Summary of Study ST003622
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 PR002238. The data can be accessed directly via it's Project DOI: 10.21228/M8BK0V 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 | ST003622 |
Study Title | A multi-omic census reveals obesity-associated microRNA miR-let-7 as novel instigator of adipose mitochondrial dysfunction and of intergenerational metabolic decline. |
Study Summary | We here describe that obesity and weight loss in male mice causes reversible abnormalities in glucose and lipid metabolism, serum metabolomes, and white adipose tissue alongside reversible reductions in activity of genes controlling mitochondrial energy dissipation. When mating obese male mice with lean females, we observed concordant reductions in mitochondrial gene expression and translation in offspring that resemble those observed in the paternal (F0) generation. When mapping miRNA responses across somatic and gametic cell types and generations, we found that obesity and weight loss reversible affected miRNA abundance, and observed miR-let7 isoforms induced in obese adipose tissues of F0 and offspring (F1) generations, as well as in sperm of obese F0 mice. Mechanistically, when overexpressing miR-let-7 in adipocytes, we found it to silence DICER1, a cellular rheostat required for adipose tissue adaptation in obesity as evidenced by functional deficiency in mitochondrial functioon following DICER1 loss. Delivery of miR-let-7 into oocytes elicited glucose intolerance and impairments in adipose mitochondrial gene expression in mice sired from miRNA-injected embryos, phenocopying aspects of paternal obesity. When performing single-cell RNA-Seq of embryos, we found that miR-let7 impaired mitochondrial gene expression, suggesting altered energy metabolism following sperm-mediated changes in zygotic miRNAs. When studying miRNA alterations in human semen, we lifestyle-induced weight loss to downregulate MIR-LET-7 in human subjects, suggesting similar roles for human MIR-LET-7 in gametic epigenomes and embryogenesis. |
Institute | University of Southern Denmark |
Last Name | Kornfeld |
First Name | Jan-Wilhelm |
Address | University of Southern Denmark (SDU), Campusvej 55, 5230 Odense M, Denmark |
janwilhelmkornfeld@bmb.sdu.dk | |
Phone | +4565503904 |
Submit Date | 2024-09-06 |
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: | PR002238 |
Project DOI: | doi: 10.21228/M8BK0V |
Project Title: | A multi-omic census reveals obesity-associated microRNA miR-let-7 as novel instigator of adipose mitochondrial dysfunction and of intergenerational metabolic decline. |
Project Summary: | We here describe that obesity and weight loss in male mice causes reversible abnormalities in glucose and lipid metabolism, serum metabolomes, and white adipose tissue alongside reversible reductions in activity of genes controlling mitochondrial energy dissipation. When mating obese male mice with lean females, we observed concordant reductions in mitochondrial gene expression and translation in offspring that resemble those observed in the paternal (F0) generation. When mapping miRNA responses across somatic and gametic cell types and generations, we found that obesity and weight loss reversible affected miRNA abundance, and observed miR-let7 isoforms induced in obese adipose tissues of F0 and offspring (F1) generations, as well as in sperm of obese F0 mice. Mechanistically, when overexpressing miR-let-7 in adipocytes, we found it to silence DICER1, a cellular rheostat required for adipose tissue adaptation in obesity as evidenced by functional deficiency in mitochondrial functioon following DICER1 loss. Delivery of miR-let-7 into oocytes elicited glucose intolerance and impairments in adipose mitochondrial gene expression in mice sired from miRNA-injected embryos, phenocopying aspects of paternal obesity. When performing single-cell RNA-Seq of embryos, we found that miR-let7 impaired mitochondrial gene expression, suggesting altered energy metabolism following sperm-mediated changes in zygotic miRNAs. When studying miRNA alterations in human semen, we lifestyle-induced weight loss to downregulate MIR-LET-7 in human subjects, suggesting similar roles for human MIR-LET-7 in gametic epigenomes and embryogenesis. |
