Summary of Study ST003483
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 PR002139. The data can be accessed directly via it's Project DOI: 10.21228/M84F91 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 | ST003483 |
| Study Title | Tissue niche influences immune and metabolic profiles to Staphylococcus aureus biofilm infection (Extracellular data) |
| Study Summary | Infection is a devastating post-surgical complication, often requiring additional procedures and prolonged antibiotic therapy. This is especially relevant for craniotomy and prosthetic joint infections (PJI), both of which are characterized by biofilm formation on the bone or implant surface, respectively, with S. aureus representing a primary cause. The local tissue microenvironment likely has profound effects on immune attributes that can influence treatment efficacy, which becomes critical to consider when developing therapeutics for biofilm infections. However, the extent to which distinct tissue niches influence immune function during biofilm development remains relatively unknown. To address this, we compare the metabolomic, transcriptomic, and functional attributes of leukocytes in mouse models of S. aureus craniotomy and PJI complemented with patient samples from both infection modalities, which reveals profound tissue niche-dependent differences in nucleic acid, amino acid, and lipid metabolism with links to immune modulation. These signatures are both spatially and temporally distinct, differing not only between infection sites but evolving over time within a single model. Collectively, this demonstrates that biofilms elicit unique immune and metabolic responses that are heavily influenced by the local tissue microenvironment, which will likely have important implications when designing therapeutic approaches targeting these infections. This submission contains the extracellular metabolomic data for the larger project. |
| Institute | University of Nebraska Medical Center |
| Department | Department of pathology, microbiology and immunology |
| Last Name | Shinde |
| First Name | Dhananjay |
| Address | DRC 2, 7066, UNMC, Emily st |
| dhananjay.shinde@unmc.edu | |
| Phone | 4025597623 |
| Submit Date | 2024-09-14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005719 | AN005720 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Relative intensities | Relative intensities |
Chromatography:
| Chromatography ID: | CH004339 |
| Chromatography Summary: | Metabolite separation was performed by liquid chromatography using a XBridge Amide analytical column (150 × 2.1mm ID; 1.7µm particle size; Waters Corporation, Milford, MA) and a binary solvent system infused at a flow rate of 0.3 mL/min. A guard XBridge Amide column (20 × 2.1mm ID; 3.5µm particle size; Waters Corporation) was connected in front of the analytical column. Mobile phase A was composed of ammonium acetate and ammonium hydroxide (10 mM each) containing 5% acetonitrile in LC-MS grade water; mobile phase B was 100% LC-MS grade acetonitrile. The pH of mobile phase A was adjusted to 8.0 using glacial acetic acid. The UHPLC pumps were operated in gradient mode. The amide column was maintained at 40°C, and the autosampler temperature was held at 5°C throughout data acquisition. The injection volume for all samples was 5 µl with the 13C15N-CAA mix as the internal standard. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40°C |
| Flow Gradient: | Started at 85% of B at 0-0.1 min, 84% B at 0.1-3.0 min; 65% B at 3.0-7.3 min, 60% B at 7.3-12.0 min, 55% B at 12.0-15.0 min, 50% B at 15.0-17.0 min, 50% B at 17.0-20.5 min, 70% B at 20.5-22.0 min. The initial conditions were recovered by 22.0 min to equilibrate the column. Total run time was 30 min. |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 95% Water/5% Acetonitrile; 10mM Ammonium acetate and 10 mM Ammonium hydroxide |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
