Summary of Study ST000869

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 PR000575. The data can be accessed directly via it's Project DOI: 10.21228/M8BM2Z 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 IDST000869
Study TitleLarge Untargeted Profiling in Kallikrein 6 Mice after SCI
Study SummaryLarge untargeted profiling mouse myelin of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Institute
Mayo Clinic
Last NameScarisbrick
First NameIsobel
Address200 First Street SW, Rochester, MN 55905
Emailscarisbrick.isobel@mayo.edu
Phone507-284-0124
Submit Date2017-08-10
Analysis Type DetailLC-MS
Release Date2021-02-17
Release Version1
Isobel Scarisbrick Isobel Scarisbrick
https://dx.doi.org/10.21228/M8BM2Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000575
Project DOI:doi: 10.21228/M8BM2Z
Project Title:Mayo Pilot and Feasibility: Targeting Myelin Metabolism to Enhance Recovery of Function after SCI
Project Summary:The loss of myelin, degeneration of the myelin producing oligodendroglia and impaired remyelination are essential features of traumatic spinal cord injury (SCI) that significantly limit patient recovery of function. The lipid rich composition of myelin, including exceptionally high levels of saturated fatty acids, underlie its essential physiological roles, including its structural and signaling properties and electrical insulation of axons to facilitate the conduction of nerve impulses. The myelin sheaths also provide metabolic support to the axons they wrap, and myelin health is therefore essential to the maintenance of axon integrity and function in the brain and spinal cord. The primary goal of this Pilot Proposal to the Mayo Clinic Metabolomics Core is to integrate highly sensitive metabolomics liquid chromatography-tandem mass spectrometry (LC/MS/MS) assays to quantify the lipid composition of the myelin membrane, with our conventional neurobehavioral approaches, enabling us to explore the metabolic basis of new interventions capable of promoting myelin regeneration and restoration of patient function. Metabolomics Core expertise in Magnetic Resonance Spectroscopy (NMR) based evaluation of key metabolites involved in CNS injury and repair (N-acetyl-L-aspartate, choline, myo-inositol, glucose/ glutamine and lactate) will also be applied to strengthen our mechanistic understanding of myelin injury and repair. Specifically, utilizing these innovative approaches we will test a novel hypothesis driven by new preliminary findings that the levels of dietary fatty acids can be optimized alone, or in combination with exercise training, to facilitate myelin regeneration and recovery of neurobehavioral function after injury to the adult spinal cord. In Aim 1, we will determine whether alterations in dietary fat, including saturated fat or omega-3 fatty acids, facilitate restoration of the myelin membrane and metabolite signatures of central nervous system repair after experimental SCI in adult mice. In Aim 2, we will determine whether exercise training alone or in combination with dietary fatty acid supplementation fosters myelin regeneration and recovery of function after experimental SCI. The proposed studies will leverage the expertise of the Mayo Metabolomics Core with that of Dr. Scarisbrick (Mayo) in myelin biology and Dr. Gomez Pinilla (UCLA) in central nervous system plasticity to investigate whether two highly targetable lifestyle variables, that is diet and exercise, can be modulated to improve myelin metabolism and functional recovery after SCI.
Institute:Mayo Clinic
Last Name:Scarisbrick
First Name:Isobel
Address:200 First St. SW, Rochester, Minnesota, 55905, USA
Email:scarisbrick.isobel@mayo.edu
Phone:507-284-0124

Subject:

Subject ID:SU000896
Subject Type:Mouse
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

