Summary of Study ST004190

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 PR002642. The data can be accessed directly via it's Project DOI: 10.21228/M84V8S 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 IDST004190
Study TitleComparative Analysis of the Metabolic Profiles of Alix−/− and Ozz−/− Soleus Skeletal Muscle
Study TypeMetabolomics
Study SummarySkeletal muscle relies on mitochondrial proteostasis for energy production, which is maintained by two key quality-control systems: the ubiquitin-proteasome system (UPS) and mitochondria-derived vesicles. This study reveals that the E3 ligase complex CRL5Ozz and its substrate Alix both localize to mitochondria and cooperate to regulate the mitochondrial ATP transporter Slc25A4. CRL5Ozz targets Slc25A4 for proteasomal degradation, while Alix promotes Slc25A4 loading into exosomes for lysosomal degradation. Loss of Ozz or Alix in mice disrupts Slc25A4 levels, causing mitochondrial dysfunction, altered metabolism, and a shift in muscle fiber type from oxidative to glycolytic. This work uncovers a coordinated role of UPS and vesicle-mediated degradation in mitochondrial quality control.
Institute
St Jude Children's Research Hospital
DepartmentGenetics
LaboratoryAlessandra d'Azzo Lab
Last NamePalacios
First NameGustavo
Address262 Danny Thomas Place, Memphis, TN 38105.
EmailGustavo.Palacios@stjude.org
Phone901-595-4448
Submit Date2025-09-08
Num Groups3
Total Subjects14
Num Males6
Num Females8
Study CommentsWe did not observe any differences in the results due to the animal's gender
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-10-06
Release Version1
Gustavo Palacios Gustavo Palacios
https://dx.doi.org/10.21228/M84V8S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002642
Project DOI:doi: 10.21228/M84V8S
Project Title:Comparative Analysis of the Metabolic Profiles of Alix−/− and Ozz−/− Soleus Skeletal Muscle
Project Type:Metabolomics
Project Summary:Skeletal muscle relies on mitochondrial proteostasis for energy production, which is maintained by two key quality-control systems: the ubiquitin-proteasome system (UPS) and mitochondria-derived vesicles. This study reveals that the E3 ligase complex CRL5Ozz and its substrate Alix both localize to mitochondria and cooperate to regulate the mitochondrial ATP transporter Slc25A4. CRL5Ozz targets Slc25A4 for proteasomal degradation, while Alix promotes Slc25A4 loading into exosomes for lysosomal degradation. Loss of Ozz or Alix in mice disrupts Slc25A4 levels, causing mitochondrial dysfunction, altered metabolism, and a shift in muscle fiber type from oxidative to glycolytic. This work uncovers a coordinated role of UPS and vesicle-mediated degradation in mitochondrial quality control. The goal of the study is to assess whether mitochondrial abnormalities observed in Alix−/− and Ozz−/− skeletal muscle are associated with impaired mitochondrial metabolism. Methods: Soleus muscles from 8-week-old mice were collected, rinsed briefly in ice-cold saline, patted dry, flash-frozen in liquid nitrogen, and stored at −80 °C. To extract both hydrophilic metabolites and lipids, an adapted three-phase solvent system (chloroform/methanol/water, 3:4:1, v/v/v) was used. Tissues were weighed and homogenized with zirconia beads using a Bead Ruptor Elite, followed by the addition of ice-cold saline and further mixing. After resting at 4 °C, samples were centrifuged at 21,000 ×g for 10 min. The aqueous phase was collected, frozen on dry ice, lyophilized, reconstituted in water/acetonitrile/formic acid (95:5:0.1, v/v/v), and analyzed by LC-MS. The organic phase was dried under nitrogen, reconstituted in chloroform/methanol (2:1, v/v), and analyzed by LC-MS. Results: High-throughput metabolomic analyses revealed approximately 87 significantly altered metabolites in Alix−/− and ccOzz−/− soleus muscles compared to WT controls. Heat maps generated using MetaboAnalyst 4.0 demonstrated distinct metabolic profiles among the three genotypes. Interestingly, several metabolites—including ADP, citrate, Citrulline, CoA, FAD, L-Acetylcarnitine, carnitine, oxoglutarate, and PEP, are regulated by the mitochondrial SLC25 solute carrier family. Pathway analysis further linked these metabolites to key metabolic pathways, including glycolysis, pyrimidine metabolism, the citric acid cycle, and others. Important, glycolysis was upregulated in Ozz−/− muscle relative to Alix−/− and WT, highlighting genotype-specific shifts in mitochondrial metabolism.
Institute:St Jude Children's Research Hospital
Department:Genetics
Laboratory:Alessandra d'Azzo Lab
Last Name:Palacios
First Name:Gustavo
Address:262 Danny Thomas Place, Memphis, TN 38105.
Email:Gustavo.Palacios@stjude.org
Phone:901-595-4448
Funding Source:NIH, the Assisi Foundation of Memphis and the American Lebanese Syrian Associated Charities (ALSAC)
Contributors:Yvan Campos, Gustavo Palacios, Elida Gomero, Diantha Van de Vlekkert, Krishnan Venkataraman, Jaison John, Jayce Weesner, Randall Wakefield, Xiaohui Qiu, Ricardo Rodriguez-Erniquez, Stephanie Rockfield, Jeroen Demmers, Joseph Opferman, Cam Robinson, Khaled Khairy, Tulio Bertorini, Gerard Grosveld, Alessandra d'Azzo*

