Summary of Study ST003890

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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003890
Study TitleRespiration defects limit serine synthesis required for lung cancer growth and survival - Effect of Polg mutation in NSCLC Tissues_Liver
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 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
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

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:SU004025
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
SA427520KP_5021_Li_C_KP_ControlControl KP
SA427521KP_5156_Li_C_KP_ControlControl KP
SA427522KP_5155_Li_C_KP_ControlControl KP
SA427523KP_5022_Li_C_KP_ControlControl KP
SA427524KP_5020_Li_C_KP_ControlControl KP
SA427525AAK_5013_Li_C_PGKP_ControlControl PGKP
SA427526AAK_5005_Li_C_PGKP_ControlControl PGKP
SA427527AAK_5004_Li_C_PGKP_ControlControl PGKP
SA427528AAK_4942_Li_C_PGKP_ControlControl PGKP
SA427529AAK_4900_Li_C_PGKP_ControlControl PGKP
SA427530AAK_4898_Li_C_PGKP_ControlControl PGKP
SA427531AAK_4896_Li_C_PGKP_ControlControl PGKP
SA427532AA_5098_Li_C_PolG_ControlControl PolG
SA427533AA_4996_Li_C_PolG_ControlControl PolG
SA427534AA_4997_Li_C_PolG_ControlControl PolG
SA427535AA_4894_Li_C_PolG_ControlControl PolG
SA427536AA_4946_Li_C_PolG_ControlControl PolG
SA427537AA_4993_Li_C_PolG_ControlControl PolG
SA427538wt_5015_Li_C_wt_ControlControl wt
SA427539wt_5017_Li_C_wt_ControlControl wt
SA427540wt_5018_Li_C_wt_ControlControl wt
SA427541wt_5019_Li_C_wt_ControlControl wt
SA427542wt_5106_Li_C_wt_ControlControl wt
SA427543KP_3425_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427544KP_3371_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427545KP_3327_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427546KP_5169_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427547KP_3370_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427548KP_3430_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427549KP_5167_Li_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427550AAK_5359_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427551AAK_4992_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427552AAK_4891_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427553AAK_4840_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427554AAK_4838_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427555AAK_4837_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427556AAK_4835_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427557AAK_4830_Li_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427558AA_5009_Li_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427559AA_4984_Li_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427560AA_4954_Li_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427561AA_4981_Li_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427562AA_4829_Li_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427563AA_4828_Li_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427564wt_6542_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427565wt_5104_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427566wt_5105_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427567wt_5107_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427568wt_5108_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427569wt_5109_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427570wt_5103_Li_woSG_wt_Ser/Gly freeSer/Gly free wt
Showing results 1 to 51 of 51

Collection:

Collection ID:CO004018
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:Liver
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:TR004034
Treatment Summary:Liver were collected from animals with and 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:SP004031
Sampleprep Summary:For Muscle: 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:CH004845
Chromatography Summary:Liver
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:AN006390
Analysis Type:MS
Chromatography ID:CH004845
Num Factors:8
Num Metabolites:419
Rt Units:Minutes
Units:ion count
  
Analysis ID:AN006391
Analysis Type:MS
Chromatography ID:CH004845
Num Factors:8
Num Metabolites:523
Rt Units:Minutes
Units:ion count
  logo