Summary of Study ST004470
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 PR002823. The data can be accessed directly via it's Project DOI: 10.21228/M8RP0M This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004470 |
| Study Title | Sex-specific effects of exogenous asparagine on colorectal tumor growth, 17β-estradiol levels, and aromatase in mice |
| Study Summary | The study aims to understand the relationship between exogenous asparagine supplementation and 17β-estradiol levels and to elucidate mechanisms underlying sex-dependent signaling during CRC development. We administered asparagine intraperitoneally to tumor-bearing male and female immunodeficient Rag2/Il2RG (R2G2) mice. We performed untargeted metabolomics and found that intraperitoneal asparagine treatment induced sex-dependent intra-tumoral metabolic changes to asparagine, aspartate, glutamine and glutamate levels. |
| Institute | Yale University |
| Last Name | Johnson |
| First Name | Caroline |
| Address | 60 College Street, LEPH, Room 509 |
| caroline.johnson@yale.edu | |
| Phone | 2037852882 |
| Submit Date | 2025-12-16 |
| Num Groups | 6 |
| Total Subjects | 29 |
| Num Males | 15 |
| Num Females | 14 |
| Publications | https://pubmed.ncbi.nlm.nih.gov/40228761/ |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2026-01-06 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002823 |
| Project DOI: | doi: 10.21228/M8RP0M |
| Project Title: | Sex-specific effects of exogenous asparagine on colorectal tumor growth, 17β-estradiol levels, and aromatase in mice |
| Project Summary: | The study aims to understand the relationship between exogenous asparagine supplementation and 17β-estradiol levels and to elucidate mechanisms underlying sex-dependent signaling during CRC development. We administered asparagine intraperitoneally to tumor-bearing male and female immunodeficient Rag2/Il2RG (R2G2) mice. We performed untargeted metabolomics and found that intraperitoneal asparagine treatment induced sex-dependent intra-tumoral metabolic changes to asparagine, aspartate, glutamine and glutamate levels. To confirm whether asparagine supplementation alters de novo asparagine synthesis in a sex-specific manner, we performed untargeted metabolomics on the tumor xenografts from the R2G2 mice. We examined abundances of metabolites that are involved in the asparagine metabolism pathway including aspartate and glutamine (substrates) and asparagine and glutamate (products). Samples were analyzed in hydrophilic interaction chromatography (HILIC) and reverse phase (RPLC) mass spectrometry (MS) modes. The mass spectrometry data was acquired using a UPLC system (H-Class ACQUITY, Waters Corporation, MA, United States) coupled to a quadrupole time-of flight (QTOF) mass spectrometer (Xevo G2-XS QTOF, Waters Corporation, MA, United States). |
| Institute: | Yale University |
| Department: | Environmental Health Sciences |
| Laboratory: | Caroline Johnson |
| Last Name: | Johnson |
| First Name: | Caroline |
| Address: | 60 College Street, LEPH, Room 509 |
| Email: | caroline.johnson@yale.edu |
| Phone: | 2037852882 |
| Funding Source: | R01 CA289440/CA/NCI NIH HHS/United States |
| Publications: | https://pubmed.ncbi.nlm.nih.gov/40228761/ |
| Contributors: | Oladimeji Aladelokun, Katherine Benitez, Yuying Wang, Abhishek Jain, Domenica Berardi, Georgio Maroun, Xinyi Shen, Jatin Roper, Joanna Gibson, Kaelyn Sumigray, Sajid A Khan, Caroline H Johnson |
Subject:
| Subject ID: | SU004646 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Rag2/IL2RG |
| Age Or Age Range: | 4-6 weeks |
| Weight Or Weight Range: | 25 g |
