Summary of Study ST001844

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 PR000667. The data can be accessed directly via it's Project DOI: 10.21228/M8FX07 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	ST001844
Study Title	Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) (part III)
Study Summary	Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
Institute	University of California, Davis
Department	Department of Internal Medicine, Division of Gastroenterology and Hepatology
Laboratory	Medici Lab
Last Name	Medici
First Name	Valentina
Address	4150 V Street - PSSB Suite 3500 - 95817 Sacramento CA
Email	vmedici@ucdavis.edu
Phone	(916) 734 3751
Submit Date	2021-06-10
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	GC-MS
Release Date	2021-07-05
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP001927
Sampleprep Summary:	Sample preparation of blood plasma or serum samples for CSH, HILIC and GC analysis Purpose: This SOP describes sample extraction and preparation of blood plasma or serum for lipid profiling on the CSH, and HILIC platform by liquid chromatography/ mass spectrometry (LC-MS) as well as primary metabolomics platform on GC/MS. This method is to be used when there is low sample volume for separate extractions, and when more than one platform is to be used in a project. References: Matyash V, Liebisch G, Kurzchalia TV, Shevchenko A and Schwudke D (2008) Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J Lip Res 2008, 49: 1137-1146 Starting material: Plasma/serum: 20 µL sample volume or aliquot Equipment: Centrifuge Eppendorf 5415 D Calibrated pipettes 20-200µL and 100-1000µL Multi-Tube Vortexer (VWR VX-2500) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Chemicals: Product Manufacturer & Part Number Eppendorf tubes 1.5 mL, uncolored Eppendorf 022363204 Eppendorf tubes 2 mL, uncolored Eppendorf 022363352 Crushed ice UC Davis Water, LC/MS Grade Fisher Optima W6-4 MTBE, HPLC Grade Acros Organics 389050010 Methanol, LC/MS Grade Fisher A456-4 Bioreclamation human plasma (disodium EDTA) Bioreclamation HMPLEDTA Acetonitrile, HPLC Grade Fisher Optima A955-4 Iso-Propanol, HPLC Grade Fisher A461-4 Sample Preparation: Preparation of extraction solvent Combine 120 mL of chilled MeOH/QC mix with 400 mL of chilled MTBE/Cholesterol Ester 22:1 in a clean 500 mL stock bottle. Mix thoroughly by swirling or stir plate and store at -20°C until use. *See SOP “QC mix for LC-MS lipid analysis” for preparation of MeOH/QC mix and MTBE/Cholesterol Ester 22:1. Preparation of Clean Up solvent For 1 L of extraction solvent, combine 375 mL of acetonitrile, 375 mL of isopropanol, and 250 mL water in a 1 L bottle conditioned with the aforementioned chemicals. If a different total volume of extraction solvent is needed, simply mix acetonitrile, isopropanol, and water in volumes in proportion 3:3:2. Purge the extraction solution mix for 5 min with nitrogen with small bubbles. Make sure that the nitrogen line is flushed out of air before using it for degassing the extraction solvent solution. Store at -20°C until use. Note: if solvent freezes, sonicate until thawed and mix before use. Extraction Thaw raw samples/controls at room temperature (or in the refrigerator at 4˚C) and either invert the tube or vortex 10 sec at low speed to homogenize. Aliquot 20 μL of plasma sample into a 1.5 mL Eppendorf tube. Keep all samples on ice. Add 975 µL ice-cold 3:10 (v/v) MeOH/MTBE + QC mix/CE 22:1 extraction solvent mixture to each aliquot, keeping the extraction solvent on ice during the procedure. Vortex samples for 10 seconds, then shake for 5 minutes at 4°C on the orbital mixer. Add 188 µL room temperature LC/MS grade water to each tube. Vortex tubes for 20 seconds and then centrifuge for 2 min at 14,000 rcf. Transfer the upper organic phase to two separate tubes (350 µL/each tube) for lipidomics analysis. Transfer 75 µL of the remaining organic phase to a 2, 15, or 50 mL tube for pools, depending on number of samples in the study. Transfer the bottom aqueous phase to two separate tubes (110 µL/each tube) for HILIC/GC-TOF analysis. Dry down one tube from each phase by centrivap, keeping the undried tubes as backups. Store all tubes at -20˚C until ready for analysis. Clean up step for GC only (and pooling) Resuspend the dried aliquot with 500 μL 3:3:2 (v/v/v) ACN:IPA:H2O (degassed as given above) and vortex for about 10 sec. Centrifuge for 2 min at 14000 rcf. Remove 450 uL supernatant to a clean 1.5 mL eppendorf tube. Tranfering remainder to a 2, 15, 50 mL Tube, dependent on number of samples. Aliquot out 1.9 mL uL of supernatant to new 2ml eppendorf tubes. Centrifuge for 2 min at 14000 rcf Aliquot out 4x450 uL of supernatant into clean 1.5 mL Eppendorf tubes. Evaporate to comeplete dryness in the Labconco Centruvap cold trap concentrator. Submit to derivatization . Pooling (CSH platform only) Transfer multiple 350 µL aliquots of pooled samples to 1.5 mL Eppendorf tubes, one aliquot for every 10 samples in the study. If there is still pool remaining, prepare additional aliquots for backup. Evaporate to complete dryness in the Labconco Centrivap cold trap concentrator. Store all tubes at -20°C until ready for analysis. Quality assurance For every 10 samples, extract a method blank (20 µL of H2O) and a sample control (20 µL human Bioreclamation or analogous species plasma) in addition to samples. For large studies (>100 samples), for every 100 samples a NIST plasma extract should be prepared in the same manner as positive controls. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules. Collect residual plasma/serum samples in specifically designed red ‘biohazard’ waste bags. Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.

