Summary of study ST001259

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 PR000845. The data can be accessed directly via it's Project DOI: 10.21228/M8G10K This work is supported by NIH grant, U2C- DK119886.

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Study IDST001259
Study TitleTargeted Metabolomic Analysis in Patients with Wilson Disease Reveals Dysregulated Choline, Methionine and Aromatic Amino Acid Metabolism: Implications for Hepatic and Neurological Phenotypes
Study TypeCross-sectional
Study SummaryThis study is comparing the plasma metabolomics profile of patients with the genetic disorder, Wilson disease, compared to healthy subjects matched by age, sex, and BMI. Wilson disease (WD) is a genetic copper overload condition characterized by hepatic and neuropsychiatric symptoms with a pathogenesis not well-understood. Choline is essential for lipid metabolism and the methionine cycle; a dysregulated methionine cycle is reported in animal models of WD, though not verified in humans. Defects in neurotransmitters, acetylcholine, and biogenic amines are reported in WD patients with neurological presentations. Precursors of these neuromodulators include choline, phenylalanine, tyrosine, and histidine. Less is known about the circulating levels of these precursors in WD. We aimed to study choline, methionine, aromatic amino acids, and phospholipids in serum profiles of WD subjects compared to healthy subjects (HC).
Institute
University of California, Davis
Last NameMedici
First NameValentina
Address4150 V St, Sacramento CA 95817
Emailvmedici@ucdavis.edu
Phone9167342011
Submit Date2019-10-01
Total Subjects76
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2020-04-02
Release Version1
Valentina Medici Valentina Medici
https://dx.doi.org/10.21228/M8G10K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000845
Project DOI:doi: 10.21228/M8G10K
Project Title:Targeted Metabolomic Analysis in Patients with Wilson Disease Reveals Dysregulated Choline, Methionine and Aromatic Amino Acid Metabolism: Implications for Hepatic and Neurological Phenotypes.
Project Summary:This study is comparing the plasma metabolomics profile of patients with the genetic disorder, Wilson disease, compared to healthy subjects matched by age, sex, and BMI. Wilson disease (WD) is a genetic copper overload condition characterized by hepatic and neuropsychiatric symptoms with a pathogenesis not well-understood. Choline is essential for lipid metabolism and the methionine cycle; a dysregulated methionine cycle is reported in animal models of WD, though not verified in humans. Defects in neurotransmitters, acetylcholine, and biogenic amines are reported in WD patients with neurological presentations. Precursors of these neuromodulators include choline, phenylalanine, tyrosine, and histidine. Less is known about the circulating levels of these precursors in WD. We aimed to study choline, methionine, aromatic amino acids, and phospholipids in serum profiles of WD subjects compared to healthy subjects (HC).
Institute:University of California, Davis
Last Name:Medici
First Name:Valentina
Address:4150 V St, Sacramento CA 95817
Email:vmedici@ucdavis.edu
Phone:9167342011

Subject:

Subject ID:SU001327
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Group Gender
SA091415Sample011Healthy Female
SA091416Sample010Healthy Female
SA091417Sample013Healthy Female
SA091418Sample014Healthy Female
SA091419Sample015Healthy Female
SA091420Sample009Healthy Female
SA091421Sample012Healthy Female
SA091422Sample008Healthy Female
SA091423Sample006Healthy Female
SA091424Sample007Healthy Female
SA091425Sample002Healthy Male
SA091426Sample001Healthy Male
SA091427Sample003Healthy Male
SA091428Sample004Healthy Male
SA091429Sample005Healthy Male
SA091430Sample064Wilson disease Female
SA091431Sample067Wilson disease Female
SA091432Sample041Wilson disease Female
SA091433Sample036Wilson disease Female
SA091434Sample047Wilson disease Female
SA091435Sample037Wilson disease Female
SA091436Sample040Wilson disease Female
SA091437Sample060Wilson disease Female
SA091438Sample054Wilson disease Female
SA091439Sample056Wilson disease Female
SA091440Sample035Wilson disease Female
SA091441Sample062Wilson disease Female
SA091442Sample052Wilson disease Female
SA091443Sample050Wilson disease Female
SA091444Sample051Wilson disease Female
SA091445Sample049Wilson disease Female
SA091446Sample029Wilson disease Female
SA091447Sample020Wilson disease Female
SA091448Sample019Wilson disease Female
SA091449Sample026Wilson disease Female
SA091450Sample072Wilson disease Female
SA091451Sample021Wilson disease Female
SA091452Sample027Wilson disease Female
SA091453Sample028Wilson disease Female
SA091454Sample032Wilson disease Female
SA091455Sample033Wilson disease Female
SA091456Sample017Wilson disease Female
SA091457Sample076Wilson disease Female
SA091458Sample030Wilson disease Female
SA091459Sample059Wilson disease Female
SA091460Sample075Wilson disease Male
SA091461Sample061Wilson disease Male
SA091462Sample074Wilson disease Male
SA091463Sample065Wilson disease Male
SA091464Sample069Wilson disease Male
SA091465Sample071Wilson disease Male
SA091466Sample068Wilson disease Male
SA091467Sample066Wilson disease Male
SA091468Sample063Wilson disease Male
SA091469Sample070Wilson disease Male
SA091470Sample073Wilson disease Male
SA091471Sample039Wilson disease Male
SA091472Sample025Wilson disease Male
SA091473Sample031Wilson disease Male
SA091474Sample034Wilson disease Male
SA091475Sample024Wilson disease Male
SA091476Sample023Wilson disease Male
SA091477Sample016Wilson disease Male
SA091478Sample018Wilson disease Male
SA091479Sample022Wilson disease Male
SA091480Sample038Wilson disease Male
SA091481Sample042Wilson disease Male
SA091482Sample053Wilson disease Male
SA091483Sample055Wilson disease Male
SA091484Sample057Wilson disease Male
SA091485Sample048Wilson disease Male
SA091486Sample046Wilson disease Male
SA091487Sample043Wilson disease Male
SA091488Sample044Wilson disease Male
SA091489Sample045Wilson disease Male
SA091490Sample058Wilson disease Male
Showing results 1 to 76 of 76

Collection:

Collection ID:CO001321
Collection Summary:Plasma samples from patients with WD and healthy subjects were obtained from the Institute of Neurology and Psychiatry in Warsaw. Subjects fasted for 8 hours prior to sampling. Plasma samples were de-identified, shipped to the University of California, Davis and stored at -80°C until further analysis.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001342
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001335
Sampleprep Summary:All samples were removed from -80°C and allowed to thaw on ice. Of the 100-250 uL of plasma shipped to the facility for analysis, 30 µL of plasma was pipetted into a new 1.5 mL Eppendorf tube. 1 mL of 3:3:2 acetonitrile:isopropanol:water was added to each sample. Samples were vortexed for 10 seconds using a MiniVortexer. Samples were then shaken on an Orbital Mixing Chilling/Heating Plate for 5 minutes at 4°C. Samples were centrifuged for 2 minutes at 14,000 rcf used the centrifuge Eppendorf 5415 D. Two 475 µL aliquots were removed from the supernatant. Both samples were dried to complete using Labconco Centrivap cold trap. 500 µL of 50:50 acetonitrile was added to each aliquot of all samples. Samples were vortexed for 10 seconds using the MiniVortexer. Samples were centrifuged for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415 D. 475 µL of supernatant was removed and evaporated to dryness using the Labconco Centrivap cold trap. One sample is submitted to derivitization, the other sample is saved for LC-MS analysis.
Extraction Method:Extraction is carried out using a bi-phasic solvent system of cold methanol, methyl tert-butyl ether (MTBE), and water. In more detail, cold methanol (225 µL is added to a 5mg tissue sample aliquot, which is placed into a 1.5 mL Eppendorf tube. Then, 750 µL of cold MTBE is added, followed by vortexing for 10 s. and shaking for 6 min. at 4ºC. Phase separation is induced by adding 188 µL of mass spec-grade water. After vortexing for 20 s. the sample is centrifuged at 14,000 rpm for 2 min. The upper organic phase is collected in two 300 µL aliquots for lipid analysis polar layer is collected in two 125 µL aliquots for HILIC analysis. One is stored at -20ºC as a backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are resuspended in acetonitrile.
Sample Derivatization:None

Combined analysis:

Analysis ID AN002089
Analysis type MS
Chromatography type HILIC
Chromatography system Waters Acquity
Column Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name ABI Sciex 6600 TripleTOF
Ion Mode POSITIVE
Units normalized peak height

Chromatography:

Chromatography ID:CH001526
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS001940
Analysis ID:AN002089
Instrument Name:ABI Sciex 6600 TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:None
Ion Mode:POSITIVE
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