| Height Or Height Range: | N/A |
| Gender: | Male and female |
| Animal Animal Supplier: | Inotiv |
| Animal Housing: | Yale School of Medicine SPF facility |
| Animal Light Cycle: | 12-hour light and dark |
| Animal Feed: | Standard rodent chow diet; Teklad #2018S |
| Animal Water: | ad libitum |
| Animal Inclusion Criteria: | N/A |
| Species Group: | N/A |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Factor |
|---|---|---|---|
| SA531921 | 614 | Tumor xenograft_Female R2G2 | 10 mg/kg asparagine |
| SA531922 | 615 | Tumor xenograft_Female R2G2 | 10 mg/kg asparagine |
| SA531923 | 611 | Tumor xenograft_Female R2G2 | 10 mg/kg asparagine |
| SA531924 | 612 | Tumor xenograft_Female R2G2 | 10 mg/kg asparagine |
| SA531925 | 613 | Tumor xenograft_Female R2G2 | 10 mg/kg asparagine |
| SA531916 | 606 | Tumor xenograft_Female R2G2 | 1 mg/kg asparagine |
| SA531917 | 607 | Tumor xenograft_Female R2G2 | 1 mg/kg asparagine |
| SA531918 | 608 | Tumor xenograft_Female R2G2 | 1 mg/kg asparagine |
| SA531919 | 609 | Tumor xenograft_Female R2G2 | 1 mg/kg asparagine |
| SA531920 | 610 | Tumor xenograft_Female R2G2 | 1 mg/kg asparagine |
| SA531926 | 602 | Tumor xenograft_Female R2G2 | Control |
| SA531927 | 601 | Tumor xenograft_Female R2G2 | Control |
| SA531928 | 605 | Tumor xenograft_Female R2G2 | Control |
| SA531929 | 604 | Tumor xenograft_Female R2G2 | Control |
| SA531935 | 626 | Tumor xenograft_Male R2G2 | 10 mg/kg asparagine |
| SA531936 | 627 | Tumor xenograft_Male R2G2 | 10 mg/kg asparagine |
| SA531937 | 628 | Tumor xenograft_Male R2G2 | 10 mg/kg asparagine |
| SA531938 | 629 | Tumor xenograft_Male R2G2 | 10 mg/kg asparagine |
| SA531939 | 630 | Tumor xenograft_Male R2G2 | 10 mg/kg asparagine |
| SA531930 | 622 | Tumor xenograft_Male R2G2 | 1 mg/kg asparagine |
| SA531931 | 625 | Tumor xenograft_Male R2G2 | 1 mg/kg asparagine |
| SA531932 | 624 | Tumor xenograft_Male R2G2 | 1 mg/kg asparagine |
| SA531933 | 623 | Tumor xenograft_Male R2G2 | 1 mg/kg asparagine |
| SA531934 | 621 | Tumor xenograft_Male R2G2 | 1 mg/kg asparagine |
| SA531940 | 620 | Tumor xenograft_Male R2G2 | Control |
| SA531941 | 616 | Tumor xenograft_Male R2G2 | Control |
| SA531942 | 619 | Tumor xenograft_Male R2G2 | Control |
| SA531943 | 618 | Tumor xenograft_Male R2G2 | Control |
| SA531944 | 617 | Tumor xenograft_Male R2G2 | Control |
| Showing results 1 to 29 of 29 |
Collection:
| Collection ID: | CO004639 |
| Collection Summary: | Tumor tissue was homogenized in UPLC-grade H2O using the Precellys Evolution cryo-homogenizer (Bertin Corp. USA) and metabolites were extracted using methanol:acetonitrile (1:1, v/v). For a comprehensive analysis of the metabolome, untargeted metabolomics was conducted as described below. Briefly, samples were analyzed in hydrophilic interaction chromatography (HILIC) mass spectrometry (MS) mode. The mass spectrometry data was acquired using a UPLC system (H-Class ACQUITY, Waters Corporation, MA, United States) coupled to a quadrupole time-of flight (QTOF) mass spectrometer (Xevo G2-XS QTOF, Waters Corporation, MA, United States). Waters ACQUITY UPLC BEH Amide column [particle size: 1.7 μm; 100 mm (length) by 2.1 mm (internal diameter)] and a BEH C18 column [particle size: 1.7 μm; 100 mm (length) by 2.1 mm (internal diameter)] were used for the UPLC-based separation of metabolites. For HILIC-MS run, the mobile phase A was 25 mM ammonium hydroxide and 25 mM ammonium acetate in water while mobile phase B was acetonitrile. For RPLC-MS run, mobile phase A was 0.1% formic acid in water, while mobile phase B was 0.1% formic acid in acetonitrile. Pooled samples were analyzed at specified injections interval during the UPLC-MS analysis which allowed monitoring of the systems’ stability. |