Institute: | University of Southern Denmark |
Department: | Department of Biochemistry and Molecular Biology |
Last Name: | Kornfeld |
First Name: | Jan-Wilhelm |
Address: | University of Southern Denmark (SDU), Campusvej 55, 5230 Odense M, Denmark |
Email: | janwilhelmkornfeld@bmb.sdu.dk |
Phone: | +4565503904 |
Subject:
Subject ID: | SU003752 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample source | Diet |
---|---|---|---|
SA393276 | IEI_Blank02 | Blank | - |
SA393277 | IEI_Blank01 | Blank | - |
SA393278 | IEI_Blank03 | Blank | - |
SA393279 | IEI_QC03 | QC | - |
SA393280 | IEI_QC01 | QC | - |
SA393281 | IEI_QC08 | QC | - |
SA393282 | IEI_QC07 | QC | - |
SA393283 | IEI_QC06 | QC | - |
SA393284 | IEI_QC04 | QC | - |
SA393285 | IEI_QC02 | QC | - |
SA393286 | IEI_QC05 | QC | - |
SA393287 | IEI_MSMS04 | Serum | - |
SA393288 | IEI_MSMS03 | Serum | - |
SA393289 | IEI_MSMS02 | Serum | - |
SA393290 | IEI_MSMS01 | Serum | - |
SA393291 | IEI_HFD01 | Serum | HFD |
SA393292 | IEI_HFD03 | Serum | HFD |
SA393293 | IEI_HFD06 | Serum | HFD |
SA393294 | IEI_HFD02 | Serum | HFD |
SA393295 | IEI_HFD05 | Serum | HFD |
SA393296 | IEI_HFD04 | Serum | HFD |
SA393297 | IEI_LFD04 | Serum | LFD |
SA393298 | IEI_LFD05 | Serum | LFD |
SA393299 | IEI_LFD01 | Serum | LFD |
SA393300 | IEI_LFD02 | Serum | LFD |
SA393301 | IEI_LFD03 | Serum | LFD |
SA393302 | IEI_LFD06 | Serum | LFD |
SA393303 | IEI_REV02 | Serum | REV |
SA393304 | IEI_REV03 | Serum | REV |
SA393305 | IEI_REV04 | Serum | REV |
SA393306 | IEI_REV05 | Serum | REV |
SA393307 | IEI_REV06 | Serum | REV |
SA393308 | IEI_REV07 | Serum | REV |
SA393309 | IEI_REV01 | Serum | REV |
Showing results 1 to 34 of 34 |
Collection:
Collection ID: | CO003745 |
Collection Summary: | For serum collection, Blood collected by the cardiac puncture was centrifuged at 2,000 g for 15 min |
Sample Type: | Blood (serum) |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR003761 |
Treatment Summary: | All animal experiments were approved by the Ministry of Environment and Agriculture Denmark (Miljø- og Fødevarestyrelsen), the license no. 2018-15-0201-01544. All mice were housed under a 12-h light/ 12-h dark cycle in a temperature and humidity-controlled facility and had ad libitum access to diets and drinking water. 4-week-old C57BL/6J male mice (Janvier Labs) were fed with a chow diet (NIH-31, Zeigler Brothers Inc., 8% calories from fat) for 2 weeks of acclimatization and then were fed with either a low-fat diet (LFD, D12450J, 10% kcal from fat, Research Diet) or a high-fat diet (HFD, D12492, 60% kcal from fat, Research Diet) for 9 weeks. After 9 weeks of feeding, half of HFD-fed mice were randomly assigned to the diet regression group which was given LFD (REV) group. |
Sample Preparation:
Sampleprep ID: | SP003759 |
Sampleprep Summary: | 100 µL of serum was mixed with 1000 µL of a 2:1 chloroform/methanol solution and 200 µL of water. Four blank samples, each containing 100 µL of water, were processed in parallel. The mixtures were shaken at 1000 rpm for 30 minutes at 4°C, followed by centrifugation at 16,000g for 10 minutes at 4°C to separate the phases. The aqueous phase was re-extracted with 350 µL of an 86:14:1 chloroform/methanol/water solution. The organic phase from this re-extraction was combined with the corresponding organic phase from the initial extraction. Aqueous fraction was dried using SpeedVac, while the organic phase was dried under a stream of nitrogen. For subsequent analysis, the dried aqueous fractions were reconstituted in 30 µL of 1% formic acid for metabolomics. The organic phase was reconstituted in 30 µL of lipidomics solvent A (5:1:4 isopropanol/methanol/water with 5 mM ammonium acetate and 0.1% acetic acid). A pooled quality control (QC) sample was prepared for each analytical setup by combining 5 µL from each sample, excluding blanks |
