Summary of Study ST004031

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 PR002523. The data can be accessed directly via it's Project DOI: 10.21228/M8HR85 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.

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Study IDST004031
Study TitleSpatial isotope deep tracing deciphers inter-tissue metabolic crosstalk
Study SummaryOrgans collaborate to maintain metabolic homeostasis in mammals. Spatial metabolomics makes strides in profiling the metabolic landscape, yet can not directly inspect the metabolic crosstalk between tissues. Here, we introduce an approach to comprehensively trace the metabolic fate of 13C-nutrients within the body and present a robust computational tool, MSITracer, to deep-probe metabolic activity in a spatial manner. By discerning spatial distribution differences between isotopically labeled metabolites from ambient mass spectrometry imaging-based isotope tracing data, this approach empowers us to characterize fatty acid metabolic crosstalk between the liver and heart, as well as glutamine metabolic exchange across the kidney, liver, and brain. Moreover, we disclose that tumor burden significantly influences the host’s hexosamine biosynthesis pathway, and that the glucose-derived glutamine released from the lung as a potential source for tumor glutamate synthesis. The developed approach facilitates the systematic characterization of metabolic activity in situ and the interpretation of tissue metabolic communications in living organisms. Each dataset was processed according to the following procedure. ProteoWizard (version 3.0.22143) was used to convert the raw MS data (.raw) files to the .mzXML format (for full scan mode) and .mgf (for ddMS2 mode) format. The R package “AutoTuner” (version 1.4.0) was utilized to select dataset-specific parameters to ensure reliable data processing. Then, these optimized key values were used to group mzXML data files from noninfusion samples for peak detection, retention time correction, and peak alignment using the R package “XCMS” (version 3.12.0). For datasets acquired under HILIC mode, the resulting MS1 peak table and MS2 files were input into the “metID” package (version 1.2.19) and MetDNA2 (version 1.4.1; http://metdna.zhulab.cn/) for metabolite annotation, with the liquid chromatography set to “HILIC”. The generated metabolite annotation tables were further filtered and modified to meet the data formatting requirements of the R package “MetTracer” (version 1.0.4).
Institute
Peking Union Medical College
Last NameLi
First NameXinzhu
AddressNo. 2, South Weilu, Xicheng District, Beijing
Emailliting@imm.ac.cn
Phone15239480561
Submit Date2025-06-29
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-07-11
Release Version1
Xinzhu Li Xinzhu Li
https://dx.doi.org/10.21228/M8HR85
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002523
Project DOI:doi: 10.21228/M8HR85
Project Title:Spatial isotope deep tracing deciphers inter-tissue metabolic crosstalk
Project Summary:Organs collaborate to maintain metabolic homeostasis in mammals. Spatial metabolomics makes strides in profiling the metabolic landscape, yet can not directly inspect the metabolic crosstalk between tissues. Here, we introduce an approach to comprehensively trace the metabolic fate of 13C-nutrients within the body and present a robust computational tool, MSITracer, to deep-probe metabolic activity in a spatial manner. By discerning spatial distribution differences between isotopically labeled metabolites from ambient mass spectrometry imaging-based isotope tracing data, this approach empowers us to characterize fatty acid metabolic crosstalk between the liver and heart, as well as glutamine metabolic exchange across the kidney, liver, and brain. Moreover, we disclose that tumor burden significantly influences the host’s hexosamine biosynthesis pathway, and that the glucose-derived glutamine released from the lung as a potential source for tumor glutamate synthesis. The developed approach facilitates the systematic characterization of metabolic activity in situ and the interpretation of tissue metabolic communications in living organisms.
Institute:Peking Union Medical College
Last Name:Li
First Name:Xinzhu
Address:No. 2, South Weilu, Xicheng District, Beijing
Email:liting@imm.ac.cn
Phone:15239480561

Subject:

Subject ID:SU004177
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id Sample source Tracer
SA464720BATT3NQC+DDMSBAT Control
SA464721BATAMIDENQC+DD590BAT Control
SA464722BATC8NQC-DD590BAT Control
SA464723BATC8NQC-DDMSBAT Control
SA464724BATC8NQC-BAT Control
SA464725BATC8N04-BAT Control
SA464726BATT3NQC+DD590BAT Control
SA464727BATT3NQC+DD290BAT Control
SA464728BATT3NQC+DD60BAT Control
SA464729BATT3NQC+BAT Control
SA464730BATAMIDENQC+DD60BAT Control
SA464731BATT3N05+BAT Control
SA464732BATT3N04+BAT Control
SA464733BATT3NQC-DD590BAT Control
SA464734BATT3NQC-DD290BAT Control
SA464735BATT3NQC-DD60BAT Control
SA464736BATT3NQC-DDMSBAT Control
SA464737BATT3NQC-BAT Control
SA464738BATT3N05-BAT Control
SA464739BATT3N04-BAT Control
SA464740BATAMIDENQC+DD290BAT Control
SA464741BATC8NQC-DD200BAT Control
SA464742BATAMIDENQC+DDMSBAT Control
SA464743BATC8NQC+BAT Control
SA464744BATC8NQC+DD890BAT Control
SA464745BATC8NQC+DD590BAT Control
SA464746BATC8NQC+DD200BAT Control
SA464747BATC8NQC+DDMSBAT Control
SA464748BATAMIDEN04-BAT Control
SA464749BATAMIDEN05-BAT Control
SA464750BATAMIDENQC-BAT Control
SA464751BATAMIDENQC-DDMSBAT Control
SA464752BATAMIDENQC-DD60BAT Control
SA464753BATAMIDENQC-DD290BAT Control
SA464754BATAMIDENQC+BAT Control
SA464755BATAMIDENQC-DD590BAT Control
SA464756BATC8N04+BAT Control
SA464757BATAMIDEN05+BAT Control
SA464758BATAMIDEN04+BAT Control
SA464759BATC8NQC-DD890BAT Control
SA464760BATC8GC49+BAT U-13C glucose
SA464761BATT3GCQC-BAT U-13C glucose
SA464762BATT3GC28-BAT U-13C glucose
SA464763BATC8GC28+BAT U-13C glucose
SA464764BATC8GCQC-BAT U-13C glucose
SA464765BATC8GCQC+BAT U-13C glucose
SA464766BATT3GC28+BAT U-13C glucose
SA464767BATT3GC49+BAT U-13C glucose
SA464768BATT3GCQC+BAT U-13C glucose
SA464769BATC8GC49-BAT U-13C glucose
SA464770BATC8GC28-BAT U-13C glucose
SA464771BATAMIDEGC49-BAT U-13C glucose
SA464772BATT3GC49-BAT U-13C glucose
SA464773BATAMIDEGC28-BAT U-13C glucose
SA464774BATAMIDEGCQC-BAT U-13C glucose
SA464775BATAMIDEGC28+BAT U-13C glucose
SA464776BATAMIDEGC49+BAT U-13C glucose
SA464777BATAMIDEGCQC+BAT U-13C glucose
SA464778BATT3GT48+BAT U-13C glutamine
SA464779BATC8GT53+BAT U-13C glutamine
SA464780BATT3GT46+BAT U-13C glutamine
SA464781BATT3GT53-BAT U-13C glutamine
SA464782BATT3GT48-BAT U-13C glutamine
SA464783BATT3GT46-BAT U-13C glutamine
SA464784BATC8GT46-BAT U-13C glutamine
SA464785BATC8GT48-BAT U-13C glutamine
SA464786BATC8GT53-BAT U-13C glutamine
SA464787BATAMIDEGT53+BAT U-13C glutamine
SA464788BATAMIDEGT46+BAT U-13C glutamine
SA464789BATT3GT53+BAT U-13C glutamine
SA464790BATC8GT46+BAT U-13C glutamine
SA464791BATC8GT48+BAT U-13C glutamine
SA464792BATAMIDEGT48+BAT U-13C glutamine
SA464793BATAMIDEGT53-BAT U-13C glutamine
SA464794BATAMIDEGT48-BAT U-13C glutamine
SA464795BATAMIDEGT46-BAT U-13C glutamine
SA464796BrainC8NQC+DD200Brain Control
SA464797BrainC8NQC-DD890Brain Control
SA464798BrainC8N04+Brain Control
SA464799BrainAMIDEN04+Brain Control
SA464800BrainAMIDEN05+Brain Control
SA464801BrainC8NQC+DD890Brain Control
SA464802BrainAMIDENQC+DDMSBrain Control
SA464803BrainAMIDENQC+DD60Brain Control
SA464804BrainAMIDENQC+DD290Brain Control
SA464805BrainAMIDENQC+DD590Brain Control
SA464806BrainAMIDEN06-Brain Control
SA464807BrainC8NQC-DD590Brain Control
SA464808BrainC8NQC-DD200Brain Control
SA464809BrainC8NQC+DDMSBrain Control
SA464810BrainAMIDEN05-Brain Control
SA464811BrainAMIDEN04-Brain Control
SA464812BrainC8NQC-DDMSBrain Control
SA464813BrainC8N06-Brain Control
SA464814BrainC8N05-Brain Control
SA464815BrainC8N04-Brain Control
SA464816BrainC8N05+Brain Control
SA464817BrainC8N06+Brain Control
SA464818BrainAMIDEN06+Brain Control
SA464819BrainC8NQC+DD590Brain Control
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Collection:

Collection ID:CO004170
Collection Summary:The BALB/c nude mice were randomly divided into noninfusion or infusion groups. Catheters were inserted into the jugular vein of mice under anaesthesia. U-13C glucose and U-13C glutamine were infused into conscious, free-moving animals for 3 h at constant rates of 80 and 30 nmol/min/g, respectively. After the infusion, blood was collected from the orbital sinus, and the mouse was euthanized. Nine organs (liver, kidney, spleen, pancreas, heart, lung, brain, brown adipose tissue, and muscle) were sequentially harvested and quickly snap-frozen in liquid nitrogen to halt metabolic processes and ensure comparability between different groups.
Sample Type:Plasma,BAT,Brain,Heart,Kidney,Liver,Lung,Muscle,Pancreas,Spleen

Treatment:

Treatment ID:TR004186
Treatment Summary:The BALB/c nude mice were randomly divided into noninfusion or infusion groups. Catheters were inserted into the jugular vein of mice under anaesthesia. U-13C glucose and U-13C glutamine were infused into conscious, free-moving animals for 3 h at constant rates of 80 and 30 nmol/min/g, respectively. After the infusion, blood was collected from the orbital sinus, and the mouse was euthanized. Nine organs (liver, kidney, spleen, pancreas, heart, lung, brain, brown adipose tissue, and muscle) were sequentially harvested and quickly snap-frozen in liquid nitrogen to halt metabolic processes and ensure comparability between different groups.

Sample Preparation:

Sampleprep ID:SP004183
Sampleprep Summary:For metabolomics analysis, 500 μL of extraction solvent (ACN:MeOH:H2O = 2:2:1, v/v/v) was added to 100 μL of serum or 25 mg of tissue sample. The mixture was vortexed for 30 s, followed by homogenization and sonication for 5 min in an ice-water bath; this process was repeated 3 times. Then, the mixture was incubated for 1 h before centrifugation at 15000 rpm for 15 min at 4 °C. An aliquot of the supernatant was used for the LC‒MS assay. For lipidomic analysis, 480 μL of extraction solution (MTBE: MeOH = 5: 1, v/v) was sequentially added to 200 μL of water. Apart from the supernatant collection, all other procedures were the same as those described above. After solution layering, the supernatant was transferred and vacuum-dried. Finally, the samples were resolubilized in ACN/IPA/H2O (65:30:5, v/v/v) containing 5 mM AmAc prior to analysis.