| Sample Type: | Tumor cells |
Treatment:
| Treatment ID: | TR004655 |
| Treatment Summary: | Pharmaceutical grade asparagine (#1043513, Sigma Aldrich, St Louis, MO, USA) was injected into the peritoneal cavity twice a week (L-asparagine in phosphate buffered saline, PBS) at 1 mg/kg and 10 mg/kg body weight for 4 weeks. |
| Treatment Compound: | asparagine |
| Treatment Route: | Intraperitoneal |
| Treatment Dose: | 1 mg/kg and 10 mg/kg asparagine body weight |
Sample Preparation:
| Sampleprep ID: | SP004652 |
| Sampleprep Summary: | Tumor tissue was homogenized in UPLC-grade H2O using the Precellys Evolution cryo-homogenizer (Bertin Corp. USA) and metabolites were extracted using methanol:acetonitrile (1:1, v/v). For a comprehensive analysis of the metabolome, untargeted metabolomics was conducted in-house. Briefly, samples were analyzed in hydrophilic interaction chromatography (HILIC) and RPLC mass spectrometry (MS) column chemistry. |
| Processing Storage Conditions: | -20℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN007493 | AN007494 |
|---|---|---|
| Chromatography ID | CH005682 | CH005683 |
| MS ID | MS007189 | MS007190 |
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Waters Acquity H-Class | Waters Acquity H-Class |
| Column | Waters ACQUITY UPLC BEH Amide (100 x 2.1 mm, 1.7 μm) | Waters ACQUITY UPLC BEH C18 (100 x 2.1 mm, 1.7 μm) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Waters Xevo-G2-XS | Waters Xevo-G2-XS |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | ion counts | ion counts |
Chromatography:
| Chromatography ID: | CH005682 |
| Chromatography Summary: | HILIC MS |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters ACQUITY UPLC BEH Amide (100 x 2.1 mm, 1.7 μm) |
| Column Temperature: | 30℃ |
| Flow Gradient: | Initial: 5% Solvent A: 95% Solvent B 0.5 min: 5% Solvent A, 95% Solvent B 7 min: 35% Solvent A, 65% Solvent B 8 min: 60% Solvent A, 40% Solvent B 9 min: 60% Solvent A, 40% Solvent B 9.10 min: 5% Solvent A, 95% Solvent B 12 min: 5% Solvent A, 95% Solvent B |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% Water; 25 mM ammonium hydroxide; 25 mM ammonium acetate |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH005683 |
| Chromatography Summary: | RP-LCMS |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1 mm, 1.7 μm) |
| Column Temperature: | 30℃ |
| Flow Gradient: | Initial: 99% Solvent A: 1% Solvent B 1 min: 99% Solvent A: 1% Solvent B 8 min: 1% Solvent A: 99% Solvent B 10 min: 1% Solvent A: 99% Solvent B 10.10 min: 99% Solvent A: 1% Solvent B 12 min: 99% Solvent A: 1% Solvent B |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS007189 |
| Analysis ID: | AN007493 |
| Instrument Name: | Waters Xevo-G2-XS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw MS data (.raw) were converted to mzML files using ProteoWizard MSConvert (http://proteowizard.sourceforge.net/). The files were then processed in R (version 4.2.1) using the XCMS package for feature detection, retention time correction and alignment |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 2.55 kV |
| Collision Energy: | not applicable |
| Collision Gas: | not applicable |
| Fragment Voltage: | not applicable |
| Fragmentation Method: | not applicable |
| Mass Accuracy: | <1ppm error |
| Source Temperature: | 150°C |
| Desolvation Gas Flow: | 1000 L/h |
| Desolvation Temperature: | 500°C |
| Scanning: | MS Full scan |
| Scanning Cycle: | 300 ms/scan |
| Scanning Range: | 50–1200 Da |
| MS ID: | MS007190 |