Subject type: Mouse; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Group Time point rep
SA048387philic-7jun16-004-r001K6+/+ P21 1
SA048388pC18-7jun16-004-r001K6+/+ P21 1
SA048389philic-7jun16-003-r001K6+/+ P21 1
SA048390nC18-8jun16-018-r001_1K6+/+ P21 1
SA048391philic-7jun16-010-r001K6+/+ P21 1
SA048392nC18-8jun16-010-r001_1K6+/+ P21 1
SA048393nC18-8jun16-015-r001_1K6+/+ P21 1
SA048394pC18-7jun16-010-r001K6+/+ P21 1
SA048395nhilic-9jun16-018-r001K6+/+ P21 1
SA048396nhilic-9jun16-003-r001K6+/+ P21 1
SA048397nhilic-9jun16-004-r001K6+/+ P21 1
SA048398nhilic-9jun16-010-r001K6+/+ P21 1
SA048399pC18-7jun16-018-r001K6+/+ P21 1
SA048400pC18-7jun16-015-r001K6+/+ P21 1
SA048401nhilic-9jun16-015-r001K6+/+ P21 1
SA048402philic-7jun16-015-r001K6+/+ P21 1
SA048403pC18-7jun16-003-r001K6+/+ P21 1
SA048404nC18-8jun16-004-r001_1K6+/+ P21 1
SA048405nC18-8jun16-003-r001_1K6+/+ P21 1
SA048406philic-7jun16-018-r001K6+/+ P21 1
SA048467nhilic-9jun16-016-r001K6-/- P21 1
SA048468philic-7jun16-020-r001K6-/- P21 1
SA048469nhilic-9jun16-020-r001K6-/- P21 1
SA048470philic-7jun16-016-r001K6-/- P21 1
SA048471philic-7jun16-001-r001K6-/- P21 1
SA048472nhilic-9jun16-009-r001K6-/- P21 1
SA048473philic-7jun16-009-r001K6-/- P21 1
SA048474philic-7jun16-005-r001K6-/- P21 1
SA048475nhilic-9jun16-001-r001K6-/- P21 1
SA048476pC18-7jun16-001-r001K6-/- P21 1
SA048477pC18-7jun16-009-r001K6-/- P21 1
SA048478pC18-7jun16-016-r001K6-/- P21 1
SA048479nC18-8jun16-020-r001_1K6-/- P21 1
SA048480nC18-8jun16-016-r001_1K6-/- P21 1
SA048481nC18-8jun16-005-r001_1K6-/- P21 1
SA048482nC18-8jun16-009-r001_1K6-/- P21 1
SA048483pC18-7jun16-020-r001K6-/- P21 1
SA048484pC18-7jun16-005-r001K6-/- P21 1
SA048485nC18-8jun16-001-r001_1K6-/- P21 1
SA048486nhilic-9jun16-005-r001K6-/- P21 1
SA048407philic-7jun16-003-r002K6+/+ P21 2
SA048408pC18-7jun16-004-r002K6+/+ P21 2
SA048409pC18-7jun16-003-r002K6+/+ P21 2
SA048410nC18-8jun16-004-r002_1K6+/+ P21 2
SA048411pC18-7jun16-018-r002K6+/+ P21 2
SA048412philic-7jun16-015-r002K6+/+ P21 2
SA048413pC18-7jun16-015-r002K6+/+ P21 2
SA048414nhilic-9jun16-015-r002K6+/+ P21 2
SA048415nhilic-9jun16-018-r002K6+/+ P21 2
SA048416pC18-7jun16-010-r002K6+/+ P21 2
SA048417nC18-8jun16-018-r002_1K6+/+ P21 2
SA048418philic-7jun16-018-r002K6+/+ P21 2
SA048419nC18-8jun16-003-r002_1K6+/+ P21 2
SA048420philic-7jun16-004-r002K6+/+ P21 2
SA048421philic-7jun16-010-r002K6+/+ P21 2
SA048422nhilic-9jun16-004-r002K6+/+ P21 2
SA048423nhilic-9jun16-003-r002K6+/+ P21 2
SA048424nC18-8jun16-010-r002_1K6+/+ P21 2
SA048425nhilic-9jun16-010-r002K6+/+ P21 2
SA048426nC18-8jun16-015-r002_1K6+/+ P21 2
SA048487pC18-7jun16-020-r002K6-/- P21 2
SA048488nC18-8jun16-020-r002_1K6-/- P21 2
SA048489pC18-7jun16-001-r002K6-/- P21 2
SA048490pC18-7jun16-005-r002K6-/- P21 2
SA048491nhilic-9jun16-020-r002K6-/- P21 2
SA048492philic-7jun16-001-r002K6-/- P21 2
SA048493philic-7jun16-009-r002K6-/- P21 2
SA048494nC18-8jun16-016-r002_1K6-/- P21 2
SA048495nC18-8jun16-005-r002_1K6-/- P21 2
