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.

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Study IDST001474
Study TitleMetabolomics of lung injury after allogeneic hematopoietic cell transplantation - Spleen ICMS
Study Typepreliminary data
Study SummaryAllogeneic 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
DepartmentMCC
Last NameHildebrandt
First NameGerhard
AddressCTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536
Emailgerhard.hildebrandt@uky.edu
Phone800-333-8874
Submit Date2020-08-22
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2020-09-10
Release Version1
Gerhard Hildebrandt Gerhard Hildebrandt
https://dx.doi.org/10.21228/M8BH7T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU001548
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 Treatment Protocol
SA12456815_C1-20_Spleen_allogenic_7days_170427_UKy_GCH_rep3-polar-ICMS_Aallogenic
SA12456914_C1-2_Spleen_allogenic_7days_170427_UKy_GCH_rep2-polar-ICMS_Aallogenic
SA12457007_C1-1_Spleen_allogenic_42days_170427_UKy_GCH_rep1-polar-ICMS_Aallogenic
SA12457109_C2-0_Spleen_allogenic_42days_170427_UKy_GCH_rep1-polar-ICMS_Aallogenic
SA12457213_C1-1_Spleen_allogenic_7days_170427_UKy_GCH_rep1-polar-ICMS_Aallogenic
SA12457308_C1-2_Spleen_allogenic_42days_170427_UKy_GCH_rep2-polar-ICMS_Aallogenic
SA12457402_A1_Spleen_naive_0days_170427_UKy_GCH_rep2-polar-ICMS_Anaive
SA12457503_A2_Spleen_naive_0days_170427_UKy_GCH_rep3-polar-ICMS_Anaive
SA12457601_A0_Spleen_naive_0days_170427_UKy_GCH_rep1-polar-ICMS_Anaive
SA12457711_B1-1_Spleen_syngenic_7days_170427_UKy_GCH_rep2-polar-ICMS_Asyngenic
SA12457804_B0_Spleen_syngenic_42days_170427_UKy_GCH_rep1-polar-ICMS_Asyngenic
SA12457905_B1_Spleen_syngenic_42days_170427_UKy_GCH_rep2-polar-ICMS_Asyngenic
SA12458006_B2_Spleen_syngenic_42days_170427_UKy_GCH_rep3-polar-ICMS_Asyngenic
SA12458110_B1-0_Spleen_syngenic_7days_170427_UKy_GCH_rep1-polar-ICMS_Asyngenic
SA12458212_B1-2_Spleen_syngenic_7days_170427_UKy_GCH_rep3-polar-ICMS_Asyngenic
Showing results 1 to 15 of 15

Collection:

Collection ID:CO001543
Collection Summary:Mouse is sacrificed and tissues are harvested.
Collection Protocol ID:mouse_tissue_collection
Sample Type:Multiple tissues

Treatment:

Treatment ID:TR001563
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

Sample Preparation:

Sampleprep ID:SP001556
Sampleprep Summary:Polar extraction from homogenate, lypholized, and frozen. Tissue is frozen in liquid nitrogen to stop metabolic processes. Before going into the IC-FTMS the frozen sample is reconstituted in water. Frozen tissue is ground in a SPEX grinder under liquid nitrogen to homogenize the sample. Protein extraction and quantification.
Sampleprep Protocol ID:frozen_tissue_grind; tissue_quench; protein_extraction; IC-FTMS_preparation; polar_extraction
Sampleprep Protocol Filename:4D_17Jun4_Fan_Prot_Quant.pdf
4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf

Combined analysis:

Analysis ID AN002450
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 abundance & normalized peak area

Chromatography:

Chromatography ID:CH001795
Chromatography Summary:Targeted IC
Instrument Name:Thermo Dionex ICS-5000+
Column Name:Dionex IonPac AS11-HC-4um 2 mm i.d. x 250 mm
Chromatography Type:Targeted IC

MS:

MS ID:MS002273
Analysis ID:AN002450
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
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