Summary of study ST000865

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 PR000602. The data can be accessed directly via it's Project DOI: 10.21228/M8VH5Q This work is supported by NIH grant, U2C- DK119886.

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Study IDST000865
Study TitleIdentification of Race-Associated Metabolite Biomarkers for Hepatocellular Carcinoma
Study SummaryIntroduction: Metabolomics provides simultaneous assessment of a broad range of metabolites that can potentially serve as indicators of the overall physiology status as well as the response to host and environmental stimuli. It has been broadly used for biomarker discovery and characterization of complex diseases such as cancer. The evaluation of the changes in the levels of metabolites in samples stratified by race could lead to the identification of more reliable biomarkers than those obtained through whole-population-based approaches. In this study, we used plasma samples collected from patients recruited at MedStar Georgetown University Hospital to investigate metabolites that may be associated with hepatocellular carcinoma (HCC) in a race-specific manner. Methods: Plasma samples were protein depleted using a solution composed of acetonitrile:isopropanol:water (3:3:2) containing a mixture of isotope-labeled internal standards. The extracted metabolites were trimethylsilyl derivatized prior to analysis by GC-MS. A quality control (QC) sample derived by pooling plasma from multiple subjects was run in between samples to assess reproducibility. A mixture of fatty acids methyl esters (FAMEs) and alkane standards was run for retention index calibration. The mixture of isotope-labeled internal standards was used to evaluate the reproducibility of the GC-MS data across multiple runs. Preliminary Data: Plasma samples collected from 40 HCC cases and 44 patients with liver cirrhosis were analyzed. The cirrhotic controls were frequency matched with the HCC cases by demographic variables. The participants included 19 African Americans (AA) and 50 European Americans (EA). The analysis targeted 46 metabolites for quantitative analysis by Agilent GC-qMS in selected ion monitoring (SIM) mode. The data were pre-processed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) for peak detection, deconvolution, and identification. The resulting peaks were aligned using Mass Profiler Professional (MPP) from Agilent Technologies. A LASSO regression model was applied to select metabolites with significant changes in HCC vs. cirrhosis in three groups: (1) AA and EA combined; (2) AA only; and (3) EA only. Also, metabolites that distinguish HCC cases from cirrhosis in the three groups were selected by considering only those subjects with Hepatitis C virus (HCV) infection. The performances of the metabolites selected by LASSO in each group were evaluated through a leave-one-out cross-validation. We identified race-specific metabolites that differentiated HCC cases from cirrhotic controls, yielding better area under the ROC curve compared to alpha-fetoprotein (AFP) - the serological marker widely used for the diagnosis of HCC. Novel Aspect: We identified race-associated metabolites that are significantly altered in HCC vs. cirrhosis, suggesting the potential role of race in HCC.
Institute
Georgetown University
DepartmentOncology
LaboratoryRessom Lab (PI: Habtom W. Ressom, email address hwr@georgetown.edu)
Last NameRessom
First NameHabtom
Address4000 Reservoir Rd. NW, Room 175, Washington, DC 20007
Emailhwr@georgetown.edu
Phone2026872283
Submit Date2017-08-14
Raw Data AvailableYes
Raw Data File Type(s).d
Analysis Type DetailGC-MS
Release Date2018-03-02
Release Version1
Habtom Ressom Habtom Ressom
https://dx.doi.org/10.21228/M8VH5Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000602
Project DOI:doi: 10.21228/M8VH5Q
Project Title:Biomarkers discovery for Hepatocellular Carcinoma (HCC)
Project Summary:Hepatocellular Carcinoma (HCC) is the most common type of liver cancer. Current diagnosis of HCC relies on the measurement of the level of the serum biomarker, α-fetoprotein (AFP). However, the sensitivity and specificity of AFP are not sufficient for diagnosis of HCC as elevated AFP levels may be seen in patients with cirrhosis or chronic hepatitis too. Therefore, reliable serological biomarkers for early detection of HCC in high-risk population of cirrhotic patients are yet to be found and validated. Metabolomics provides simultaneous assessment of a broad range of metabolites that can potentially serve as indicators of the overall physiology status as well as the response to host and environmental stimuli. It has been broadly used for biomarker discovery and characterization of complex diseases such as cancer.
Institute:Georgetown University
Department:Oncology
Laboratory:Ressom Lab (PI: Habtom W. Ressom, email address hwr@georgetown.edu)
Last Name:Di Poto
First Name:Cristina
Address:3970 Reservoir Rd., NW, Research Bldg, Room W325, Washington, DC, 20007, USA
Email:cd329@georgetown.edu
Phone:2026872926

