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
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

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.

Combined analysis:

Analysis ID AN002407 AN002408 AN002409
Analysis type MS MS MS
Chromatography type HILIC HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters Xbridge amide (100 × 2.1 mm i.d., 3.5 μm) Waters Xbridge amide (100 × 2.1 mm i.d., 3.5 μm) Phenomenex Luna C18 (100 × 2.0 mm i.d., 3 μm)
MS Type ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap Thermo Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE
Units peak area peak area peak area

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 × 2.1 mm i.d., 3.5 μm)
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 × 2.0 mm i.d., 3 μm)
Chromatography Type:Reversed phase

MS:

MS ID:MS002248
Analysis ID:AN002407
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:It was operated in the full-scan mode with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:POSITIVE
  
MS ID:MS002249
Analysis ID:AN002408
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:It was operated in the full-scan mode with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:NEGATIVE
  
MS ID:MS002250
Analysis ID:AN002409
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:It was operated in the full-scan mode with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:POSITIVE
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