| Analysis ID: | AN007494 |
| Instrument Name: | Waters Xevo-G2-XS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | raw MS data (.raw) were converted to mzML files using ProteoWizard MSConvert (http://proteowizard.sourceforge.net/). The files were then processed in R (version 4.2.1) using the XCMS package for feature detection, retention time correction and alignment |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 2.55 kV |
| Collision Energy: | not applicable |
| Collision Gas: | not applicable |
| Mass Accuracy: | <1ppm error |
| Source Temperature: | 150°C |
| Desolvation Gas Flow: | 1000 L/h |
| Desolvation Temperature: | 500°C |
| Scanning: | MS Full scan |
| Scanning Cycle: | 300 ms/scan |
| Scanning Range: | 100–1200 Da |
| MS ID: | MS007191 |
| Analysis ID: | AN007493 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolites identified through stable isotope tracing were analyzed using a Vanquish Horizon UHPLC System (Thermo Fisher Scientific) coupled to an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific). The sample injection volume was 5 μL. ESI source parameters were set as follows: spray voltage, 3,200 V or −2,800 V, in positive or negative modes, respectively; sheath gas, 35 arb; aux gas, 10 arb; sweep gas, 0.5 arb; ion transfer tube temperature, 300 °C; vaporizer temperature, 35°C. LC–MS data acquisition was operated under a full-scan polarity switching mode for all samples. The full scan was set as orbitrap resolution, 120,000 at m/z 200; AGC target, 1× 107; maximum injection time, 200 ms; scan range, 60–1,000 m/z. LC-MS raw data files (.raw) were converted to mzXML format using ProteoWizard (version 3.0.20315). El-MAVEN (version 0.12.0) was used to generate a peak table containing m/z, retention time, and intensity for the peaks. Parameters for peak picking were the defaults except for the following: mass domain resolution, 5 ppm; time domain resolution, 10 scans; minimum intensity, 10,000; and minimum peak width, 5 scans. The resulting peak table was exported as a .csv file. Peak annotation of untargeted metabolomics data was performed using NetID with default parameters. |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS007192 |
| Analysis ID: | AN007494 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolites identified through stable isotope tracing were analyzed using a Vanquish Horizon UHPLC System (Thermo Fisher Scientific) coupled to an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific). The sample injection volume was 5 μL. ESI source parameters were set as follows: spray voltage, 3,200 V or −2,800 V, in positive or negative modes, respectively; sheath gas, 35 arb; aux gas, 10 arb; sweep gas, 0.5 arb; ion transfer tube temperature, 300 °C; vaporizer temperature, 35°C. LC–MS data acquisition was operated under a full-scan polarity switching mode for all samples. The full scan was set as orbitrap resolution, 120,000 at m/z 200; AGC target, 1× 107; maximum injection time, 200 ms; scan range, 60–1,000 m/z. LC-MS raw data files (.raw) were converted to mzXML format using ProteoWizard (version 3.0.20315). El-MAVEN (version 0.12.0) was used to generate a peak table containing m/z, retention time, and intensity for the peaks. Parameters for peak picking were the defaults except for the following: mass domain resolution, 5 ppm; time domain resolution, 10 scans; minimum intensity, 10,000; and minimum peak width, 5 scans. The resulting peak table was exported as a .csv file. Peak annotation of untargeted metabolomics data was performed using NetID with default parameters. |
| Ion Mode: | UNSPECIFIED |
