Summary of Study ST003703
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 PR002298. The data can be accessed directly via it's Project DOI: 10.21228/M8KR8S 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 ID | ST003703 |
| Study Title | NAD Depletion in Skeletal Muscle does not Compromise Muscle Function or Accelerate Aging |
| Study Summary | NAD is a ubiquitous electron carrier essential for energy metabolism and the posttranslational modification of numerous regulatory proteins. Perturbation of NAD metabolism is considered detrimental to health, with NAD depletion commonly thought to promote aging. However, the extent to which cellular NAD concentration can be decreased without deleterious repercussions is unclear. We generated a mouse model where nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis is disrupted in adult skeletal muscle. The resulting 85% decrease in muscle NAD+ abundance was associated with preserved tissue integrity and functionality, as demonstrated by its unchanged morphology, contractility, and exercise tolerance. This lack of defects was corroborated by intact mitochondrial respiratory capacity and unaffected muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings indicate that NAD depletion does not contribute to agerelated declines in skeletal muscle function. |
| Institute | University of Copenhagen |
| Last Name | Treebak |
| First Name | Jonas Thue |
| Address | Blegdamsvej 3B, Mærsk Tårnet, 7. sal 2200 København N. |
| jttreebak@sund.ku.dk | |
| Phone | +4524805398 |
| Submit Date | 2025-02-03 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-02-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002298 |
| Project DOI: | doi: 10.21228/M8KR8S |
| Project Title: | NAD Depletion in Skeletal Muscle does not Compromise Muscle Function or Accelerate Aging |
| Project Summary: | NAD is a ubiquitous electron carrier essential for energy metabolism and the posttranslational modification of numerous regulatory proteins. Perturbation of NAD metabolism is considered detrimental to health, with NAD depletion commonly thought to promote aging. However, the extent to which cellular NAD concentration can be decreased without deleterious repercussions is unclear. We generated a mouse model where nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis is disrupted in adult skeletal muscle. The resulting 85% decrease in muscle NAD+ abundance was associated with preserved tissue integrity and functionality, as demonstrated by its unchanged morphology, contractility, and exercise tolerance. This lack of defects was corroborated by intact mitochondrial respiratory capacity and unaffected muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings indicate that NAD depletion does not contribute to age related declines in skeletal muscle function. This submission contains lipidomics data. |
| Institute: | University of Copenhagen |
| Department: | Novo Nordisk Foundation Center for Basic Metabolic Research |
| Laboratory: | TREEBAK GROUP |
| Last Name: | Treebak |
| First Name: | Jonas Thue |
| Address: | Blegdamsvej 3B, Mærsk Tårnet, 7. sal 2200 København N. |
| Email: | jttreebak@sund.ku.dk |
| Phone: | +4524805398 |
Subject:
| Subject ID: | SU003835 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | skeletal muscle-specific Nampt knockout |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Treatment |
|---|---|---|---|---|
| SA405343 | iSMNKO _Blank02 | Blank | - | - |
| SA405344 | iSMNKO _Blank01 | Blank | - | - |
| SA405351 | iSMNKO _34 | Muscle | ko | run |
| SA405352 | iSMNKO _11 | Muscle | ko | run |
| SA405353 | iSMNKO _30 | Muscle | ko | run |
| SA405354 | iSMNKO _6 | Muscle | ko | run |
| SA405355 | iSMNKO _23 | Muscle | ko | run |
| SA405356 | iSMNKO _16 | Muscle | ko | run |
| SA405357 | iSMNKO _17 | Muscle | ko | run |
| SA405358 | iSMNKO _10 | Muscle | ko | run |
| SA405359 | iSMNKO _22 | Muscle | ko | run |
| SA405360 | iSMNKO _24 | Muscle | ko | sed |
| SA405361 | iSMNKO _18 | Muscle | ko | sed |
| SA405362 | iSMNKO _33 | Muscle | ko | sed |
| SA405363 | iSMNKO _4 | Muscle | ko | sed |
| SA405364 | iSMNKO _5 | Muscle | ko | sed |
| SA405365 | iSMNKO _28 | Muscle | ko | sed |
| SA405366 | iSMNKO _12 | Muscle | ko | sed |
| SA405367 | iSMNKO _29 | Muscle | ko | sed |
| SA405345 | iSMNKO _MSMS05 | Muscle | - | - |
| SA405346 | iSMNKO _MSMS01 | Muscle | - | - |
| SA405347 | iSMNKO _MSMS02 | Muscle | - | - |
| SA405348 | iSMNKO _MSMS04 | Muscle | - | - |
| SA405349 | iSMNKO _MSMS03 | Muscle | - | - |