Subject:

Subject ID:SU000892
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Patient group RACE
SA04779444_Sample_112_082914CIRR AA
SA04779546_Sample_114_082914CIRR AA
SA04779628_Sample_57_082614CIRR AA
SA04779741_Sample_66_082614CIRR AA
SA04779852_Sample_75_082614CIRR AA
SA04779932_Sample_102_082914CIRR AA
SA04780034_Sample_104_082914CIRR AA
SA04780156_Sample_79_082614CIRR AA
SA04780226_Sample_98_082914CIRR Asian
SA04780354_Sample_77_082614CIRR EA
SA04780424_Sample_96_082914CIRR EA
SA04780520_Sample_94_082914CIRR EA
SA04780618_Sample_92_082914CIRR EA
SA04780724_Sample_53_082614CIRR EA
SA04780826_Sample_55_082614CIRR EA
SA04780914_Sample_45_082614CIRR EA
SA04781064_Sample_85_082614CIRR EA
SA04781118_Sample_49_082614CIRR EA
SA04781216_Sample_90_082914CIRR EA
SA04781360_Sample_81_082614CIRR EA
SA04781462_Sample_83_082614CIRR EA
SA04781528_Sample_100_082914CIRR EA
SA04781647_Sample_72_082614CIRR EA
SA04781760_Sample_124_082914CIRR EA
SA04781856_Sample_122_082914CIRR EA
SA04781954_Sample_120_082914CIRR EA
SA04782032_Sample_59_082614CIRR EA
SA04782162_Sample_126_082914CIRR EA
SA04782220_Sample_51_082614CIRR EA
SA04782366_Sample_130_082914CIRR EA
SA04782452_Sample_118_082914CIRR EA
SA04782537_Sample_64_082614CIRR EA
SA04782645_Sample_70_082614CIRR EA
SA04782736_Sample_106_082914CIRR EA
SA04782816_Sample_47_082614CIRR EA
SA04782938_Sample_108_082914CIRR EA
SA04783043_Sample_68_082614CIRR EA
SA04783150_Sample_116_082914CIRR EA
SA04783242_Sample_110_082914CIRR EA
SA04783350_Sample_73_082614CIRR EA
SA04783414_Sample_88_082914CIRR Hisp
SA04783565_Sample_86_082614CIRR Hisp
SA04783634_Sample_61_082614CIRR Other
SA04783764_Sample_128_082914CIRR Other
SA04783846_Sample_71_082614HCC AA
SA04783941_Sample_109_082914HCC AA
SA04784017_Sample_48_082614HCC AA
SA04784135_Sample_62_082614HCC AA
SA04784219_Sample_50_082614HCC AA
SA04784329_Sample_58_082614HCC AA
SA04784417_Sample_91_082914HCC AA
SA04784553_Sample_119_082914HCC AA
SA04784635_Sample_105_082914HCC AA
SA04784763_Sample_84_082614HCC AA
SA04784815_Sample_46_082614HCC AA
SA04784959_Sample_80_082614HCC Asian
SA04785044_Sample_69_082614HCC Asian
SA04785123_Sample_95_082914HCC Asian
SA04785265_Sample_129_082914HCC Asian
SA04785325_Sample_54_082614HCC Asian
SA04785437_Sample_107_082914HCC EA
SA04785533_Sample_103_082914HCC EA
SA04785629_Sample_101_082914HCC EA
SA04785743_Sample_111_082914HCC EA
SA04785838_Sample_65_082614HCC EA
SA04785951_Sample_117_082914HCC EA
SA04786047_Sample_115_082914HCC EA
SA04786145_Sample_113_082914HCC EA
SA04786251_Sample_74_082614HCC EA
SA04786342_Sample_67_082614HCC EA
SA04786466_Sample_87_082614HCC EA
SA04786519_Sample_93_082914HCC EA
SA04786655_Sample_78_082614HCC EA
SA04786723_Sample_52_082614HCC EA
SA04786827_Sample_99_082914HCC EA
SA04786961_Sample_82_082614HCC EA
SA04787025_Sample_97_082914HCC EA
SA04787115_Sample_89_082914HCC EA
SA04787253_Sample_76_082614HCC EA
SA04787361_Sample_125_082914HCC Hisp
SA04787433_Sample_60_082614HCC Hisp
SA04787555_Sample_121_082914HCC Other
SA04787659_Sample_123_082914HCC Other
SA04787763_Sample_127_082914HCC Other
SA04788022_QC_CIRR_B3_02_082914Pool CIRR -
SA04788168_QC_CIRR_B3_07_082914Pool CIRR -
SA04788213_QC_CIRR_B3_01_082914Pool CIRR -
SA04788322_QC_CIRR_B2_02_082614Pool CIRR -
SA04788440_QC_CIRR_B2_04_082614Pool CIRR -
SA04788513_QC_CIRR_B2_01_082614Pool CIRR -
SA04788640_QC_CIRR_B3_04_082914Pool CIRR -
SA04788731_QC_CIRR_B3_03_082914Pool CIRR -
SA04788868_QC_CIRR_B2_07_082614Pool CIRR -
SA04788958_QC_CIRR_B2_06_082614Pool CIRR -
SA04789049_QC_CIRR_B2_05_082614Pool CIRR -
SA04789131_QC_CIRR_B2_03_082614Pool CIRR -
SA04789249_QC_CIRR_B3_05_082914Pool CIRR -
SA04789358_QC_CIRR_B3_06_082914Pool CIRR -
SA04789467_QC_HCC_B2_07_082614Pool HCC -
SA04789567_QC_HCC_B3_07_082914Pool HCC -
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Collection:

Collection ID:CO000886
Collection Summary:Blood collection Adult patients were recruited from the hepatology clinic at MedStar Georgetown University Hospital (MGUH).All participants provided informed consent to the study approved by the Institutional Review Board (IRB) at Georgetown University. The patients were diagnosed to have liver cirrhosis on the basis of established clinical, laboratory and/or imaging criteria. Cases were diagnosed to have HCC based on well-established diagnostic imaging criteria and/or histology. Clinical stages for HCC cases were determined based on the tumor-node-metastasis (TNM) staging system. Controls were required to be HCC free for at least 6 months from the time of study entry. Race information was collected from patients’ self-report. Through peripheral venipuncture, single blood sample was drawn into 10 mL BD Vacutainer sterile vacuum tube in the presence of EDTA anticoagulant.
Collection Protocol ID:1_Collection
Sample Type:Blood

Treatment:

Treatment ID:TR000906
Treatment Summary:Blood treatment The blood was immediately centrifuged at 1000g for 10 minutes at room temperature. The plasma supernatant was carefully collected and centrifuged at 2500g for 10 minutes at room temperature. After aliquoting, plasma was kept frozen at −80°C until use.
Treatment Protocol ID:2_Treatment

Sample Preparation:

Sampleprep ID:SP000899
Sampleprep Summary:Metabolite extraction Plasma metabolites were extracted by adding 1mL of a working solution composed of acetonitrile, isopropanol and water (3:3:2) containing isotope-labeled internal standards at a concentration of 1.25 μg/mL (Tyrosine-d2, L-glutamic-2,3,3,4,4-d5 acid, L-alanine-2,3,3,3-d4, L-phenyl-d5-alanine-2,3,3,-d3, Glycine-d5, Myristic acid d27) to 30μL of plasma in order to evaluate the quality of metabolites extraction. After vortexing, samples were centrifuged at 14,500g for 15 minutes at room temperature. Each supernatant was then concentrated to dryness in speedvac. The dried samples were kept at -20°C until derivatization prior to analysis by GC-MS. 20μL of a 20mg/mL methoxyamine hydrochloride in pyridine was added to the dried extracts, vortexed and incubated at 30°C for 90 minutes. After returning the samples at room temperature, 80μL of MSTFA was added, vortexed and incubated at 30°C for 30 minutes. Samples were then centrifuged at 14,500rpm for 15 minutes, and 60μL of the supernatant was transferred into 250μL clear glass autosampler vials.
Sampleprep Protocol ID:3_SamplePrep

Combined analysis:

Analysis ID AN001390
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Agilent DB_5MS + DG
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975C
Ion Mode POSITIVE
Units RAW intensity

Chromatography:

Chromatography ID:CH000974
Instrument Name:Agilent 7890A
Column Name:Agilent DB_5MS + DG
Chromatography Type:GC

MS:

MS ID:MS001282
Analysis ID:AN001390
Instrument Name:Agilent 5975C
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
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