Summary of Study ST000607
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 PR000444. The data can be accessed directly via it's Project DOI: 10.21228/M8NW2H This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000607 |
| Study Title | 1D-1H-Nuclear Magnetic Resonance Metabolomics Reveals Age-related Changes in Metabolites Associated with Experimental Venous Thrombosis |
| Study Type | Experimental venous thrombosis |
| Study Summary | Sodium heparin preserved whole blood samples were collected from young and old mice with and without induced VT. Samples were subjected to MeOH:CHCl3 extraction and the MeOH was assayed by 1H-NMR. Chenomx software was used for spectral analysis. |
| Institute | University of Michigan |
| Department | Clinical Pharmacy |
| Laboratory | The NMR Metabolomics Laboratory (Stringer) |
| Last Name | Stringer |
| First Name | Kathleen |
| Address | College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109 |
| NMRmetabolomics@umich.edu | |
| Phone | NA |
| Submit Date | 2016-12-08 |
| Num Groups | 4 |
| Total Subjects | 31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2017-07-10 |
| Release Version | 1 |
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Project:
| Project ID: | PR000444 |
| Project DOI: | doi: 10.21228/M8NW2H |
| Project Title: | Metabolomics of Murine Age-related Deep Vein Thrombosis |
| Project Type: | Quantitative 1D-1H-NMR metabolomics |
| Project Summary: | Objective: Age is a significant risk factor for the development of venous thrombosis (VT), but the mechanism(s) that underlie this risk remain(s) undefined and poorly understood. Aging is known to adversely influence inflammation and affect metabolism. Untargeted metabolomics permits an agnostic assessment of the physiological landscape and lends insight into the mechanistic underpinnings of clinical phenotypes. The objective of this exploratory study was to test the feasibility of a metabolomics approach for identifying potential metabolic mechanisms of age-related VT. Methods: We subjected whole blood samples collected from young and old nonthrombosed controls and VT mice 2 days after thrombus induction using the electrolytic inferior vena cava, to a methanol:chloroform extraction and assayed the resulting aqueous fractions using 1D-1H- nuclear magnetic resonance. Normalized mouse metabolite data were compared across groups using analysis of variance (ANOVA) with Holm-Sidak post-testing. In addition, associations between metabolite concentrations and parameters of thrombosis such as thrombus and vein wall weights, and markers of inflammation, vein wall P- and E-selectin levels, were assessed using linear regression. The relatedness of the found significant metabolites was visually assessed using a bioinformatics tool, Metscape, which generates compound-reaction-enzyme-gene networks to aid in the interpretation of metabolomics data. Results: Old mice with VT had a greater mean vein wall weight compared with young mice with VT (P < .05). Clot weight differences between old and young mice followed the same trend as vein wall weight (0.011 % 0.04 g vs 0.008 % 0.003 g; P [ not significant). Glutamine (ANOVA, P < .01), proline (ANOVA, P < .01), and phenylalanine (ANOVA, P <.05) levels were increased in old VT mice compared with age-matched controls and young VT mice. Betaine and/or trimethylamine N-oxide levels were increased in aged mice compared with young animals. Vein wall weight was strongly associated with glutamine (P < .05), and phenylalanine (P <.01) concentrations and there was a trend toward an association with proline (P [ .09) concentration. Vein wall Pselectin, but not E-selectin levels, were increased in old VT mice and were associated with the three found metabolites of age-related VT. Collectively, with the addition of glutamate, these metabolites form a single compound-reaction-enzyme gene network that was generated by Metscape. Conclusions: We used 1D-1H-nuclear magnetic resonance metabolite profiling to identify, for the first time, in an experimental model, three potential metabolites, glutamine, phenylalanine, and proline, associated with age-related VT. These metabolites are metabolically related and their levels are associated with vein wall weight and P-selectin concentrations. In aggregate, these findings provide a “roadmap” of pathways that could be interrogated in future studies, which could include provocation of the glutamine, phenylalanine, and proline pathways in the vein wall. This study introduces metabolomics as a new approach to furthering knowledge about the mechanisms of age-related VT. This study has been published: J Vasc Surg Venous Lymphat Disord. 2016 Apr;4(2):221-30. doi: 10.1016/j.jvsv.2015.09.010. Epub 2015 Nov 24. |
