Summary of Study ST001256
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 PR000842. The data can be accessed directly via it's Project DOI: 10.21228/M8V694 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 | ST001256 |
| Study Title | Metabolic landscape remodeling in dystrophic muscle through glucocorticoid steroid regimens |
| Study Summary | Duchenne muscular dystrophy is caused by genetic defects in the gene encoding dystrophin and leads to progressive muscle degeneration. Glucocorticoid steroids are current mainstay pharmacological regimen to decrease muscle inflammation and prolong the ambulatory period in these patients, but daily intake of glucocorticoids like prednisone and deflazacort causes adverse side effects like osteoporosis, adrenal suppression, insulin resistance and obesity. Intermittent steroid dosing has been proposed as alternative to maintain benefits and limit side effects, but a detailed understanding of the mechanisms underpinning the regimen-specific effects in muscle is still missing. Here we explore how once-daily versus once-weekly prednisone (4 week-long treatment) affect the metabolomic landscape in mdx mouse muscle (genetic model of Duchenne muscular dystrophy; DBA/2J background) through metabolomics profiling. |
| Institute | Northwestern University |
| Last Name | Quattrocelli |
| First Name | Mattia |
| Address | 303 East Superior St, SQBRC 5-500, Chicago, IL, 60611, USA |
| mattia.quattrocelli@northwestern.edu | |
| Phone | 3125037450 |
| Submit Date | 2019-09-26 |
| Num Groups | 3 |
| Total Subjects | 9 |
| Num Males | 9 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-01-06 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000842 |
| Project DOI: | doi: 10.21228/M8V694 |
| Project Title: | Metabolic landscape remodeling in dystrophic muscle through glucocorticoid steroid regimens |
| Project Summary: | Duchenne muscular dystrophy is caused by genetic defects in the gene encoding dystrophin and leads to progressive muscle degeneration. Glucocorticoid steroids are current mainstay pharmacological regimen to decrease muscle inflammation and prolong the ambulatory period in these patients, but daily intake of glucocorticoids like prednisone and deflazacort causes adverse side effects like osteoporosis, adrenal suppression, insulin resistance and obesity. Intermittent steroid dosing has been proposed as alternative to maintain benefits and limit side effects, but a detailed understanding of the mechanisms underpinning the regimen-specific effects in muscle is still missing. Here we explore how once-daily versus once-weekly prednisone (4 week-long treatment) affect the metabolomic landscape in mdx mouse muscle (genetic model of Duchenne muscular dystrophy; DBA/2J background) through metabolomics profiling. |
| Institute: | Northwestern University |
| Department: | Center for Genetic Medicine |
| Laboratory: | McNally Laboratory |
| Last Name: | Quattrocelli |
| First Name: | Mattia |
| Address: | 303 East Superior St, SQBRC 5-500, Chicago, IL, 60611, USA |
| Email: | mattia.quattrocelli@northwestern.edu |
| Phone: | 3125037450 |
| Funding Source: | NIH, PPMD, MDA |
| Contributors: | Quattrocelli, McNally |
Subject:
| Subject ID: | SU001324 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | DBA/2J-mdx |
| Age Or Age Range: | 6 months |
| Gender: | Male |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA091299 | McN-Mat-20180411-07 | daily prednisone |
| SA091300 | McN-Mat-20180411-09 | daily prednisone |
| SA091301 | McN-Mat-20180411-08 | daily prednisone |
| SA091302 | McN-Mat-20180411-03 | vehicle |
| SA091303 | McN-Mat-20180411-02 | vehicle |
| SA091304 | McN-Mat-20180411-01 | vehicle |
| SA091305 | McN-Mat-20180411-05 | weekly prednisone |
| SA091306 | McN-Mat-20180411-04 | weekly prednisone |
| SA091307 | McN-Mat-20180411-06 | weekly prednisone |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO001318 |
| Collection Summary: | 3 vehicle control samples; 3 once-daily prednisone (1mg/kg i.p.) samples; 3 once-weekly prednisone (1mg/kg i.p.) samples. Each sample was extracted from ~100mg quadriceps muscle mass (one per mouse). Total hydrophilic metabolite content was extracted from quadriceps muscle tissue at treatment endpoint through methanol:water (80:20) extraction, adapting conditions described previously (Bruno et al., 2018). Briefly, total metabolite content from quadriceps muscle was obtained from ~100mg (wet weight) quadriceps muscle tissue per animal. Frozen (-80°C) muscle was pulverized in liquid nitrogen and homogenized with ~250l 2.3mm zirconia/silica beads (Cat # 11079125z, BioSpec, Bartlesville, OK) in 1ml methanol/water 80:20 (vol/vol) by means of Mini-BeadBeater-16 (Cat # 607, Biospec, Bartlesville, OK) for 1 minute. After centrifuging at 5000rpm for 5 minutes, 200l of supernatant were transferred into a tube pre-added with 800L of ice-cold methanol/water 80% (vol/vol). Samples were vortexed for 1 min, and then centrifuged at ~20,160 xg for 15 min at 4°C. Metabolite-containing extraction solution was then dried using SpeedVac (medium power). |