| SA405350 | iSMNKO _MSMS06 | Muscle | - | - |
| SA405368 | iSMNKO _31 | Muscle | wt | run |
| SA405369 | iSMNKO _27 | Muscle | wt | run |
| SA405370 | iSMNKO _26 | Muscle | wt | run |
| SA405371 | iSMNKO _3 | Muscle | wt | run |
| SA405372 | iSMNKO _7 | Muscle | wt | run |
| SA405373 | iSMNKO _8 | Muscle | wt | run |
| SA405374 | iSMNKO _20 | Muscle | wt | run |
| SA405375 | iSMNKO _15 | Muscle | wt | run |
| SA405376 | iSMNKO _19 | Muscle | wt | run |
| SA405377 | iSMNKO _2 | Muscle | wt | sed |
| SA405378 | iSMNKO _9 | Muscle | wt | sed |
| SA405379 | iSMNKO _13 | Muscle | wt | sed |
| SA405380 | iSMNKO _14 | Muscle | wt | sed |
| SA405381 | iSMNKO _1 | Muscle | wt | sed |
| SA405382 | iSMNKO _21 | Muscle | wt | sed |
| SA405383 | iSMNKO _32 | Muscle | wt | sed |
| SA405384 | iSMNKO _25 | Muscle | wt | sed |
| SA405385 | iSMNKO _QC06 | QC | - | - |
| SA405386 | iSMNKO _QC08 | QC | - | - |
| SA405387 | iSMNKO _QC09 | QC | - | - |
| SA405388 | iSMNKO _QC05 | QC | - | - |
| SA405389 | iSMNKO _QC04 | QC | - | - |
| SA405390 | iSMNKO _QC03 | QC | - | - |
| SA405391 | iSMNKO _QC02 | QC | - | - |
| SA405392 | iSMNKO _QC01 | QC | - | - |
| SA405393 | iSMNKO _QC07 | QC | - | - |
| Showing results 1 to 51 of 51 |
Collection:
| Collection ID: | CO003828 |
| Collection Summary: | All animal experiments were performed following the European directive 2010/63/EU of the European Parliament and the Council of the protection of animals used for scientific purposes, approved by the Danish Animal Experiments Inspectorate (license numbers: 2015-15-0201-00796, 2018-15-0201-01493, 2020-15-0201-00764). Previously generated homozygous Nampt-floxed carrying mice (Nampttm1Jtree) were crossed with animals heterozygous for the inducible human α-skeletal actin promoter-driven MCM Cre (HSACreMCM), so that the target transgenic strain HSACreMCM-Nampttm1Jtree was obtained after crossing with Nampttm1Jtree. After induction, Cre-/+ mice were knockouts (i.e., iSMNKO), while the Cre-/- littermates were used as controls. All animals used in the experiments were on a C57BL/6JBomTac background (Taconic, Denmark). Both iSMNKO and control animals at the age of 9-15 weeks were dosed orally with 2 mg/day of tamoxifen (Sigma-Aldrich T5648) suspended in corn oil (Sigma-Aldrich C8267) for three consecutive days. All animals were housed in standard conditions with controlled temperature (22 ± 1ºC) and a 12 h light-dark cycle and received water and chow diet (Altromin 1310 or equivalent SAFE DS D30) ad libitum. Experiments were performed on male 16-25-week-old mice unless stated otherwise Briefly, SOL and EDL muscles were obtained from 23-week-old (12 weeks after tamoxifen) control and mutant animals anaesthetized with an intraperitoneal injection of Avertin (2,2,2-Tribromoehtanol and 2- methyl-2-butanol (Sigma Aldrich #T48402 and #152463))Mitochondria isolation Mitochondrial fraction was isolated from muscle tissue with nagarse digestion and differential centrifugation, as previously described46. Briefly, 100 mg of the freshly dissected muscle tissue was homogenized after crude mechanical and enzymatic digestion. Followed by two centrifugation steps, the mitochondria-enriched pellet was washed, resuspended, and its protein content was determined with the Bradford method (BioRad #5000205). After the final centrifugation, the mitochondrial pellet was either snap-frozen in liquid nitrogen or suspended in an appropriate assay buffer. When a large quantity of the mitochondrial material was required (more than 250 µg), isolation was performed on up to 1 g of muscle tissue per isolation round, with the according upscaling of the reagents’ volumes. |
| Sample Type: | Biopsy |
Treatment:
| Treatment ID: | TR003844 |
| Treatment Summary: | Acutely exercised animals were used for several experiments in the current study. In preparation for those experiments, mice were familiarized with treadmill running for 3 days (day 1: 5 min, no running; day 2: 5 min, belt speed 6 m/min, 5 min at 10 m/min, no electric grid stimulation; day 3: 2 min at 6 m/min, 3 min at 10 m/min, 2 min from 10 to 16 m/min, 3 min at 16 m/min, electric grid at 1 Hz, 0.1 mA). Animals were then used for experiments 2 days after acclimation. The treadmill belt inclination was set to 10º. The treadmill used was Exer 3/6 Treadmill (Columbus Instruments, USA). The exercise tolerance test was performed on non-fasted animals roughly in the middle of the light phase at ZT 6. The running protocol included a warm-up stage (5 min