Summary of Study ST003887

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.

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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 IDST003887
Study TitleRespiration defects limit serine synthesis required for lung cancer growth and survival - Effect of Polg mutation in NSCLC conditioned medium
Study SummaryThis 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 conditioned medium. 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 NameCararo Lopes
First NameEduardo
Address195 Little Albany Street
Emailedu.llopes@gmail.com
Phone732-235-5795
Submit Date2025-03-20
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-05-06
Release Version1
Eduardo Cararo Lopes Eduardo Cararo Lopes
https://dx.doi.org/10.21228/M8RN89
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

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:SU004022
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 Medium Medium Genotype
SA427272Ctrol+SG_2_Fresh Medium_ControlControl Fresh Medium control
SA427273Ctrol+SG_1_Fresh Medium_ControlControl Fresh Medium control
SA427274KP_+SG_483M12_3_KP_ControlControl KP
SA427275KP_+SG_313M4_3_KP_ControlControl KP
SA427276KP_+SG_483M8_3_KP_ControlControl KP
SA427277KP_+SG_483M8_2_KP_ControlControl KP
SA427278KP_+SG_483M8_1_KP_ControlControl KP
SA427279KP_+SG_483M4_3_KP_ControlControl KP
SA427280KP_+SG_483M4_2_KP_ControlControl KP
SA427281KP_+SG_483M4_1_KP_ControlControl KP
SA427282KP_+SG_483M12_2_KP_ControlControl KP
SA427283KP_+SG_483M12_1_KP_ControlControl KP
SA427284KP_+SG_313M8_3_KP_ControlControl KP
SA427285KP_+SG_311M12_1_KP_ControlControl KP
SA427286KP_+SG_313M8_1_KP_ControlControl KP
SA427287KP_+SG_313M8_2_KP_ControlControl KP
SA427288KP_+SG_313M4_2_KP_ControlControl KP
SA427289KP_+SG_311M8_1_KP_ControlControl KP
SA427290KP_+SG_311M12_2_KP_ControlControl KP
SA427291KP_+SG_311M12_3_KP_ControlControl KP
SA427292KP_+SG_311M4_1_KP_ControlControl KP
SA427293KP_+SG_313M4_1_KP_ControlControl KP
SA427294KP_+SG_311M4_3_KP_ControlControl KP
SA427295KP_+SG_311M4_2_KP_ControlControl KP
SA427296KP_+SG_311M8_2_KP_ControlControl KP
SA427297KP_+SG_311M8_3_KP_ControlControl KP
SA427298KP_+SG_313M12_1_KP_ControlControl KP
SA427299KP_+SG_313M12_2_KP_ControlControl KP
SA427300KP_+SG_313M12_3_KP_ControlControl KP
SA427301PG_+SG_263M8_2_PGKP_ControlControl PGKP
SA427302PG_+SG_263M8_1_PGKP_ControlControl PGKP
SA427303PG_+SG_263M4_3_PGKP_ControlControl PGKP
SA427304PG_+SG_263M4_2_PGKP_ControlControl PGKP
SA427305PG_+SG_263M4_1_PGKP_ControlControl PGKP
SA427306PG_+SG_263M12_3_PGKP_ControlControl PGKP
SA427307PG_+SG_263M12_2_PGKP_ControlControl PGKP
SA427308PG_+SG_262M8_2_PGKP_ControlControl PGKP
SA427309PG_+SG_262M8_3_PGKP_ControlControl PGKP
SA427310PG_+SG_262M8_1_PGKP_ControlControl PGKP
SA427311PG_+SG_262M4_3_PGKP_ControlControl PGKP
SA427312PG_+SG_262M4_2_PGKP_ControlControl PGKP
SA427313PG_+SG_262M4_1_PGKP_ControlControl PGKP
SA427314PG_+SG_262M12_3_PGKP_ControlControl PGKP
SA427315PG_+SG_41M12_1_PGKP_ControlControl PGKP
SA427316PG_+SG_263M8_3_PGKP_ControlControl PGKP
SA427317PG_+SG_693M4_3_PGKP_ControlControl PGKP
SA427318PG_+SG_41M12_2_PGKP_ControlControl PGKP
SA427319PG_+SG_693M12_3_PGKP_ControlControl PGKP
SA427320PG_+SG_693M8_3_PGKP_ControlControl PGKP
SA427321PG_+SG_693M8_2_PGKP_ControlControl PGKP
SA427322PG_+SG_693M8_1_PGKP_ControlControl PGKP
SA427323PG_+SG_262M12_1_PGKP_ControlControl PGKP
SA427324PG_+SG_693M4_2_PGKP_ControlControl PGKP
SA427325PG_+SG_693M4_1_PGKP_ControlControl PGKP
SA427326PG_+SG_693M12_2_PGKP_ControlControl PGKP
SA427327PG_+SG_41M12_3_PGKP_ControlControl PGKP
SA427328PG_+SG_693M12_1_PGKP_ControlControl PGKP
