Summary of Study ST000977
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
| Study ID | ST000977 |
| Study Title | Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) |
| Study Type | Populations comparison |
| 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 | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2018-05-24 |
| Num Groups | 8 |
| Total Subjects | 40 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-07-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000667 |
| Project DOI: | doi: 10.21228/M8FX07 |
| Project Title: | Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) |
| Project 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: | GI and Hepatology Division Academic Office - 4150 V Street - PSSB Suite 3500 - 95817 Sacramento CA |
| Email: | vmedici@ucdavis.edu |
| Phone: | (916) 734 3751 |
Subject:
| Subject ID: | SU001016 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 23-73 |
| Gender: | Male and female |
| Human Race: | Hispanic and Caucasian |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Ethnicity | Gender | Group |
|---|---|---|---|---|
| SA059409 | RB14 E05 | Caucasian | Female | Healthy Control |
| SA059410 | RB14 C06 | Caucasian | Female | Healthy Control |
| SA059411 | RB14 E07 | Caucasian | Female | Healthy Control |
| SA059412 | RB14 G05 | Caucasian | Female | Healthy Control |
| SA059413 | RB14 D08 | Caucasian | Female | NAFLD |
| SA059414 | RB14 D07 | Caucasian | Female | NAFLD |
| SA059415 | RB14 G06 | Caucasian | Female | NAFLD |
| SA059416 | RB14 B08 | Caucasian | Female | NAFLD |
| SA059417 | RB14 A04 | Caucasian | Male | Healthy Control |
| SA059418 | RB14 G03 | Caucasian | Male | Healthy Control |
| SA059419 | RB14 E04 | Caucasian | Male | Healthy Control |
| SA059420 | RB14 C05 | Caucasian | Male | Healthy Control |
| SA059421 | RB14 F03 | Caucasian | Male | NAFLD |
| SA059422 | RB14 A07 | Caucasian | Male | NAFLD |
| SA059423 | RB14 D05 | Caucasian | Male | NAFLD |
| SA059424 | RB14 F08 | Caucasian | Male | NAFLD |
| SA059425 | RB14 C08 | Hispanic | Female | Healthy Control |
| SA059426 | RB14 A06 | Hispanic | Female | Healthy Control |
| SA059427 | RB14 A05 | Hispanic | Female | Healthy Control |
| SA059428 | RB14 B07 | Hispanic | Female | Healthy Control |
| SA059429 | RB14 G08 | Hispanic | Female | Healthy Control |
| SA059430 | RB14 A09 | Hispanic | Female | Healthy Control |
| SA059431 | RB14 F05 | Hispanic | Female | NAFLD |
| SA059432 | RB14 B04 | Hispanic | Female | NAFLD |
| SA059433 | RB14 D06 | Hispanic | Female | NAFLD |
| SA059434 | RB14 H05 | Hispanic | Female | NAFLD |
| SA059435 | RB14 H08 | Hispanic | Female | NAFLD |
| SA059436 | RB14 H07 | Hispanic | Female | NAFLD |
| SA059437 | RB14 H03 | Hispanic | Female | NAFLD |
| SA059438 | RB14 H06 | Hispanic | Male | Healthy Control |
| SA059439 | RB14 E08 | Hispanic | Male | Healthy Control |
| SA059440 | RB14 C04 | Hispanic | Male | Healthy Control |
| SA059441 | RB14 C07 | Hispanic | Male | Healthy Control |
| SA059442 | RB14 E06 | Hispanic | Male | Healthy Control |
| SA059443 | RB14 F06 | Hispanic | Male | Healthy Control |
| SA059444 | RB14 A08 | Hispanic | Male | Healthy Control |
| SA059445 | RB14 G04 | Hispanic | Male | Healthy Control |
| SA059446 | RB14 F04 | Hispanic | Male | NAFLD |
| SA059447 | RB14 D04 | Hispanic | Male | NAFLD |
| SA059448 | RB14 B05 | Hispanic | Male | NAFLD |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO001010 |
| Collection Summary: | Blood was collected as a part of a routine/pre-operation check up, not more than 2 weeks prior to operation day (bariatric surgery) for the NAFLD group and among normal BMI healthy volunteers for the control group. All volunteers were fasted 10-12 hours before collection. |
| Sample Type: | Blood (plasma) |
| Collection Method: | Venipuncture |
| Storage Conditions: | -80℃ |
| Collection Vials: | EDTA Vacutainer tubes |
| Collection Tube Temp: | Ambient |
| Additives: | EDTA |
Treatment:
| Treatment ID: | TR001030 |
| Treatment Summary: | Subjects were divided into two groups either: Healthy control or Nonalcoholic fatty liver disease (NAFLD) |
Sample Preparation:
| Sampleprep ID: | SP001023 |
| Sampleprep Summary: | After sample randomization, 50 µl plasma aliquots were enriched with deuterated surrogates in 10 µL methanol (Table S1 from Agrawal, K., L.A. Hassoun, N. Foolad, T.L. Pedersen, R.K. Sivamani, J.W. Newman. 2017. Sweat lipid mediator profiling: a non-invasive approach for cutaneous research. J. Lipid Res. 58:188–195 [EPub: Nov 7, 2016]. doi: 10.1194/jlr.M071738) and 5 μl of BHT/EDTA in 1:1 methanol/water (v/v). A total of 200 μl 1-cyclohexyl uredio, 3-dodecanoic acid / 1-phenyl ureido, 3-hexanoic acid (CUDA / PUHA) in 1:1 methanol:acetonitrile was added. Protein precipitate and debris were removed by centrifugation for 10 min at 4,500 RCF. The supernatant was filtered by centrifugation through 0.2 µm PVDF membranes (Agilent Technologies, Santa Clara, CA, USA) at 500 RCF for 5 min. |
| Sampleprep Protocol Filename: | V_Medici_Plasma_Oxy-EC_analysis_protocol.pdf |
Combined analysis:
| Analysis ID | AN001598 | AN001599 | AN001600 | AN001601 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 6500 QTrap | ABI Sciex 6500 QTrap | ABI Sciex 6500 QTrap | ABI Sciex 6500 QTrap |
| Ion Mode | NEGATIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | Concentration (pmol/gram) | Concentration (pmol/gram) | % | % |
Chromatography:
| Chromatography ID: | CH001123 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 60 °C |
| Flow Gradient: | See protocol/methods file |
| Flow Rate: | 0.25 mL/min |
| Internal Standard: | See protocol/methods file |
| Retention Time: | See protocol/methods file |
| Sample Injection: | 5 µL |
| Solvent A: | 100% water; 0.1% acetic acid |
| Solvent B: | 90% acetonitrile/ 10% isopropanol |
| Analytical Time: | 20 min |
| Weak Wash Solvent Name: | 20% methanol, 10% isopropanol |
| Weak Wash Volume: | 600 µL |
| Strong Wash Solvent Name: | 50:50 Acetonitrile:Methanol |
| Strong Wash Volume: | 600 µL |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001476 |
| Analysis ID: | AN001598 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Concentration (pmol/gram) |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001477 |
| Analysis ID: | AN001599 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Concentration (pmol/gram) |
| Ion Mode: | POSITIVE |
| MS ID: | MS001478 |
| Analysis ID: | AN001600 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | % |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001479 |
| Analysis ID: | AN001601 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | % |
| Ion Mode: | POSITIVE |
