Summary of Study ST001441

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 PR000991. The data can be accessed directly via it's Project DOI: 10.21228/M8M116 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 IDST001441
Study TitleMetabolomics of patient-derived fibroblasts
Study Summary7 control fibroblasts samples and 7 patient-derived fibroblasts samples were collected at day 0 and day 5. Intracellular metabolites were extracted from cells cultured in 6 well plate while acyl-CoA and 5-methyltetrahydrofolate were extracted from cells cultured in 60 mm dish.
Institute
North Carolina State University
Last NameLiu
First NameXiaojing
AddressPolk Hall, RM 128
Emailxliu68@ncsu.edu
Phone9195154387
Submit Date2020-06-11
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-08-06
Release Version1
Xiaojing Liu Xiaojing Liu
https://dx.doi.org/10.21228/M8M116
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000991
Project DOI:doi: 10.21228/M8M116
Project Title:SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease
Project Summary:Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients carrying recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit beta (SUCLA2) causing global protein hyper-succinylation. Using mass spectrometry, we quantified nearly 1000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper-succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper-succinylation to disease progression, we developed a zebrafish model of the SCL deficiency, and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications.
Institute:North Carolina State University
Last Name:Liu
First Name:Xiaojing
Address:Polk Hall, RM 128
Email:xliu68@ncsu.edu
Phone:9195154387

Subject:

Subject ID:SU001515
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample Source Treatment Duration
SA122335D0-control3_lunaControl Day0
SA122336D0-control2_lunaControl Day0
SA122337D0-control4_lunaControl Day0
SA122338D0-control6_lunaControl Day0
SA122339D0-control7_lunaControl Day0
SA122340D0-control1Control Day0
SA122341D0-control5_lunaControl Day0
SA122342D0-control1_lunaControl Day0
SA122343D0-control6Control Day0
SA122344D0-control4Control Day0
SA122345D0-control3Control Day0
SA122346D0-control2Control Day0
SA122347D0-control7Control Day0
SA122348D0-control5Control Day0
SA122349D5-control3_lunaControl Day5
SA122350D5-control5_lunaControl Day5
SA122351D5-control2_lunaControl Day5
SA122352D5-control1_lunaControl Day5
SA122353D5-control2Control Day5
SA122354D5-control1Control Day5
SA122355D5-control6_lunaControl Day5
SA122356D5-control4_lunaControl Day5
SA122357D5-control7_lunaControl Day5
SA122358D5-control4Control Day5
SA122359D5-control5Control Day5
SA122360D5-control6Control Day5
SA122361D5-control3Control Day5
SA122362D5-control7Control Day5
SA122363D0-patient4_lunaPatient Day0
SA122364D0-patient3_lunaPatient Day0
SA122365D0-patient5_lunaPatient Day0
SA122366D0-patient7_lunaPatient Day0
SA122367D0-patient4Patient Day0
SA122368D0-patient2_lunaPatient Day0
SA122369D0-patient6_lunaPatient Day0
SA122370D0-patient1_lunaPatient Day0
SA122371D0-patient5Patient Day0
SA122372D0-patient2Patient Day0
SA122373D0-patient7Patient Day0
SA122374D0-patient1Patient Day0
SA122375D0-patient3Patient Day0
SA122376D0-patient6Patient Day0
SA122377D5-patient5_lunaPatient Day5
SA122378D5-patient3_lunaPatient Day5
SA122379D5-patient4_lunaPatient Day5
SA122380D5-patient1Patient Day5
SA122381D5-patient2_lunaPatient Day5
SA122382D5-patient7_lunaPatient Day5
SA122383D5-patient6_lunaPatient Day5
SA122384D5-patient4Patient Day5
SA122385D5-patient6Patient Day5
SA122386D5-patient7Patient Day5
SA122387D5-patient5Patient Day5
SA122388D5-patient3Patient Day5
SA122389D5-patient2Patient Day5
SA122390D5-patient1_lunaPatient Day5
Showing results 1 to 56 of 56

Collection:

Collection ID:CO001510
Collection Summary:7 control fibroblasts samples and 7 patient-derived fibroblasts samples were collected at day 0 and day 5. Intracellular metabolites were extracted from cells cultured in 6 well plate while acyl-CoA and 5-methyltetrahydrofolate were extracted from cells cultured in 60 mm dish. Intracellular metabolites and acyl-CoA from cells were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For acyl-CoA and 5-methyltetrahydrofolate analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate), and 10 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 3 μL was injected into the LC-MS.
Sample Type:Cultured fibroblasts

Treatment:

Treatment ID:TR001530
Treatment Summary:Patient-derived fibroblasts cultured in standard culture conditions (proliferative condition) and cells cultured for 5 days in low-serum conditions (non-proliferative condition). Patients carry disease-causing mutations in SUCLA2. Controls are fibroblasts from age-matched patients with other mitochondrial diseases.

Sample Preparation:

Sampleprep ID:SP001523
Sampleprep Summary:Intracellular metabolites and acyl-CoA from cells were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For acyl-CoA and 5-methyltetrahydrofolate analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate), and 10 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 3 μL was injected into the LC-MS.

Chromatography:

Chromatography ID:CH001769
Chromatography Summary:HILIC method is for general metabolomics analysis.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Xbridge amide (100 x 2.1mm,3.5um)
Chromatography Type:HILIC
  
Chromatography ID:CH001770
Chromatography Summary:RPLC is for acyl-CoA and folate analysis.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Luna C18 (100 x 2.0mm,3um)
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN002407
Analysis Type:MS
Chromatography ID:CH001769
Num Factors:4
Num Metabolites:150
Units:peak area
  
Analysis ID:AN002408
Analysis Type:MS
Chromatography ID:CH001769
Num Factors:4
Num Metabolites:192
Units:peak area
  
Analysis ID:AN002409
Analysis Type:MS
Chromatography ID:CH001770
Num Factors:4
Num Metabolites:7
Units:peak area
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