Subject:

Subject ID:SU004342
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:8 weeks
Weight Or Weight Range:20-24 grams
Gender:Male and female
Animal Animal Supplier:Jackson Labs
Animal Housing:4-5 individual per cage
Animal Light Cycle:12 h day-time, 12-5 Night-time
Animal Feed:ad libitum
Animal Water:ad libitum
Animal Inclusion Criteria:homozygous WT or homozygous for the gene deletion Alix or Ozz
Species Group:WT, Alix, Ozz

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Sample source
SA483383Alix_R4_NegAlix-KO Soleus
SA483384Alix_R1_PosAlix-KO Soleus
SA483385Alix_R4_PosAlix-KO Soleus
SA483386Alix_R1_NegAlix-KO Soleus
SA483387Alix_R3_PosAlix-KO Soleus
SA483388Alix_R2_NegAlix-KO Soleus
SA483389Alix_R2_PosAlix-KO Soleus
SA483390Alix_R3_NegAlix-KO Soleus
SA483391Ozz_R6_PosOzz-KO Soleus
SA483392Ozz_R6_NegOzz-KO Soleus
SA483393Ozz_R5_NegOzz-KO Soleus
SA483394Ozz_R4_PosOzz-KO Soleus
SA483395Ozz_R5_PosOzz-KO Soleus
SA483396Ozz_R3_PosOzz-KO Soleus
SA483397Ozz_R3_NegOzz-KO Soleus
SA483398Ozz_R2_PosOzz-KO Soleus
SA483399Ozz_R2_NegOzz-KO Soleus
SA483400Ozz_R1_PosOzz-KO Soleus
SA483401Ozz_R1_NegOzz-KO Soleus
SA483402Ozz_R4_NegOzz-KO Soleus
SA483403WT_R1_NegWT Soleus
SA483404WT_R1_PosWT Soleus
SA483405WT_R2_NegWT Soleus
SA483406WT_R2_PosWT Soleus
SA483407WT_R3_NegWT Soleus
SA483408WT_R3_PosWT Soleus
SA483409WT_R4_NegWT Soleus
SA483410WT_R4_PosWT Soleus
Showing results 1 to 28 of 28

Collection:

Collection ID:CO004335
Collection Summary:Soleus muscles from 8-week-old mice were collected, rinsed briefly in ice-cold saline, patted dry, flash-frozen in liquid nitrogen, and stored at −80 °C.
Collection Protocol Filename:Protocol_of_Untargeted_Metabolomics_04032020.pdf
Collection Protocol Comments:The PDF file contains he description of the samples processing procedure, as well as details of the LC & MS conditions
Sample Type:Muscle
Storage Conditions:-80℃
Additives:None, flash frozen in liquid nitrogen

Treatment:

Treatment ID:TR004351
Treatment Summary:The performed metabolomics work does not contain treatment conditions managed by the investigators. The compared conditions were determined by the genotypes of the animals evaluated in this study.

Sample Preparation:

Sampleprep ID:SP004348
Sampleprep Summary:To extract both hydrophilic metabolites and lipids, an adapted three-phase solvent system (chloroform/methanol/water, 3:4:1, v/v/v) was used. Tissues were weighed and homogenized with zirconia beads using a Bead Ruptor Elite, followed by the addition of ice-cold saline and further mixing. After resting at 4 °C, samples were centrifuged at 21,000 ×g for 10 min. The aqueous phase was collected, frozen on dry ice, lyophilized, reconstituted in water/acetonitrile/formic acid (95:5:0.1, v/v/v), and analyzed by LC-MS. The organic phase was dried under nitrogen, reconstituted in chloroform/methanol (2:1, v/v), and analyzed by LC-MS.
Sampleprep Protocol Filename:Protocol_of_Untargeted_Metabolomics 04032020.pdf
Sampleprep Protocol Comments:The uploaded file contain details about the samples collection and processing for metabolomics analysis.

Chromatography:

Chromatography ID:CH005286
Chromatography Summary:Negative ion mode LC/MS conditions
Methods Filename:Protocol_of_Untargeted_Metabolomics_04032020.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 1 mm, 1.7 um)
Column Temperature:40 °C
Flow Gradient:Time(min), %B: 0.0, 1; 16.5, 50; 18.0, 99; 36.0, 99; 39.0, 1; 45.0, 1
Flow Rate:50 µL/min
Solvent A:100% Water; 10mM ammonium formate; 0.1% formic acid
Solvent B:100% Acetonitrile; 0.1% formic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006961
Laboratory Name:Immuno-Metabolomics Core
Analysis Type:MS
Software Version:Xcalibur 2.8 SP1
Operator Name:Gustavo Palacios
Detector Type:MS
Chromatography ID:CH005286
Num Factors:3
Num Metabolites:1942
Units:Peak area
  
Analysis ID:AN006962
Laboratory Name:Immuno-Metabolomics Core
Analysis Type:MS
Software Version:Xcalibur 2.8 SP1
Operator Name:Gustavo Palacios
Detector Type:MS
Chromatography ID:CH005286
Num Factors:3
Num Metabolites:2419
Units:Peak area
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