| Institute: | University of Michigan |
| Department: | Department of Surgery |
| Laboratory: | NMR Metabolomics Laboratory, University of Michigan |
| Last Name: | Stringer |
| First Name: | Kathleen |
| Address: | College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109 |
| Email: | NMRmetabolomics@umich.edu |
| Phone: | NA |
| Funding Source: | NIH (DK097153; HL076123), College of Pharmacy Upjohn Award |
Subject:
| Subject ID: | SU000630 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl6 |
| Age Or Age Range: | 10 weeks and 12-24 months (young & old) |
| Weight Or Weight Range: | ~25 g and ~34 g |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Condition |
|---|---|---|
| SA033501 | CH14WB | Cntrl young |
| SA033502 | CH13WB | Cntrl young |
| SA033503 | CH11WB | Cntrl young |
| SA033504 | CH15WB | Cntrl young |
| SA033505 | CH12WB | Cntrl young |
| SA033506 | CH16WB | Cntrol old |
| SA033507 | CH20WB | Cntrol old |
| SA033508 | CH19WB | Cntrol old |
| SA033509 | CH18WB | Cntrol old |
| SA033510 | CH17WB | Cntrol old |
| SA033511 | CH31WB | DVT old |
| SA033512 | CH29WB | DVT old |
| SA033513 | CH28WB | DVT old |
| SA033514 | CH8WB | DVT old |
| SA033515 | CH10WB | DVT old |
| SA033516 | CH7WB | DVT old |
| SA033517 | CH21WB | DVT old |
| SA033518 | CH27WB | DVT old |
| SA033519 | CH5WB | DVT young |
| SA033520 | CH4WB | DVT young |
| SA033521 | CH22WB | DVT young |
| SA033522 | CH25WB | DVT young |
| SA033523 | CH1WB | DVT young |
| SA033524 | CH26WB | DVT young |
| SA033525 | CH24WB | DVT young |
| Showing results 1 to 25 of 25 |
Collection:
| Collection ID: | CO000624 |
| Collection Summary: | None |
| Collection Protocol Filename: | SOP_for_whole_blood_collection_exp._animals_v1.3.pdf |
| Sample Type: | Whole blood |
| Collection Tube Temp: | 4C |
| Additives: | Sodium heparin |
| Blood Serum Or Plasma: | Whole blood |
Treatment:
| Treatment ID: | TR000644 |
| Treatment Summary: | None |
| Animal Vet Treatments: | Electrolytic inferior vena cava (IVC) model (EIM to induce thrombogenesis |
| Animal Anesthesia: | 2-5% isoflurane with 100% oxygen |
| Animal Fasting: | No |
| Animal Endp Euthanasia: | Per IUCUCA and 2d following induction of VT |
| Animal Endp Tissue Coll List: | Blood sampling, thrombus and vein wall |
Sample Preparation:
| Sampleprep ID: | SP000637 |
| Sampleprep Summary: | Methanol:cholorform extraction |
| Sampleprep Protocol Filename: | Wakefield_Mouse_WB_Extraction_Protocol.pdf |
| Sampleprep Protocol Comments: | Lipid fractions saved, stored at -20°C |
| Processing Method: | Methanol:Chloroform Extraction |
| Processing Storage Conditions: | 0-4°C |
| Extraction Method: | Methanol:chloroform extraction |
| Extract Cleanup: | N/A |
| Extract Storage: | -80°C |
Analysis:
| Analysis ID: | AN000928 |
| Laboratory Name: | University of Michigan Biochemical NMR Core Laboratory |
| Analysis Type: | NMR |
| Software Version: | VNMRJ 3.2 |
| Operator Name: | Michael Finkel |
| Data Format: | .fid |
| Num Factors: | 4 |
| Num Metabolites: | 54 |
| Units: | uM |
NMR:
| NMR ID: | NM000104 |
| Analysis ID: | AN000928 |
| Instrument Name: | Agilent 500/54 Premium Shielded VNMRS system |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Standard Concentration: | 10% (~0.5mM) |
| Spectrometer Frequency: | 500 MHz |
| NMR Probe: | ONE-Probe |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm |
| Shimming Method: | Auto shim (gradient shimming) |
| Pulse Sequence: | 1D-NOESY |
| Water Suppression: | saturation at 80 Hz induced field strength |
| Pulse Width: | 5.5ms |
| Offset Frequency: | around -178Hz |
| Chemical Shift Ref Cpd: | 6mM Formate |
| Temperature: | 25°C |
| Number Of Scans: | 32 |
