Summary of study ST000284

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 PR000226. The data can be accessed directly via it's Project DOI: 10.21228/M8FG61 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000284
Study TitleColorectal Cancer Detection Using Targeted Serum Metabolic Profiling
Study SummaryColorectal cancer (CRC) is one of the most prevalent and deadly cancers in the world. Despite an expanding knowledge of its molecular pathogenesis during the past two decades, robust biomarkers to enable screening, surveillance, and therapy monitoring of CRC are still lacking. In this study, we present a targeted liquid chromatography-tandem mass spectrometry-based metabolic profiling approach for identifying biomarker candidates that could enable highly sensitive and specific CRC detection using human serum samples. In this targeted approach, 158 metabolites from 25 metabolic pathways of potential significance were monitored in 234 serum samples from three groups of patients (66 CRC patients, 76 polyp patients, and 92 healthy controls). Partial least squares-discriminant analysis (PLS-DA) models were established, which proved to be powerful for distinguishing CRC patients from both healthy controls and polyp patients. Receiver operating characteristic curves generated based on these PLS-DA models showed high sensitivities (0.96 and 0.89, respectively, for differentiating CRC patients from healthy controls or polyp patients); good specificities (0.80 and 0.88), and excellent areas under the curve (0.93 and 0.95) were also obtained. Monte Carlo cross validation (MCCV) was also applied, demonstrating the robust diagnostic power of this metabolic profiling approach.
Institute
University of Washington
DepartmentAnesthesiology and Pain Medicine
LaboratoryNorthwest Metabolomics Research Center
Last NameGu
First NameHaiwei
Address850 Republican St.
Emailhaiwei@uw.edu
Phone7654919481
Submit Date2015-12-15
Num Groups3
Total Subjects234
Num Males118
Num Females116
PublicationsColorectal Cancer Detection Using Targeted Serum Metabolic Profiling, J. Proteome. Res., 2014, 13, 4120-4130
Analysis Type DetailLC-MS
Release Date2015-12-16
Release Version1
Haiwei Gu Haiwei Gu
https://dx.doi.org/10.21228/M8FG61
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000226
Project DOI:doi: 10.21228/M8FG61
Project Title:Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling
Project Summary:Colorectal cancer (CRC) is one of the most prevalent and deadly cancers in the world. Despite an expanding knowledge of its molecular pathogenesis during the past two decades, robust biomarkers to enable screening, surveillance, and therapy monitoring of CRC are still lacking. In this study, we present a targeted liquid chromatography-tandem mass spectrometry-based metabolic profiling approach for identifying biomarker candidates that could enable highly sensitive and specific CRC detection using human serum samples. In this targeted approach, 158 metabolites from 25 metabolic pathways of potential significance were monitored in 234 serum samples from three groups of patients (66 CRC patients, 76 polyp patients, and 92 healthy controls). Partial least squares-discriminant analysis (PLS-DA) models were established, which proved to be powerful for distinguishing CRC patients from both healthy controls and polyp patients. Receiver operating characteristic curves generated based on these PLS-DA models showed high sensitivities (0.96 and 0.89, respectively, for differentiating CRC patients from healthy controls or polyp patients); good specificities (0.80 and 0.88), and excellent areas under the curve (0.93 and 0.95) were also obtained. Monte Carlo cross validation (MCCV) was also applied, demonstrating the robust diagnostic power of this metabolic profiling approach.
Institute:University of Washington
Department:Anesthesiology and Pain Medicine
Laboratory:Northwest Metabolomics Research Center
Last Name:Gu
First Name:Haiwei
Address:850 Republican St.
Email:haiwei@uw.edu
Phone:7654919481
Funding Source:AMRMC grant W81XWH-10-1- 0540, The China Scholarship Council is also gratefully acknowledged (Grant to L.D.).
Publications:Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling, J. Proteome. Res., 2014, 13, 4120-4130

Subject:

Subject ID:SU000304
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:18-88
Gender:Femal(116), Male(118)
Human Smoking Status:67 nonsmokers and 167 smokers
Human Alcohol Drug Use:14 no alcohol and 220 alcohol
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Patient group
SA012337575CRC
SA01233812CRC
SA01233953CRC
SA012340561CRC
SA012341312CRC
SA012342263CRC
SA012343289CRC
SA012344156CRC
SA012345187CRC
SA012346448CRC
SA012347562CRC
SA012348491CRC
SA012349276CRC
SA012350193CRC
SA012351214CRC
SA012352168CRC
SA01235334CRC
SA012354133CRC
SA012355250CRC
SA012356109CRC
SA012357200CRC
SA012358157CRC
SA012359132CRC
SA012360177CRC
SA01236177CRC
SA012362173CRC
SA012363279CRC
SA01236411CRC
SA012365281CRC
SA012366292CRC
SA012367284CRC
SA012368283CRC
SA012369447CRC
SA01237013CRC
SA012371202CRC
SA012372152CRC
SA012373115CRC
SA012374253CRC
SA012375277CRC
SA012376310CRC
SA012377304CRC
SA01237824CRC
SA012379457CRC
SA012380282CRC
SA012381257CRC
SA012382300CRC
SA012383285CRC
SA012384291CRC
SA012385295CRC
SA01238614CRC
SA0123875CRC
SA012388452CRC
SA012389454CRC
SA012390427CRC
SA01239120CRC
SA012392455CRC
SA012393278CRC
SA012394469CRC
SA01239549CRC
SA01239628CRC
SA012397122CRC
SA012398139CRC
SA012399162CRC
SA012400154CRC
SA01240145Healthy
SA012402483Healthy
SA01240379Healthy
SA01240440Healthy
SA01240576Healthy
SA012406466Healthy
SA01240798Healthy
SA01240863Healthy
SA012409433Healthy
SA012410437Healthy
SA012411485Healthy
SA012412482Healthy
SA01241387Healthy
SA012414205Healthy
SA012415141Healthy
SA012416244Healthy
SA012417406Healthy
SA012418163Healthy
SA012419213Healthy
SA01242093Healthy
SA012421118Healthy
SA01242257Healthy
SA012423120Healthy
SA012424119Healthy
SA012425179Healthy
SA012426442Healthy
SA012427294Healthy
SA012428409Healthy
SA012429108Healthy
SA01243046Healthy
SA01243178Healthy
SA012432272Healthy
SA012433288Healthy
SA0124346Healthy
SA012435159Healthy
SA012436216Healthy
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Collection:

Collection ID:CO000298
Collection Summary:Patient recruitment and sample collection protocols were University and Indiana University Boards. Informed according (both were evaluated, and blood samples from the overnight fasting and bowel polyp status were polyp patients (n = 76), and healthy controls (n = 92) biopsied tissue. Patients were age- and the gender/age group suggesting sample was allowed to clot for 45 min and then All samples were stored at -80C
Sample Type:Blood serum
Blood Serum Or Plasma:Serum

Treatment:

Treatment ID:TR000318
Treatment Summary:Patient recruitment and sample collection protocols were University and Indiana University Boards. Informed according (both were evaluated, and blood samples from the overnight fasting and bowel polyp status were polyp patients (n = 76), and healthy controls (n = 92) biopsied tissue. Patients were age- and the gender/age group suggesting sample was allowed to clot for 45 min and then All samples were stored at -80C

Sample Preparation:

Sampleprep ID:SP000312
Sampleprep Summary:Frozen samples were first thawed at room temperature (25 °C) and 50 uL of each serum sample was placed in a 2 Scientific). The initial step for extraction was performed vortexed centrifuged at 20 800g for 10 min, and the supernatant was Eppendorf vial. To the first vial containing methanol was added, and the metabolite the supernatant was collected in the same vial that supernatant. The resulting supernatants dried using a Vacufuge dried mM ammonium acetate in 40% water/60% acetonitrile 5.13 ?M L-tyrosine-13C2 and 22.5 Laboratory). each through 0.45 ?m PVDF filters (Phenomenex, Torrance, analysis. A pooled sample, which was a polyp patients, and as sample and was analyzed once every 10 patient

Combined analysis:

Analysis ID AN000452
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1260
Column SeQuant ZIC-cHILIC
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode UNSPECIFIED
Units cps

Chromatography:

Chromatography ID:CH000323
Chromatography Summary:The LC system was composed of two Agilent 1260 binary autosampler, and Agilent 1290 column valve (Agilent 10 ?L for analysis using negative ionization mode and 2 positive ionization mode. Both chromatographic hydrophilic interaction ZIC-cHILIC KGaA, to perform the separation, while the other column for the next injection. The flow temperature was kept the phase was composed of Solvents A (5 mM acetonitrile +0.2% acetic acetonitrile/ confirmed by spiking the with metabolites). However, some metabolites that could had similar m/z values (<1 Da) were acid and 3- samples not undergo any significant shift (each peak was of analysis), which proved the
Instrument Name:Agilent 1260
Column Name:SeQuant ZIC-cHILIC
Column Temperature:40oC
Flow Gradient:0-2 min: 90%B; 2-5 min: to 50%B; 5-9 min: 50%B
Flow Rate:0.3 mL/min
Injection Temperature:4oC
Sample Injection:2 uL for positive and 10 uL for negative
Solvent A:(5 mM ammonium acetate in 90% H2O/10% acetonitrile +0.2% acetic acid
Solvent B:5 mM ammonium acetate in 90% acetonitrile/ 10% H2O + 0.2% acetic acid
Analytical Time:18 min
Capillary Voltage:3.8kV
Chromatography Type:HILIC

MS:

MS ID:MS000393
Analysis ID:AN000452
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:UNSPECIFIED
Capillary Voltage:3.8kV
Ion Source Temperature:500oC
Reagent Gas:N2
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