Summary of Study ST001474
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 PR000993. The data can be accessed directly via it's Project DOI: 10.21228/M8BH7T 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.
| Study ID | ST001474 |
| Study Title | Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Spleen ICMS |
| Study Summary | Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs. |
| Institute | University of Kentucky |
| Department | MCC |
| Last Name | Hildebrandt |
| First Name | Gerhard |
| Address | CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536 |
| gerhard.hildebrandt@uky.edu | |
| Phone | 800-333-8874 |
| Submit Date | 2020-08-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-02 |
| Release Version | 2 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000993 |
| Project DOI: | doi: 10.21228/M8BH7T |
| Project Title: | Metabolomics of lung injury after allogeneic hematopoietic cell transplantation |
| Institute: | University of Kentucky |
| Department: | Markey Cancer Center |
| Last Name: | Hildebrandt |
| First Name: | Gerhard |
| Address: | Gerhard C. Hildebrandt, MD, Room no. CC401A, Ben Roach Building, Markey Cancer Center University of Kentucky, Lexington, 40536 |
| Email: | gerhard.hildebrandt@uky.edu |
| Phone: | 800-333-8874 |
Subject:
| Subject ID: | SU002825 |
| Subject Type: | Mouse |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mouse; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Time Point |
|---|---|---|---|
| SA273737 | 09_C2-0_Spleen_allogenic_42days_170427_UKy_GCH_rep1-polar-ICMS_A | allogenic | 42 |
| SA273738 | 07_C1-1_Spleen_allogenic_42days_170427_UKy_GCH_rep1-polar-ICMS_A | allogenic | 42 |
| SA273739 | 08_C1-2_Spleen_allogenic_42days_170427_UKy_GCH_rep2-polar-ICMS_A | allogenic | 42 |
| SA273740 | 15_C1-20_Spleen_allogenic_7days_170427_UKy_GCH_rep3-polar-ICMS_A | allogenic | 7 |
| SA273741 | 13_C1-1_Spleen_allogenic_7days_170427_UKy_GCH_rep1-polar-ICMS_A | allogenic | 7 |
| SA273742 | 14_C1-2_Spleen_allogenic_7days_170427_UKy_GCH_rep2-polar-ICMS_A | allogenic | 7 |
| SA273743 | 02_A1_Spleen_naive_0days_170427_UKy_GCH_rep2-polar-ICMS_A | naive | 0 |
| SA273744 | 03_A2_Spleen_naive_0days_170427_UKy_GCH_rep3-polar-ICMS_A | naive | 0 |
| SA273745 | 01_A0_Spleen_naive_0days_170427_UKy_GCH_rep1-polar-ICMS_A | naive | 0 |
| SA273746 | 06_B2_Spleen_syngenic_42days_170427_UKy_GCH_rep3-polar-ICMS_A | syngenic | 42 |
| SA273747 | 04_B0_Spleen_syngenic_42days_170427_UKy_GCH_rep1-polar-ICMS_A | syngenic | 42 |
| SA273748 | 05_B1_Spleen_syngenic_42days_170427_UKy_GCH_rep2-polar-ICMS_A | syngenic | 42 |
| SA273749 | 10_B1-0_Spleen_syngenic_7days_170427_UKy_GCH_rep1-polar-ICMS_A | syngenic | 7 |
| SA273750 | 11_B1-1_Spleen_syngenic_7days_170427_UKy_GCH_rep2-polar-ICMS_A | syngenic | 7 |
| SA273751 | 12_B1-2_Spleen_syngenic_7days_170427_UKy_GCH_rep3-polar-ICMS_A | syngenic | 7 |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO002818 |
| Collection Summary: | Mouse is sacrificed and tissues are harvested. |
| Collection Protocol ID: | mouse_tissue_collection |
| Collection Protocol Filename: | mouse_tissue_procedure.pdf |
| Sample Type: | Multiple tissues |
Treatment:
| Treatment ID: | TR002834 |
| Treatment Summary: | Mouse with allogenic bone marrow transplant. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest.;Mouse with no treatment. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest.;Mouse with syngenic bone marrow transplant. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest. |
| Treatment Protocol ID: | allogenic;naive;syngenic |
| Treatment Protocol Filename: | study_treatments.pdf |
Sample Preparation:
| Sampleprep ID: | SP002831 |
| Sampleprep Summary: | Tissue is frozen in liquid nitrogen to stop metabolic processes.;Frozen tissue is ground in a SPEX grinder under liquid nitrogen to homogenize the sample.;Polar extraction from homogenate, lypholized, and frozen.;Protein extraction and quantification.;Before going into the IC-FTMS the frozen sample is reconstituted in water. |
| Sampleprep Protocol ID: | tissue_quench;frozen_tissue_grind;polar_extraction;protein_extraction;IC-FTMS_preparation |
| Sampleprep Protocol Filename: | No tissue_quench file. No frozen_tissue_grind file. 4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf ['4D_17Jun4_Fan_Prot_Quant.pdf', '4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf'] No IC-FTMS_preparation file. |
Combined analysis:
| Analysis ID | AN004409 |
|---|---|
| Analysis type | MS |
| Chromatography type | Targeted IC |
| Chromatography system | Thermo Dionex ICS-5000+ |
| Column | Dionex IonPac AS11-HC-4um 2 mm i.d. x 250 mm |
| MS Type | ESI |
| MS instrument type | IC-FTMS |
| MS instrument name | Orbitrap Fusion |
| Ion Mode | NEGATIVE |
| Units | natural abundance corrected and dry residue normalized peak area |
Chromatography:
| Chromatography ID: | CH003309 |
| Chromatography Summary: | Targeted IC |
| Instrument Name: | Thermo Dionex ICS-5000+ |
| Column Name: | Dionex IonPac AS11-HC-4um 2 mm i.d. x 250 mm |
| Column Temperature: | -- |
| Flow Gradient: | -- |
| Flow Rate: | -- |
| Solvent A: | -- |
| Solvent B: | -- |
| Chromatography Type: | Targeted IC |
MS:
| MS ID: | MS004157 |
| Analysis ID: | AN004409 |
| Instrument Name: | Orbitrap Fusion |
| Instrument Type: | IC-FTMS |
| MS Type: | ESI |
| MS Comments: | ICMS Analytical Experiment with detection of compounds by comparison to standards. Thermo RAW files are loaded into TraceFinder and peaks are manually curated. The area under the chromatograms is then exported to an Excel file. The area is then corrected for natural abundance. The natural abundance corrected area is then used to calculate the concentration of each compound for each sample. This calculation is done using standards. The first sample ran on the ICMS is a standard that has known concentrations of certain compounds. Then a number of samples are ran (typically 3-4) followed by another standard. The equation to calculate the concentration is "intensity in sample"/("intensity in first standard" + (("intensity in second standard" - "intensity in first standard")/# of samples) * "known concentration in standard", where the "intensity" is the aforementioned natural abundance corrected area, and the unlabeled intensity from the standard is used for all isotopologues of the compound. The reconstitution volume is simply the volume that the polar part of the sample was reconstituted to before going into the ICMS. The injection volume is how much of the reconstitution volume was injected into the ICMS. The protein is how much protein was in the entire sample (not only the small portion that was aliquoted for the ICMS). The polar split ratio is the fraction of the polar part of the sample that was aliquoted for the ICMS. This is calculated by dividing the weight of the polar aliquot for ICMS by the total weight of the polar portion of the sample. The protein normalized concentration is calculated using the equation, concentration * (reconstitution volume / 1000 / polar split ratio / protein). |
| Ion Mode: | NEGATIVE |