Combined analysis:
Analysis ID | AN005949 | AN005950 | AN005951 | AN005952 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | Reversed phase | Reversed phase | Reversed phase | Reversed phase |
Chromatography system | Agilent 1290 | Agilent 1290 | Agilent 1290 | Agilent 1290 |
Column | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | QTOF | QTOF | QTOF | QTOF |
MS instrument name | Agilent 6530 QTOF | Agilent 6530 QTOF | Agilent 6530 QTOF | Agilent 6530 QTOF |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | Peak intensity | Peak intensity | Peak intensity | Peak intensity |
Chromatography:
Chromatography ID: | CH004521 |
Chromatography Summary: | Lipidomics |
Instrument Name: | Agilent 1290 |
Column Name: | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) |
Column Temperature: | 50 |
Flow Gradient: | 0% B from 0 to 1 min, 0-25% B from 1 to 1.5 min, 25-95% B from 1.5 to 12 min, 95% B from 12 to 14 min, and 95-0% B from 14 to 15 min, followed by a 3-minute equilibration |
Flow Rate: | 400 uL/min |
Solvent A: | 95% isopropanol/1% methanol/4% water; 5 mM ammonium acetate; 0.1% acetic acid |
Solvent B: | 99% isopropanol/1% water; 5 mM ammonium acetate; 0.1% acetic acid |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH004522 |
Chromatography Summary: | Metabolomics |
Instrument Name: | Agilent 1290 |
Column Name: | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) |
Column Temperature: | 40 |
Flow Gradient: | 3% B from 0 to 1.5 min, 3-40% B from 1.5 to 4.5 min, 40-95% B from 4.5 to 7.5 min, 95% B from 7.5 to 10.1 min, and 95-3% B from 10.1 to 10.5 min, followed by a 3.5-minute equilibration |
Flow Rate: | 400 uL/min |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS005664 |
Analysis ID: | AN005949 |
Instrument Name: | Agilent 6530 QTOF |
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: | MS005665 |
Analysis ID: | AN005950 |
Instrument Name: | Agilent 6530 QTOF |
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 |
MS ID: | MS005666 |
Analysis ID: | AN005951 |
Instrument Name: | Agilent 6530 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
MS Comments: | Metabolomics: Data were acquired in MS-only mode, while MS/MS spectra were obtained exclusively from a pooled sample for annotation. Scan range: 50-1050 CID energy: 20V and 40V All data was converted. mzML format using ProteoWizard. Metabolomics data was processed in MzMine (v2.59) utilizing modules such as ADAP chromatogram builder and deconvolution. Compounds were annotated at Metabolomics Standards Initiative (MSI) levels 3 using the libraries of National Institute of Standards and Technology 2017 (NIST17) and MassBank of North America (MoNa). 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: | MS005667 |
Analysis ID: | AN005952 |
Instrument Name: | Agilent 6530 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
MS Comments: | Metabolomics: Data were acquired in MS-only mode, while MS/MS spectra were obtained exclusively from a pooled sample for annotation. Scan range: 50-1050 CID energy: 20V and 40V All data was converted. mzML format using ProteoWizard. Metabolomics data was processed in MzMine (v2.59) utilizing modules such as ADAP chromatogram builder and deconvolution. Compounds were annotated at Metabolomics Standards Initiative (MSI) levels 3 using the libraries of National Institute of Standards and Technology 2017 (NIST17) and MassBank of North America (MoNa). 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 |