SA427329PG_+SG_41M8_3_PGKP_ControlControl PGKP
SA427330PG_+SG_41M8_2_PGKP_ControlControl PGKP
SA427331PG_+SG_41M8_1_PGKP_ControlControl PGKP
SA427332PG_+SG_41M4_3_PGKP_ControlControl PGKP
SA427333PG_+SG_41M4_2_PGKP_ControlControl PGKP
SA427334PG_+SG_41M4_1_PGKP_ControlControl PGKP
SA427335PG_+SG_262M12_2_PGKP_ControlControl PGKP
SA427336PG_+SG_263M12_1_PGKP_ControlControl PGKP
SA427337PG_+SG_261M8_3_PGKP_ControlControl PGKP
SA427338PG_+SG_261M12_1_PGKP_ControlControl PGKP
SA427339PG_+SG_261M8_1_PGKP_ControlControl PGKP
SA427340PG_+SG_261M4_3_PGKP_ControlControl PGKP
SA427341PG_+SG_261M4_2_PGKP_ControlControl PGKP
SA427342PG_+SG_261M4_1_PGKP_ControlControl PGKP
SA427343PG_+SG_261M12_3_PGKP_ControlControl PGKP
SA427344PG_+SG_261M12_2_PGKP_ControlControl PGKP
SA427345PG_+SG_261M8_2_PGKP_ControlControl PGKP
SA427346Ctrol-SG_2_Fresh Medium woSer/Gly_woSer/GlywoSer/Gly Fresh Medium no Ser/Gly
SA427347Ctrol-SG_1_Fresh Medium woSer/Gly_woSer/GlywoSer/Gly Fresh Medium no Ser/Gly
SA427348KP_-SG_483M8_3_KP_woSer/GlywoSer/Gly KP
SA427349KP_-SG_313M12_3_KP_woSer/GlywoSer/Gly KP
SA427350KP_-SG_483M8_2_KP_woSer/GlywoSer/Gly KP
SA427351KP_-SG_311M12_1_KP_woSer/GlywoSer/Gly KP
SA427352KP_-SG_311M12_2_KP_woSer/GlywoSer/Gly KP
SA427353KP_-SG_311M4_1_KP_woSer/GlywoSer/Gly KP
SA427354KP_-SG_311M4_2_KP_woSer/GlywoSer/Gly KP
SA427355KP_-SG_311M4_3_KP_woSer/GlywoSer/Gly KP
SA427356KP_-SG_311M8_1_KP_woSer/GlywoSer/Gly KP
SA427357KP_-SG_311M8_2_KP_woSer/GlywoSer/Gly KP
SA427358KP_-SG_311M8_3_KP_woSer/GlywoSer/Gly KP
SA427359KP_-SG_313M12_1_KP_woSer/GlywoSer/Gly KP
SA427360KP_-SG_313M12_2_KP_woSer/GlywoSer/Gly KP
SA427361KP_-SG_311M12_3_KP_woSer/GlywoSer/Gly KP
SA427362KP_-SG_313M4_1_KP_woSer/GlywoSer/Gly KP
SA427363KP_-SG_483M12_2_KP_woSer/GlywoSer/Gly KP
SA427364KP_-SG_313M4_2_KP_woSer/GlywoSer/Gly KP
SA427365KP_-SG_483M4_3_KP_woSer/GlywoSer/Gly KP
SA427366KP_-SG_483M4_1_KP_woSer/GlywoSer/Gly KP
SA427367KP_-SG_483M12_3_KP_woSer/GlywoSer/Gly KP
SA427368KP_-SG_483M4_2_KP_woSer/GlywoSer/Gly KP
SA427369KP_-SG_483M12_1_KP_woSer/GlywoSer/Gly KP
SA427370KP_-SG_313M8_3_KP_woSer/GlywoSer/Gly KP
SA427371KP_-SG_313M8_2_KP_woSer/GlywoSer/Gly KP
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Collection:

Collection ID:CO004015
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). For Kinect release, the conditioned medium was collected at three-time points every 4 hours after the introduction of [U-13C]D-glucose, followed by metabolite extraction as previously described.
Sample Type:Culture Media
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:TR004031
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). For Kinect release, the conditioned medium was collected at three-time points every 4 hours after the introduction of [U-13C]D-glucose, followed by metabolite extraction as previously described.

Sample Preparation:

Sampleprep ID:SP004028
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. In the table, where the genotype of the samples is specified as “Fresh medium control” and “Fresh medium no Ser/Gly” it refers to unconditioned culture medium (not exposed to cells), which serves as a baseline for metabolite analysis of the conditioned medium with and without Ser/Gly from KP and PGKP TDCLs.

Chromatography:

Chromatography ID:CH004842
Chromatography Summary:TDCLs from NSCLC. BOX I Pos
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:AN006384
Analysis Type:MS
Chromatography ID:CH004842
Num Factors:6
Num Metabolites:157
Units:ion count
  
Analysis ID:AN006385
Analysis Type:MS
Chromatography ID:CH004842
Num Factors:6
Num Metabolites:153
Units:ion count
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