#METABOLOMICS WORKBENCH hormel101_20170810_143044_mwtab.txt DATATRACK_ID:1207 STUDY_ID:ST000856 ANALYSIS_ID:AN001381 PROJECT_ID:PR000575 VERSION 1 CREATED_ON August 11, 2017, 12:09 pm #PROJECT PR:PROJECT_TITLE Mayo Pilot and Feasiblity: Targeting Myelin Metabolism of Kallikrein 6 Signals PR:PROJECT_TITLE through PAR1 and PAR2 to Enchance Recovery of Function after SCI PR:PROJECT_SUMMARY CNS trauma generates a proteolytic imbalance contributing to secondary injury, PR:PROJECT_SUMMARY including axonopathy and neuron degeneration. Kallikrein 6 (Klk6) is a serine PR:PROJECT_SUMMARY protease implicated in neurodegeneration and here we investigate the role of PR:PROJECT_SUMMARY protease activated receptors 1 (PAR1) and PAR2 in mediating these effects in PR:PROJECT_SUMMARY mice with spinal cord injury (SCI). This project conducts untargeted Profiling PR:PROJECT_SUMMARY (unbiased metabolomics assay) and targeted lipid analysis. The lipid assays are PR:PROJECT_SUMMARY 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) PR:PROJECT_SUMMARY cholesterol concentration (free and bound); 4) Ceramides, including galactosyl PR:PROJECT_SUMMARY and glucosyl; 5) sphingomyelin. PR:INSTITUTE Mayo Clinic PR:LAST_NAME Scarisbrick PR:FIRST_NAME Isobel PR:ADDRESS 200 First Street SW, Rochester, MN 55905 PR:EMAIL scarisbrick.isobel@mayo.edu PR:PHONE 507-284-0124 #STUDY ST:STUDY_TITLE Targeted NEFA in Kallikrein 6 Mice after SCI ST:STUDY_SUMMARY Targeted NEFA in Kallikrein 6 Mice after SCI. The samples submitted are purified ST:STUDY_SUMMARY myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). ST:STUDY_SUMMARY There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or ST:STUDY_SUMMARY P90. ST:INSTITUTE Mayo Clinic ST:LAST_NAME Scarisbrick ST:FIRST_NAME Isobel ST:ADDRESS 200 First Street SW, Rochester, MN 55905 ST:EMAIL scarisbrick.isobel@mayo.edu ST:PHONE 507-284-0124 #SUBJECT SU:SUBJECT_TYPE Mouse SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - ms6022-1 group:K6+/+ | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-2 group:K6+/+ | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-3 group:K6+/+ | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-4 group:K6+/+ | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-5 group:K6+/+ | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-6 group:K6+/+ | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-7 group:K6+/+ | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-8 group:K6+/+ | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-9 group:K6+/+ | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-10 group:K6+/+ | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-11 group:K6-/- | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-12 group:K6-/- | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-13 group:K6-/- | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-14 group:K6-/- | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-15 group:K6-/- | time:P21 SUBJECT_SAMPLE_FACTORS - ms6022-16 group:K6-/- | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-17 group:K6-/- | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-18 group:K6-/- | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-19 group:K6-/- | time:P90 SUBJECT_SAMPLE_FACTORS - ms6022-20 group:K6-/- | time:P90 #COLLECTION CO:COLLECTION_SUMMARY Tissue is from adult mouse spinal cord (SC). We are submitting these samples for CO:COLLECTION_SUMMARY Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The CO:COLLECTION_SUMMARY lipid assays we request are 1) free fatty acid composition of lipids; 2) free CO:COLLECTION_SUMMARY fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, CO:COLLECTION_SUMMARY including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is CO:COLLECTION_SUMMARY our top priority, followed by the lipid assays as listed. All samples were snap CO:COLLECTION_SUMMARY frozen at the point of harvest and approximate weights are provided. The samples CO:COLLECTION_SUMMARY are submitted as intact pieces of tissue. There are two different genotypes CO:COLLECTION_SUMMARY (K6+/+ and K6-/-) and 20 samples total, n=5 for each group that includes CO:COLLECTION_SUMMARY P21(K6+/+); P90 (K6+/+); P21 (K6-/-); and P90 (K6-/-). We would like to make CO:COLLECTION_SUMMARY comparisons across the 4 groups. #TREATMENT TR:TREATMENT_SUMMARY A 3g Clip produces moderate SCI including demyelination and clinical impairment TR:TREATMENT_SUMMARY and we recently published a detailed methodology. At 1 week after injury, the 3g TR:TREATMENT_SUMMARY injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on TR:TREATMENT_SUMMARY a 9 point scale such that they have frequent plantar stepping with no or some TR:TREATMENT_SUMMARY coordination. This level of impairment was chosen to provide a sufficient window TR:TREATMENT_SUMMARY to observe recovery. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY "NEFA of mouse spinal cord Lipids will be quantified in myelin isolated in high SP:SAMPLEPREP_SUMMARY yield and purity by subcellular fractionation from the lumbosacral spinal cord. SP:SAMPLEPREP_SUMMARY While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside SP:SAMPLEPREP_SUMMARY is the most typical of myelin in the adult nervous system being directly SP:SAMPLEPREP_SUMMARY proportional to the amount of myelin. Sulfatide is another galactolipid enriched SP:SAMPLEPREP_SUMMARY in myelin. Together with cholesterol, these form 78% of the total amount of SP:SAMPLEPREP_SUMMARY lipid in the myelin membrane and each will be quantified using LC/MS/MS. A SP:SAMPLEPREP_SUMMARY highly sensitive assay for galactocerebroside was recently established by the SP:SAMPLEPREP_SUMMARY Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel SP:SAMPLEPREP_SUMMARY for free fatty acids, including the very long chain fatty acids found in myelin SP:SAMPLEPREP_SUMMARY is also routinely performed by the Core. Cholesterol will be quantified using an SP:SAMPLEPREP_SUMMARY NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. SP:SAMPLEPREP_SUMMARY Additionally, we have a plan in place with the Metabolomics Core to develop SP:SAMPLEPREP_SUMMARY LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. SP:SAMPLEPREP_SUMMARY Having quantitative assays for each of these key myelin lipids will facilitate SP:SAMPLEPREP_SUMMARY our goal to comprehensively profile myelin lipid metabolism and will form SP:SAMPLEPREP_SUMMARY foundational assays for a future NIH grant focused on myelin metabolism." #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Waters Acquity BEH C18 (150 x 2.1mm, 1.7um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6460 QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS unit = nmol/vial MS_METABOLITE_DATA_START Samples ms6022-1 ms6022-2 ms6022-3 ms6022-4 ms6022-5 ms6022-6 ms6022-7 ms6022-8 ms6022-9 ms6022-10 ms6022-11 ms6022-12 ms6022-13 ms6022-14 ms6022-15 ms6022-16 ms6022-17 ms6022-18 ms6022-19 ms6022-20 Factors group:K6+/+ | time:P21 group:K6+/+ | time:P21 group:K6+/+ | time:P21 group:K6+/+ | time:P21 group:K6+/+ | time:P21 group:K6+/+ | time:P90 group:K6+/+ | time:P90 group:K6+/+ | time:P90 group:K6+/+ | time:P90 group:K6+/+ | time:P90 group:K6-/- | time:P21 group:K6-/- | time:P21 group:K6-/- | time:P21 group:K6-/- | time:P21 group:K6-/- | time:P21 group:K6-/- | time:P90 group:K6-/- | time:P90 group:K6-/- | time:P90 group:K6-/- | time:P90 group:K6-/- | time:P90 myristic 0.03 0.03 0.02 0.03 0.03 0.01 0.02 0.02 0.02 0.02 0.04 0.04 0.05 0.04 0.02 0.03 0.02 0.02 0.02 0.01 palmitic 0.49 0.60 0.47 0.56 0.54 0.69 0.59 0.64 0.74 0.83 0.58 0.64 0.78 0.78 0.40 1.17 0.82 0.80 0.72 0.64 stearic 0.52 0.67 0.56 0.65 0.60 0.76 0.73 0.78 0.75 0.89 0.68 0.71 0.87 0.89 0.60 1.25 1.02 1.02 0.88 0.82 cis-palmitoleic 0.05 0.06 0.04 0.05 0.05 0.04 0.03 0.03 0.06 0.05 0.05 0.06 0.07 0.06 0.04 0.06 0.04 0.04 0.03 0.03 trans-palmitoleic 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 cis-oleic 1.02 1.00 0.89 0.95 1.02 1.28 1.14 1.22 1.60 1.59 1.01 1.16 1.33 1.42 0.88 1.88 1.51 1.40 1.13 1.22 trans-oleic 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 linoleic 0.10 0.10 0.08 0.09 0.10 0.07 0.08 0.07 0.10 0.08 0.12 0.12 0.14 0.13 0.09 0.10 0.10 0.11 0.07 0.08 linolenic 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.01 0.00 0.01 0.00 0.01 0.00 0.00 0.01 0.01 0.01 0.00 0.01 arachidonic 0.62 0.59 0.52 0.54 0.56 0.75 0.70 0.74 0.89 0.89 0.57 0.64 0.71 0.82 0.44 1.06 0.83 0.92 0.72 0.66 EPA 0.04 0.03 0.03 0.03 0.03 0.05 0.04 0.04 0.05 0.05 0.03 0.04 0.04 0.03 0.02 0.06 0.04 0.05 0.03 0.03 DHA 0.41 0.38 0.32 0.32 0.36 0.41 0.33 0.35 0.51 0.55 0.36 0.37 0.44 0.42 0.30 0.61 0.44 0.44 0.35 0.36 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name myristic palmitic stearic cis-palmitoleic trans-palmitoleic cis-oleic trans-oleic linoleic linolenic arachidonic EPA DHA METABOLITES_END #END