at 6 m/min, 5 min at 10 m/min, 3 min at 12 m/min, 3 min at 14 m/min) and a test stage (speed increases by 2 m/min every 3rd min). The treadmill belt inclination was set to 10º, and the electric grid stimulation was at 3 Hz and 1.5 mA. A mouse was deemed fatigued when it did not resume running after three consecutive stimuli (contact with the electric grid or a gentle nudge). After running, the animals were returned to their home cages, and sometimes their tail blood was drawn for direct lactate (Lactate Pro 2, Arkray, Japan) and glucose (Contour XT, Bayer, Germany) checks. Moderate-intensity running exercise consisted of a brief warm-up (2 min at 6 m/min, 2 min at 10 m/min, 1 min from 10 to 16 m/min) and a 30 min long bout (10 min at 16 m/min followed by 20 min at 18 m/min). The treadmill belt inclination was set to 10º, and the electric grid stimulation was at 3 Hz and 0.5-1.0 mA. In TSE indirect calorimetry after an acute exercise bout experiment, as well as in the glucose oxidation experiment, mice ran a 1-hour-long moderate-intensity exercise bout, which consisted of a warm-up (2 min at 6 m/min, 2 min at 10 m/min, 1 min from 10 to 16 m/min) and a 55 min long bout at 16 m/min, with other settings as described above. |
Sample Preparation:
| Sampleprep ID: | SP003841 |
| Sampleprep Summary: | Lipids were extracted from the muscle mitochondrial fraction (isolated as described above) using Folch extraction with 8-12 replicates from each experimental group at each time point. Prior to tissue lysis, Splash mix (Merck) was added to the extraction solvent, and tissue samples (except for plasma) were lysed by bead beating in a FastPrep-24 homogenizer. After centrifugation and phase separation, the apolar and polar phases were transferred to separate tubes, and the apolar phase was dried under N₂. |
Combined analysis:
| Analysis ID | AN006075 | AN006076 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 µm) | Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 µm) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Bruker timsTOF fleX | Bruker timsTOF fleX |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Intensity | Intensity |
Chromatography:
| Chromatography ID: | CH004614 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 µm) |
| Column Temperature: | 55℃ |
| Flow Gradient: | from 0 to 0.5 min, 40–43% B from 0.5 to 0.7 min, 43‐65% B from 0.7 to 0.8 min, 65-70% B from 0.8 to 2.3 min, 70-99% B from 2.3 to 6 min, 99% B from 6-6.8 min, 99-40% B from 6.8-7 min before equilibration for 3 min with the initial conditions |
| Flow Rate: | 400 µL/min |
| Solvent A: | 60% Acetonitrile/40% Water; 10 mM Ammonium formate; 0.1% formic acid |
| Solvent B: | 90% Isopropanol/10% Acetonitrile; 10 mM Ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005782 |
| Analysis ID: | AN006075 |
| Instrument Name: | Bruker timsTOF fleX |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics: Data were acquired in MS-only mode, while MS/MS spectra were obtained exclusively from a pooled sample for annotation. Scan range: 50-1700 CID energy: 40V All data was converted. mzML format using ProteoWizard. Data was annotated in MS-Dial (v. 4.9) against the incorporated lipid-blast database with an MS1/MS2 mass tolerance of 0.005/0.01 Da and a minimum identification score of 70%. The annotated compounds were exported to PCDL manager B.08.00 (Agilent Technologies) to create a database for area extraction in Profinder 10.0 (Agilent Technologies). Features with signals less than 5 times those in blanks or missing in more than 20% of QC samples were removed and signals were QC corrected |
| Ion Mode: | POSITIVE |
| MS ID: | MS005783 |
| Analysis ID: | AN006076 |
| Instrument Name: | Bruker timsTOF fleX |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics: Data were acquired in MS-only mode, while MS/MS spectra were obtained exclusively from a pooled sample for annotation. Scan range: 50-1700 CID energy: 40V All data was converted. mzML format using ProteoWizard. Data was annotated in MS-Dial (v. 4.9) against the incorporated lipid-blast database with an MS1/MS2 mass tolerance of 0.005/0.01 Da and a minimum identification score of 70%. The annotated compounds were exported to PCDL manager B.08.00 (Agilent Technologies) to create a database for area extraction in Profinder 10.0 (Agilent Technologies). Features with signals less than 5 times those in blanks or missing in more than 20% of QC samples were removed and signals were QC corrected |
| Ion Mode: | NEGATIVE |