Chromatography:

Chromatography ID:CH005063
Chromatography Summary:For metabolome analysis, a Waters BEH Amide column (2.1 mm × 100 mm, 1.7 μm), the mobile phase consisted of water containing 25 mmol/L AmAc, 25 mmol/L NH4OH (A) and ACN (B) in both positive and negative ion modes. The gradient program was set as follows: 0-0.5 min, 5% A; 0.5-7.0 min, 5% A-35% A; 7.0-8.0 min, 35%-60% A; 8.0-9.0 min, 60% A; and 9.0-12.0 min, 5% A. The flow rate was 0.5 mL/min, and the sample injection volume was 5 μL.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
Column Temperature:30
Flow Gradient:0-0.5 min, 5% A; 0.5-7.0 min, 5% A-35% A; 7.0-8.0 min, 35%-60% A; 8.0-9.0 min, 60% A; and 9.0-12.0 min, 5% A
Flow Rate:0.5 mL/min
Solvent A:100% water; 25 mmol/L Ammonium acetate; 25 mmol/L Ammonium hydroxide
Solvent B:100% Acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH005064
Chromatography Summary:In RP mode, the mobile phase consisted of water containing 0.1% formic acid (A) and ACN (B) for both positive and negative ion modes. The gradient program was set as follows: 0-1.5 min, 98% A; 1.5-15 min, 98-0% A; 15-22 min, 0% A; 22-22.1 min, 0-98% A; 22.1-27 min, 98% A. The flow rate was 0.25 mL/min, and the sample injection volume was 5 μL.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:35
Flow Gradient:0-1.5 min, 98% A; 1.5-15 min, 98-0% A; 15-22 min, 0% A; 22-22.1 min, 0-98% A; 22.1-27 min, 98% A.
Flow Rate:0.25 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% Acetonitrile
Chromatography Type:Reversed phase
  
Chromatography ID:CH005065
Chromatography Summary:For lipid analysis, the mobile phase consisted of ACN/H2O (60:40, v/v) (A) and IPA/ACN (90:10, v/v) (B), both containing 10 mM AmAc, for positive and negative ion modes. The gradient program was set as follows: 0-1.5 min, 68% A; 1.5-15.5 min, 15% A; 15.5-15.6 min, 3% A; 15.6-18 min, 3% A; 18-18.1 min, 68% A; and 18.1-20 min, 68% A. The flow rate was 0.26 mL/min, and the sample injection volume was 5 μL.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
Column Temperature:55
Flow Gradient:0-1.5 min, 68% A; 1.5-15.5 min, 15% A; 15.5-15.6 min, 3% A; 15.6-18 min, 3% A; 18-18.1 min, 68% A; and 18.1-20 min, 68% A.
Flow Rate:0.26 mL/min
Solvent A:60% acetonitrile/40% water; 10mM ammonium acetate
Solvent B:90% isopropanol/10% acetonitrile; 10mM ammonium acetate
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006662
Analysis Type:MS
Chromatography ID:CH005063
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004031_AN006662_Results.txt
Units:Peak area
  
Analysis ID:AN006663
Analysis Type:MS
Chromatography ID:CH005063
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004031_AN006663_Results.txt
Units:Peak area
  
Analysis ID:AN006664
Analysis Type:MS
Chromatography ID:CH005064
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004031_AN006664_Results.txt
Units:Peak area
  
Analysis ID:AN006665
Analysis Type:MS
Chromatography ID:CH005064
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004031_AN006665_Results.txt
Units:Peak area
  
Analysis ID:AN006666
Analysis Type:MS
Chromatography ID:CH005065
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004031_AN006666_Results.txt
Units:Peak area
  
Analysis ID:AN006667
Analysis Type:MS
Chromatography ID:CH005065
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004031_AN006667_Results.txt
Units:Peak area
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