Summary of Study ST003145
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 PR001956. The data can be accessed directly via it's Project DOI: 10.21228/M8WF0F 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 | ST003145 |
Study Title | Muscle-type specific stress responses explain the onset of external ophthalmoplegia in mitochondrial disease |
Study Summary | Mitochondrial dysfunctions elicit progressive tissue-specific stress responses that can be protective or deleterious. Here, we show that even different muscles of an individual react differently to mitochondrial disease. In mitochondrial myopathy (MM), the extraocular muscles (EOMs) are affected first, followed by exercise intolerance in the large lower limb muscles. Both muscle types show clear signs of respiratory chain deficiency. However, the limbs upregulate the mitochondrial integrated stress response (ISRmt) that drives glucose carbons to anabolic repair pathways, while EOMs present no signs of ISRmt. In contrast, in EOMs, Pdk4 activation inhibits pyruvate metabolism, while beta-oxidation of fatty acids is induced - despite the reliance of beta-oxidation on a functional respiratory chain for ATP production. The data suggest that the inability to upregulate ISRmt and consequent deleterious fuel choices sensitize EOMs to early weakness and atrophy, explaining ophthalmoplegia, the most common MM sign. The distinct responses to disease even in muscles of a single individual predict different responses to treatment, which is essential knowledge when designing interventions. |
Institute | University of Helsinki |
Department | Faculty of Medicine |
Laboratory | Anu Wartiovaara Lab |
Last Name | Pradhan |
First Name | Swagat |
Address | C519b, Biomedicum 1, Haartmaninkatu 8, Helsinki |
swagat.pradhan@helsinki.fi | |
Phone | +358465287359 |
Submit Date | 2024-02-21 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2025-01-02 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001956 |
Project DOI: | doi: 10.21228/M8WF0F |
Project Title: | Muscle-type specific stress responses explain external ophthalmoplegia in mitochondrial disease |
Project Summary: | Mitochondrial dysfunctions elicit progressive tissue-specific stress responses that can be protective or deleterious. Here, we show that even different muscles of an individual react differently to mitochondrial disease. In mitochondrial myopathy (MM), the extraocular muscles (EOMs) are affected first, followed by exercise intolerance in the large lower limb muscles. Both muscle types show clear signs of respiratory chain deficiency. However, the limbs upregulate the mitochondrial integrated stress response (ISRmt) that drives glucose carbons to anabolic repair pathways, while EOMs present no signs of ISRmt. In contrast, in EOMs, Pdk4 activation inhibits pyruvate metabolism, while beta-oxidation of fatty acids is induced - despite the reliance of beta-oxidation on a functional respiratory chain for ATP production. The data suggest that the inability to upregulate ISRmt and consequent deleterious fuel choices sensitize EOMs to early weakness and atrophy, explaining ophthalmoplegia, the most common MM sign. The distinct responses to disease even in muscles of a single individual predict different responses to treatment, which is essential knowledge when designing interventions. |
Institute: | University of Helsinki |
Laboratory: | Anu Wartiovaara Lab |
Last Name: | Pradhan |
First Name: | Swagat |
Address: | C519b, Biomedicum 1, Haartmaninkatu 8, Helsinki, Uusimaa, 00290, Finland |
Email: | swagat.pradhan@helsinki.fi |
Phone: | +358465287359 |
Subject:
Subject ID: | SU003262 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample source | Genotype |
---|---|---|---|
SA340691 | Del_2_EOM | Extra-ocular muscle | Deletor |
SA340692 | Del_3_EOM | Extra-ocular muscle | Deletor |
SA340693 | Del_5_EOM | Extra-ocular muscle | Deletor |
SA340694 | Del_1_EOM | Extra-ocular muscle | Deletor |
SA340695 | Del_4_EOM | Extra-ocular muscle | Deletor |
SA340696 | Del_6_EOM | Extra-ocular muscle | Deletor |
SA340697 | WT_1_EOM | Extra-ocular muscle | Wild type |
SA340698 | WT_7_EOM | Extra-ocular muscle | Wild type |
SA340699 | WT_3_EOM | Extra-ocular muscle | Wild type |
SA340700 | WT_2_EOM | Extra-ocular muscle | Wild type |
SA340701 | WT_6_EOM | Extra-ocular muscle | Wild type |
SA340702 | WT_5_EOM | Extra-ocular muscle | Wild type |
SA340703 | WT_4_EOM | Extra-ocular muscle | Wild type |
SA340704 | Del_1_QF | Quadriceps femoris | Deletor |
SA340705 | Del_4_QF | Quadriceps femoris | Deletor |
SA340706 | Del_3_QF | Quadriceps femoris | Deletor |
SA340707 | Del_5_QF | Quadriceps femoris | Deletor |