SA048496philic-7jun16-020-r002K6-/- P21 2
SA048497philic-7jun16-016-r002K6-/- P21 2
SA048498nhilic-9jun16-005-r002K6-/- P21 2
SA048499nhilic-9jun16-001-r002K6-/- P21 2
SA048500nC18-8jun16-009-r002_1K6-/- P21 2
SA048501nC18-8jun16-001-r002_1K6-/- P21 2
SA048502philic-7jun16-005-r002K6-/- P21 2
SA048503pC18-7jun16-009-r002K6-/- P21 2
SA048504pC18-7jun16-016-r002K6-/- P21 2
SA048505nhilic-9jun16-016-r002K6-/- P21 2
SA048506nhilic-9jun16-009-r002K6-/- P21 2
SA048427pC18-7jun16-008-r001K6+/+ P90 1
SA048428philic-7jun16-011-r001K6+/+ P90 1
SA048429nhilic-9jun16-014-r001K6+/+ P90 1
SA048430philic-7jun16-014-r001K6+/+ P90 1
SA048431nC18-8jun16-011-r001_1K6+/+ P90 1
SA048432pC18-7jun16-014-r001K6+/+ P90 1
SA048433philic-7jun16-019-r001K6+/+ P90 1
SA048434pC18-7jun16-011-r001K6+/+ P90 1
SA048435pC18-7jun16-007-r001K6+/+ P90 1
SA048436nhilic-9jun16-019-r001K6+/+ P90 1
SA048437nC18-8jun16-014-r001_1K6+/+ P90 1
SA048438nC18-8jun16-007-r001_1K6+/+ P90 1
SA048439philic-7jun16-008-r001K6+/+ P90 1
SA048440pC18-7jun16-019-r001K6+/+ P90 1
SA048441philic-7jun16-007-r001K6+/+ P90 1
SA048442nhilic-9jun16-007-r001K6+/+ P90 1
SA048443nhilic-9jun16-011-r001K6+/+ P90 1
SA048444nC18-8jun16-019-r001_1K6+/+ P90 1
SA048445nhilic-9jun16-008-r001K6+/+ P90 1
SA048446nC18-8jun16-008-r001_1K6+/+ P90 1
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Collection:

Collection ID:CO000890
Collection Summary:Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are two different genotypes (K6+/+ and K6-/-) and 20 samples total, n=5 for each group that includes P21(K6+/+); P90 (K6+/+); P21 (K6-/-); and P90 (K6-/-). We would like to make comparisons across the 4 groups.
Sample Type:Spinal cord

Treatment:

Treatment ID:TR000910
Treatment Summary:A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery.

Sample Preparation:

Sampleprep ID:SP000903
Sampleprep Summary:large scale profiling of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism.

Combined analysis:

Analysis ID AN001399 AN001400 AN001401
Analysis type MS MS MS
Chromatography type Reversed phase HILIC HILIC
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters Acquity HSS C18 (150 x 2.1mm,1.8um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI
MS instrument type QTOF QTOF QTOF
MS instrument name Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode NEGATIVE POSITIVE NEGATIVE
Units intensity intensity intensity

Chromatography:

Chromatography ID:CH000980
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity HSS C18 (150 x 2.1mm,1.8um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH000981
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS001291
Analysis ID:AN001399
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001292
Analysis ID:AN001400
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001293
Analysis ID:AN001401
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
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