Summary of Study ST003888

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

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Study IDST003888
Study TitleRespiration defects limit serine synthesis required for lung cancer growth and survival - Effect of Polg mutation in NSCLC Tissues_Muscle
Study SummaryHere 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:SU004023
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
SA427420KP_5021_Mu_C_KP_ControlControl KP
SA427421KP_5156_Mu_C_KP_ControlControl KP
SA427422KP_5155_Mu_C_KP_ControlControl KP
SA427423KP_5022_Mu_C_KP_ControlControl KP
SA427424KP_5020_Mu_C_KP_ControlControl KP
SA427425AAK_5013_Mu_C_PGKP_ControlControl PGKP
SA427426AAK_5005_Mu_C_PGKP_ControlControl PGKP
SA427427AAK_5004_Mu_C_PGKP_ControlControl PGKP
SA427428AAK_4942_Mu_C_PGKP_ControlControl PGKP
SA427429AAK_4900_Mu_C_PGKP_ControlControl PGKP
SA427430AAK_4898_Mu_C_PGKP_ControlControl PGKP
SA427431AAK_4896_Mu_C_PGKP_ControlControl PGKP
SA427432AA_5098_Mu_C_PolG_ControlControl PolG
SA427433AA_4996_Mu_C_PolG_ControlControl PolG
SA427434AA_4997_Mu_C_PolG_ControlControl PolG
SA427435AA_4894_Mu_C_PolG_ControlControl PolG
SA427436AA_4946_Mu_C_PolG_ControlControl PolG
SA427437AA_4993_Mu_C_PolG_ControlControl PolG
SA427438wt_5015_Mu_C_wt_ControlControl wt
SA427439wt_5017_Mu_C_wt_ControlControl wt
SA427440wt_5018_Mu_C_wt_ControlControl wt
SA427441wt_5019_Mu_C_wt_ControlControl wt
SA427442wt_5106_Mu_C_wt_ControlControl wt
SA427443KP_3425_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427444KP_3371_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427445KP_3327_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427446KP_5169_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427447KP_3370_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427448KP_3430_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427449KP_5167_Mu_woSG_KP_Ser/Gly freeSer/Gly free KP
SA427450AAK_5359_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427451AAK_4992_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427452AAK_4891_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427453AAK_4840_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427454AAK_4838_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427455AAK_4837_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427456AAK_4835_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427457AAK_4830_Mu_woSG_PGKP_Ser/Gly freeSer/Gly free PGKP
SA427458AA_5009_Mu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427459AA_4984_Mu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427460AA_4954_Mu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427461AA_4981_Mu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427462AA_4829_Mu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427463AA_4828_Mu_woSG_PolG_Ser/Gly freeSer/Gly free PolG
SA427464wt_6542_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427465wt_5104_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427466wt_5105_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427467wt_5107_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427468wt_5108_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427469wt_5109_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
SA427470wt_5103_Mu_woSG_wt_Ser/Gly freeSer/Gly free wt
Showing results 1 to 51 of 51

Collection:

Collection ID:CO004016
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:Muscle
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:TR004032
Treatment Summary: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:SP004029
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.

Combined analysis:

Analysis ID AN006386 AN006387
Chromatography ID CH004843 CH004843
MS ID MS006087 MS006088
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters XBridge BEH Amide (150 × 2.1mm, 2.5um) Waters XBridge BEH Amide (150 × 2.1mm, 2.5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE
Units ion count ion count

Chromatography:

Chromatography ID:CH004843
Chromatography Summary:Muscle
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

MS:

MS ID:MS006087
Analysis ID:AN006386
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Maven
Ion Mode:POSITIVE
  
MS ID:MS006088
Analysis ID:AN006387
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Maven
Ion Mode:NEGATIVE
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