| Sample Type: | Muscle |
Treatment:
| Treatment ID: | TR001339 |
| Treatment Summary: | 3 vehicle control samples; 3 once-daily prednisone (1mg/kg i.p.) samples; 3 once-weekly prednisone (1mg/kg i.p.) samples. Each sample was extracted from ~100mg quadriceps muscle mass (one per mouse). Treatment duration was four weeks. Samples were collected 48 hours after last prednisone injection. |
Sample Preparation:
| Sampleprep ID: | SP001332 |
| Sampleprep Summary: | Total hydrophilic metabolite content was extracted from quadriceps muscle tissue at treatment endpoint through methanol:water (80:20) extraction, adapting conditions described previously (Bruno et al., 2018). Briefly, total metabolite content from quadriceps muscle was obtained from ~100mg (wet weight) quadriceps muscle tissue per animal. Frozen (-80°C) muscle was pulverized in liquid nitrogen and homogenized with ~250l 2.3mm zirconia/silica beads (Cat # 11079125z, BioSpec, Bartlesville, OK) in 1ml methanol/water 80:20 (vol/vol) by means of Mini-BeadBeater-16 (Cat # 607, Biospec, Bartlesville, OK) for 1 minute. After centrifuging at 5000rpm for 5 minutes, 200l of supernatant were transferred into a tube pre-added with 800L of ice-cold methanol/water 80% (vol/vol). Samples were vortexed for 1 min, and then centrifuged at ~20,160 xg for 15 min at 4°C. Metabolite-containing extraction solution was then dried using SpeedVac (medium power). |
Combined analysis:
| Analysis ID | AN002085 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Ultimate3000 |
| Column | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q-Exactive |
| Ion Mode | UNSPECIFIED |
| Units | peak area values |
Chromatography:
| Chromatography ID: | CH001522 |
| Chromatography Summary: | 200ul of 50% Acetonitrile were added to the tube for reconstitution following by overtaxing for 1 min. Samples solution were then centrifuged for 15 min @ 20,000g, 4°C. Supernatant was collected for LC-MS analysis for Hydrophilic Metabolites Profiling as follows. Samples were analyzed by High-Performance Liquid Chromatography and High-Resolution Mass Spectrometry and Tandem Mass Spectrometry (HPLC-MS/MS). Specifically, system consisted of a Thermo Q-Exactive in line with an electrospray source and an Ultimate3000 (Thermo) series HPLC consisting of a binary pump, degasser, and auto-sampler outfitted with a Xbridge Amide column (Waters; dimensions of 4.6 mm × 100 mm and a 3.5 µm particle size). The mobile phase A contained 95% (vol/vol) water, 5% (vol/vol) acetonitrile, 20 mM ammonium hydroxide, 20 mM ammonium acetate, pH = 9.0; B was 100% Acetonitrile. The gradient was as following: 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1-18 min, 75% A; 18-25 min, 15% A with a flow rate of 400 μL/min. |
| Instrument Name: | Thermo Ultimate3000 |
| Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| Flow Gradient: | 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1-18 min, 75% A; 18-25 min, 15% A |
| Flow Rate: | 400 µL/min |
| Solvent A: | 95% water/5% acetonitrile; 20 mM ammonium hydroxide; 20 mM ammonium acetate, pH 9.0 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001936 |
| Analysis ID: | AN002085 |
| Instrument Name: | Thermo Q-Exactive |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The capillary of the ESI source was set to 275 °C, with sheath gas at 45 arbitrary units, auxiliary gas at 5 arbitrary units and the spray voltage at 4.0 kV. In positive/negative polarity switching mode, an m/z scan range from 70 to 850 was chosen and MS1 data was collected at a resolution of 70,000. The automatic gain control (AGC) target was set at 1 × 106 and the maximum injection time was 200 ms. The top 5 precursor ions were subsequently fragmented, in a data-dependent manner, using the higher energy collisional dissociation (HCD) cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. The sample volumes of 25 μl were injected. Data acquisition and analysis were carried out by Xcalibur 4.0 software and Tracefinder 2.1 software, respectively (both from Thermo Fisher Scientific). |
| Ion Mode: | UNSPECIFIED |
