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.

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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 IDST003622
Study TitleA multi-omic census reveals obesity-associated microRNA miR-let-7 as novel instigator of adipose mitochondrial dysfunction and of intergenerational metabolic decline.
Study SummaryWe 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 NameKornfeld
First NameJan-Wilhelm
AddressUniversity of Southern Denmark (SDU), Campusvej 55, 5230 Odense M, Denmark
Emailjanwilhelmkornfeld@bmb.sdu.dk
Phone+4565503904
Submit Date2024-09-06
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-01-02
Release Version1
Jan-Wilhelm Kornfeld Jan-Wilhelm Kornfeld
https://dx.doi.org/10.21228/M8BK0V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA393276IEI_Blank02Blank -
SA393277IEI_Blank01Blank -
SA393278IEI_Blank03Blank -
SA393279IEI_QC03QC -
SA393280IEI_QC01QC -
SA393281IEI_QC08QC -
SA393282IEI_QC07QC -
SA393283IEI_QC06QC -
SA393284IEI_QC04QC -
SA393285IEI_QC02QC -
SA393286IEI_QC05QC -
SA393287IEI_MSMS04Serum -
SA393288IEI_MSMS03Serum -
SA393289IEI_MSMS02Serum -
SA393290IEI_MSMS01Serum -
SA393291IEI_HFD01Serum HFD
SA393292IEI_HFD03Serum HFD
SA393293IEI_HFD06Serum HFD
SA393294IEI_HFD02Serum HFD
SA393295IEI_HFD05Serum HFD
SA393296IEI_HFD04Serum HFD
SA393297IEI_LFD04Serum LFD
SA393298IEI_LFD05Serum LFD
SA393299IEI_LFD01Serum LFD
SA393300IEI_LFD02Serum LFD
SA393301IEI_LFD03Serum LFD
SA393302IEI_LFD06Serum LFD
SA393303IEI_REV02Serum REV
SA393304IEI_REV03Serum REV
SA393305IEI_REV04Serum REV
SA393306IEI_REV05Serum REV
SA393307IEI_REV06Serum REV
SA393308IEI_REV07Serum REV
SA393309IEI_REV01Serum 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
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