Sample Type:	Cultured cells
Volumeoramount Collected:	400uL 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:	TR004030
Treatment Summary:	TDCLs were plated in 6-well plates (Corning) and cultured for 72 hours to reach 60-80% confluence at the time of incubation. For this period the KP and PGKP TDCLs were incubated in complete RPMI medium (Control) and in RPMI without serine and glycine (woSer/Gly). Cells were then incubated with 2 g/L of [U-¹³C]D-glucose (Cambridge Isotope Laboratories) for 12 hours before metabolite extraction. For tracing, cells were incubated with 2g/L of [U-13C]D-glucose (Cambridge Isotope Laboratories) for 12h before metabolite extraction. Three wells were used for the metabolite extraction, and the other three were harvested using trypsin 0.25% to measure the wet cell volume using a PCV-packed cell volume tube (TPP).

Treatment ID:

TR004030

Treatment Summary:

TDCLs were plated in 6-well plates (Corning) and cultured for 72 hours to reach 60-80% confluence at the time of incubation. For this period the KP and PGKP TDCLs were incubated in complete RPMI medium (Control) and in RPMI without serine and glycine (woSer/Gly). Cells were then incubated with 2 g/L of [U-¹³C]D-glucose (Cambridge Isotope Laboratories) for 12 hours before metabolite extraction. For tracing, cells were incubated with 2g/L of [U-13C]D-glucose (Cambridge Isotope Laboratories) for 12h before metabolite extraction. Three wells were used for the metabolite extraction, and the other three were harvested using trypsin 0.25% to measure the wet cell volume using a PCV-packed cell volume tube (TPP).

Sample Preparation:

Sampleprep ID:	SP004027
Sampleprep Summary:	TDCLs the metabolites extraction was performed by washing the wells twice with cold PBS, and 400 µL of extraction buffer 40:40:20 with 0.05% formic acid was added to each well. The plate was allowed to rest on ice for 5 minutes, and then the cells and buffer were scraped. The samples, extraction from medium and cells, were placed in a 1.5 mL microtube with 22 µL of 15% NH4HCO3 vortexed and centrifuged for 10 min at 15,000g at 4° C. 380 µL of the supernatant were collected and stored in -80° C freezer until analysis by LC-MS. The conditioned medium generated in this study was used for the analyses presented in study 5751.

Sampleprep ID:

SP004027

Sampleprep Summary:

TDCLs the metabolites extraction was performed by washing the wells twice with cold PBS, and 400 µL of extraction buffer 40:40:20 with 0.05% formic acid was added to each well. The plate was allowed to rest on ice for 5 minutes, and then the cells and buffer were scraped. The samples, extraction from medium and cells, were placed in a 1.5 mL microtube with 22 µL of 15% NH4HCO3 vortexed and centrifuged for 10 min at 15,000g at 4° C. 380 µL of the supernatant were collected and stored in -80° C freezer until analysis by LC-MS. The conditioned medium generated in this study was used for the analyses presented in study 5751.

Chromatography:

Chromatography ID:	CH004841
Chromatography Summary:	TDCLs from NSCLC.
Methods Filename:	Chromatography_method.pdf
Instrument Name:	Thermo Vanquish
Column Name:	Waters 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% water/80% acetonitrile; 20mM acetic acid, 40mM ammonium hydroxide (pH 9.4)
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006382
Analysis Type:	MS
Chromatography ID:	CH004841
Num Factors:	4
Num Metabolites:	264
Units:	ion count

Analysis ID:	AN006383
Analysis Type:	MS
Chromatography ID:	CH004841
Num Factors:	4
Num Metabolites:	338
Units:	ion count