SA340708 | Del_2_QF | Quadriceps femoris | Deletor |
SA340709 | Del_6_QF | Quadriceps femoris | Deletor |
SA340710 | WT_4_QF | Quadriceps femoris | Wild type |
SA340711 | WT_1_QF | Quadriceps femoris | Wild type |
SA340712 | WT_2_QF | Quadriceps femoris | Wild type |
SA340713 | WT_3_QF | Quadriceps femoris | Wild type |
SA340714 | WT_5_QF | Quadriceps femoris | Wild type |
SA340715 | WT_6_QF | Quadriceps femoris | Wild type |
Showing results 1 to 25 of 25 |
Collection:
Collection ID: | CO003255 |
Collection Summary: | Muscles were extracted by excision and snap frozen in liquid nitrogen |
Sample Type: | Muscle |
Treatment:
Treatment ID: | TR003271 |
Treatment Summary: | The experimental mouse model used in this study (Deletor) are transgenic for Twnk, encoding Twinkle, a nuclear-encoded mtDNA helicase that carries a dominant mutation (homologous to a MM patient mutation, leading into a 13-amino acid duplication of amino acids p.353-365 in the protein). The controls were wild-type (WT) littermates of Deletor mice. WT mice are used as controls. The genotype and tissue specific differences were studied by analysing metabolites from Quadriceps femoris(QF) and extra-ocular muscles(EOM). |
Sample Preparation:
Sampleprep ID: | SP003269 |
Sampleprep Summary: | The samples were added to 2 ml Precellys homogenization tube (Bertin Technologies, Montigny-le-Bretonneux, France) with 2.8 mm ceramic (zirconium oxide) beads with 500µl of cold extraction solvent (Acetonitrile:Methanol:Milli-Q Water; 40:40:20). Subsequently, samples were homogenized using a tissue homogenizer (Bertin Technologies, France) for 3 cycles (30sec at 5500rpm with 60sec pause at 4°C). It was then followed by centrifugation at 14000rpm at 4°C for 5 minutes. The supernatant was then loaded into a Phenomenex, Phree Phospholipid removal 96 well plate 30mg (Part No. 8E-S133-TGB) and passed through using a robotic vacuum. The resulting filtrate was then transferred into polypropylene tubes and placed into a Nitrogen gas evaporator to completely dry the solvent. |
Combined analysis:
Analysis ID | AN005161 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Thermo Vanquish |
Column | Merck SeQuant ZIC-pHILIC (100 x 2.1mm,5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap |
Ion Mode | UNSPECIFIED |
Units | Peak intensity |
Chromatography:
Chromatography ID: | CH003906 |
Instrument Name: | Thermo Vanquish |
Column Name: | Merck SeQuant ZIC-pHILIC (100 x 2.1mm,5um) |
Column Temperature: | 40 ± 3 |
Flow Gradient: | gradient elution began with 20% mobile phase A and 80% mobile phase B and was maintained until 2 minutes. Then, mobile phase A was gradually increased from 20% to 80% until 17 minutes, followed by a decrease from 80% to 20% in mobile phase A from 17.1 minutes and maintained up to 24 minutes. |
Flow Rate: | 0.100 mL/minute |
Solvent A: | 100% water, 20mM Ammonium hydrogen carbonate, pH 9.4 |
Solvent B: | 100% acetonitrile |
Chromatography Type: | HILIC |
MS:
MS ID: | MS004897 |
Analysis ID: | AN005161 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Mass spectrometry (MS) was used with a heated electrospray ionization (H-ESI) source using polarity switching and the following settings: resolution of 70,000, spray voltages of 4250 V for positive mode and 3250 V for negative mode, sheath gas flow rate of 25 arbitrary units (AU), auxiliary gas flow rate of 15 AU, sweep gas flow rate of 0, capillary temperature of 275°C, and S-lens RF level of 50.0. The instrument was controlled with the Xcalibur 4.1.31.9 software (Thermo Fischer Scientific, Waltham, MA, USA). In data processing, peak integration was performed using TraceFinder 5.1 software (Thermo Fischer Scientific), and the confirmed retention times of 462 metabolites in an in-house library developed using the library kit MSMLS-1EA (Merck) were used. The peak area data were exported as an excel file for further analysis. Data quality was monitored throughout the run using a pooled sample as Quality Control (QC), which was prepared by pooling 5µL from each suspended sample and interspersed throughout the run as every 10th sample. After integration of QC data with TraceFinder 5.1, detected metabolites were checked for peak, and % RSD were calculated. An acceptance limit was set at ≤20%. Blank samples for carryover were injected after every fifth randomized sample to monitor the metabolites' carryover effect and were calculated against the mean QC area. The acceptance limit was set at ≤20% for each metabolite. Background % noise was calculated with respect to the first blank against the mean QC area, and the acceptance limit was set at ≤20% for each metabolite. |
Ion Mode: | UNSPECIFIED |