Sampleprep ID:

SP001927

Sampleprep Summary:

Sample preparation of blood plasma or serum samples for CSH, HILIC and GC analysis Purpose: This SOP describes sample extraction and preparation of blood plasma or serum for lipid profiling on the CSH, and HILIC platform by liquid chromatography/ mass spectrometry (LC-MS) as well as primary metabolomics platform on GC/MS. This method is to be used when there is low sample volume for separate extractions, and when more than one platform is to be used in a project. References: Matyash V, Liebisch G, Kurzchalia TV, Shevchenko A and Schwudke D (2008) Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J Lip Res 2008, 49: 1137-1146 Starting material: Plasma/serum: 20 µL sample volume or aliquot Equipment: Centrifuge Eppendorf 5415 D Calibrated pipettes 20-200µL and 100-1000µL Multi-Tube Vortexer (VWR VX-2500) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Chemicals: Product Manufacturer & Part Number Eppendorf tubes 1.5 mL, uncolored Eppendorf 022363204 Eppendorf tubes 2 mL, uncolored Eppendorf 022363352 Crushed ice UC Davis Water, LC/MS Grade Fisher Optima W6-4 MTBE, HPLC Grade Acros Organics 389050010 Methanol, LC/MS Grade Fisher A456-4 Bioreclamation human plasma (disodium EDTA) Bioreclamation HMPLEDTA Acetonitrile, HPLC Grade Fisher Optima A955-4 Iso-Propanol, HPLC Grade Fisher A461-4 Sample Preparation: Preparation of extraction solvent Combine 120 mL of chilled MeOH/QC mix with 400 mL of chilled MTBE/Cholesterol Ester 22:1 in a clean 500 mL stock bottle. Mix thoroughly by swirling or stir plate and store at -20°C until use. *See SOP “QC mix for LC-MS lipid analysis” for preparation of MeOH/QC mix and MTBE/Cholesterol Ester 22:1. Preparation of Clean Up solvent For 1 L of extraction solvent, combine 375 mL of acetonitrile, 375 mL of isopropanol, and 250 mL water in a 1 L bottle conditioned with the aforementioned chemicals. If a different total volume of extraction solvent is needed, simply mix acetonitrile, isopropanol, and water in volumes in proportion 3:3:2. Purge the extraction solution mix for 5 min with nitrogen with small bubbles. Make sure that the nitrogen line is flushed out of air before using it for degassing the extraction solvent solution. Store at -20°C until use. Note: if solvent freezes, sonicate until thawed and mix before use. Extraction Thaw raw samples/controls at room temperature (or in the refrigerator at 4˚C) and either invert the tube or vortex 10 sec at low speed to homogenize. Aliquot 20 μL of plasma sample into a 1.5 mL Eppendorf tube. Keep all samples on ice. Add 975 µL ice-cold 3:10 (v/v) MeOH/MTBE + QC mix/CE 22:1 extraction solvent mixture to each aliquot, keeping the extraction solvent on ice during the procedure. Vortex samples for 10 seconds, then shake for 5 minutes at 4°C on the orbital mixer. Add 188 µL room temperature LC/MS grade water to each tube. Vortex tubes for 20 seconds and then centrifuge for 2 min at 14,000 rcf. Transfer the upper organic phase to two separate tubes (350 µL/each tube) for lipidomics analysis. Transfer 75 µL of the remaining organic phase to a 2, 15, or 50 mL tube for pools, depending on number of samples in the study. Transfer the bottom aqueous phase to two separate tubes (110 µL/each tube) for HILIC/GC-TOF analysis. Dry down one tube from each phase by centrivap, keeping the undried tubes as backups. Store all tubes at -20˚C until ready for analysis. Clean up step for GC only (and pooling) Resuspend the dried aliquot with 500 μL 3:3:2 (v/v/v) ACN:IPA:H2O (degassed as given above) and vortex for about 10 sec. Centrifuge for 2 min at 14000 rcf. Remove 450 uL supernatant to a clean 1.5 mL eppendorf tube. Tranfering remainder to a 2, 15, 50 mL Tube, dependent on number of samples. Aliquot out 1.9 mL uL of supernatant to new 2ml eppendorf tubes. Centrifuge for 2 min at 14000 rcf Aliquot out 4x450 uL of supernatant into clean 1.5 mL Eppendorf tubes. Evaporate to comeplete dryness in the Labconco Centruvap cold trap concentrator. Submit to derivatization . Pooling (CSH platform only) Transfer multiple 350 µL aliquots of pooled samples to 1.5 mL Eppendorf tubes, one aliquot for every 10 samples in the study. If there is still pool remaining, prepare additional aliquots for backup. Evaporate to complete dryness in the Labconco Centrivap cold trap concentrator. Store all tubes at -20°C until ready for analysis. Quality assurance For every 10 samples, extract a method blank (20 µL of H2O) and a sample control (20 µL human Bioreclamation or analogous species plasma) in addition to samples. For large studies (>100 samples), for every 100 samples a NIST plasma extract should be prepared in the same manner as positive controls. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules. Collect residual plasma/serum samples in specifically designed red ‘biohazard’ waste bags. Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.