Summary of Study ST003889

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 IDST003889
Study TitleRespiration defects limit serine synthesis required for lung cancer growth and survival - Effect of Polg mutation in NSCLC Tissues_Lung
Study TypeIn vivo Isotope Tracing
Study SummaryThis study investigates the impact of mtDNA mutation burden induced by the PolGD256A mutation in NSCLC. Using in vivo, we characterized the metabolic profile of NSCLC harboring this mutation compared to controls after submitting 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
DepartmentRutgers Cancer Institute
LaboratoryEileen White
Last NameLopes
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 Lopes Eduardo Lopes
https://dx.doi.org/10.21228/M8RN89
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:SU004024
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 Diet Genotype
SA427471AA_4894_LuII_C__PolG_ControlControl PolG
SA427472AA_5098_Lu_C_PolG_ControlControl PolG
SA427473AA_4997_Lu_C_PolG_ControlControl PolG
SA427474AA_4997_LuII_C_PolG_ControlControl PolG
SA427475AA_4996_Lu_C_PolG_ControlControl PolG
SA427476AA_4996_LuII_C_PolG_ControlControl PolG
SA427477AA_4993_Lu_C_PolG_ControlControl PolG
SA427478AA_4993_LuII_C__PolG_ControlControl PolG
SA427479AA_4946_Lu_C_PolG_ControlControl PolG
SA427480AA_4946_LuII_C_PolG_ControlControl PolG
SA427481AA_4897_Lu_C_PolG_ControlControl PolG
SA427482AA_4897_LuII_C__PolG_ControlControl PolG
SA427483AA_4894_Lu_C_PolG_ControlControl PolG
SA427484wt_5015_LuII_C__wt_ControlControl wt
SA427485wt_5015_Lu_C_wt_ControlControl wt
SA427486wt_5017_LuII_C__wt_ControlControl wt
SA427487wt_5017_Lu_C_wt_ControlControl wt
SA427488wt_5018_LuII_C__wt_ControlControl wt
SA427489wt_5018_Lu_C_wt_ControlControl wt
SA427490wt_5019_Lu_C_repeat_wt_ControlControl wt
SA427491wt_5106_LuII_C__wt_ControlControl wt
SA427492wt_5106_Lu_C_wt_ControlControl wt
SA427493wt_5019_LuII_C__wt_ControlControl wt
SA427494AA_4828_LuII_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427495AA_4828_Lu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427496AA_5009_Lu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427497AA_5009_LuII_woSG__PolG_Ser/Gly freeSer/Gly free PolG
SA427498AA_4984_Lu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427499AA_4984_LuII_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427500AA_4981_Lu_woSG__PolG_Ser/Gly freeSer/Gly free PolG
SA427501AA_4981_LuII_woSG__PolG_Ser/Gly freeSer/Gly free PolG
SA427502AA_4954_Lu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427503AA_4954_LuII_woSG__PolG_Ser/Gly freeSer/Gly free PolG
SA427504AA_4829_Lu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427505AA_4829_LuII_woSG__PolG_Ser/Gly freeSer/Gly free PolG
SA427506wt_5104_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427507wt_6542_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427508wt_5107_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427509wt_5107_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427510wt_5108_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427511wt_5108_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427512wt_5105_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427513wt_5109_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427514wt_5109_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427515wt_6542_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427516wt_5103_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427517wt_5103_Lu_woSG__wt_Ser/Gly freeSer/Gly free wt
SA427518wt_5104_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427519wt_5105_LuII_woSG_wt_Ser/Gly freeSer/Gly free wt
Showing results 1 to 49 of 49

Collection:

Collection ID:CO004017
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:Lung
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:TR004033
Treatment Summary:Lung were collected from animals without 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:SP004030
Sampleprep Summary:For Lung: 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:CH004844
Chromatography Summary:Lung
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:AN006388
Analysis Type:MS
Chromatography ID:CH004844
Num Factors:4
Num Metabolites:291
Units:ion count
  
Analysis ID:AN006389
Analysis Type:MS
Chromatography ID:CH004844
Num Factors:4
Num Metabolites:358
Units:ion count
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