Summary of Study ST003025

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 PR001876. The data can be accessed directly via it's Project DOI: 10.21228/M87426 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.

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Study IDST003025
Study TitleNMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma (part-Ⅴ)
Study SummaryMetabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. We conducted NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning, logistic regression and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, and were reflected in 16 serum and 10 urine metabolic signatures that were consistently identified by NMR and MS in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperformed clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and were effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613).
Institute
Shantou University Medical College
DepartmentRadiology Department, Second Affiliated Hospital
Last NameLin
First NameYan
AddressNo. 69, Dongxia North Road, Shantou, Guangdong, China
Email994809889@qq.com
Phone+86 18823992148
Submit Date2023-12-18
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2024-02-08
Release Version1
Yan Lin Yan Lin
https://dx.doi.org/10.21228/M87426
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001876
Project DOI:doi: 10.21228/M87426
Project Title:NMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma
Project Summary:Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. We conducted NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning, logistic regression and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, and were reflected in 16 serum and 10 urine metabolic signatures that were consistently identified by NMR and MS in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperformed clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and were effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613).
Institute:Radiology Department, Second Affiliated Hospital, Shantou University Medical College
Last Name:Lin
First Name:Yan
Address:No. 69, Dongxia North Road, Shantou, Guangdong, China
Email:994809889@qq.com
Phone:+86 18823992148

Subject:

Subject ID:SU003139
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Fator
SA32785913Early stage ESCC
SA32786011Early stage ESCC
SA32786114Early stage ESCC
SA32786216Early stage ESCC
SA3278631Early stage ESCC
SA32786410Early stage ESCC
SA32786515Early stage ESCC
SA32786612Early stage ESCC
SA3278674Early stage ESCC
SA3278689Early stage ESCC
SA3278692Early stage ESCC
SA3278705Early stage ESCC
SA3278713Early stage ESCC
SA3278728Early stage ESCC
SA3278737Early stage ESCC
SA3278746Early stage ESCC
SA32787528Normal tissue
SA32787627Normal tissue
SA32787729Normal tissue
SA32787832Normal tissue
SA32787926Normal tissue
SA32788031Normal tissue
SA32788130Normal tissue
SA32788217Normal tissue
SA32788320Normal tissue
SA32788419Normal tissue
SA32788518Normal tissue
SA32788621Normal tissue
SA32788722Normal tissue
SA32788824Normal tissue
SA32788923Normal tissue
SA32789025Normal tissue
Showing results 1 to 32 of 32

Collection:

Collection ID:CO003132
Collection Summary:Tissue samples, including tumor and normal areas 5 cm away, were obtained under the guidance of experienced pathologists without compromising the patients' pathology examinations. The collected tissue was rinsed with PBS to avoid contamination, excess moisture was removed, and it was rapidly frozen in liquid nitrogen to arrest enzymatic or chemical reactions. Samples were stored at −80°C until metabolite extraction.
Sample Type:Tissue

Treatment:

Treatment ID:TR003148
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP003145
Sampleprep Summary:GC-MS Analysis mainly detects seven short-chain and four medium-chain fatty acids. Qualitative and quantitative analysis was also performed using internal standard method. Metabolic extracts were analyzed using the SHIMADZU GC2030-QP2020 NX gas chromatography-mass spectrometer. The system employed an HP-FFAP capillary column, and a 1 μL aliquot of the analyte was injected in split mode (5:1). Helium was used as the carrier gas with a front inlet purge flow of 3 mL/min and a gas flow rate of 1 mL/min through the column. The initial temperature was maintained at 50 °C for 1 min, then increased to 150 °C at a rate of 50 °C/min for 1 min. Subsequently, it was raised to 170 °C at a rate of 10 °C/min for 1 min, further increased to 210 °C at a rate of 20 °C/min for 1 min, and finally raised to 240 °C at a rate of 40 °C/min for 1 min. The injection, transfer line, quad, and ion source temperatures were set at 220 °C, 240 °C, 150 °C, and 200 °C, respectively. The energy used was -70 eV in electron impact mode. Mass spectrometry data were acquired in Scan/SIM mode within the m/z range of 33-150 after a solvent delay of 3 min. Metabolite identification was performed using an in-house MS database. The pre-processing of MS raw data involved filtering individual metabolites to retain those with no more than 50% missing values. Missing values in the original data were simulated by multiplying the minimum value by a random number between 0.1 and 0.5.

Combined analysis:

Analysis ID AN004960
Analysis type MS
Chromatography type GC
Chromatography system SHIMADZU GC2030
Column Agilent HP5-MS (30m x 0.25mm, 0.25 um)
MS Type EI
MS instrument type GC2030-QP2020
MS instrument name SHIMADZU
Ion Mode POSITIVE
Units m/z

Chromatography:

Chromatography ID:CH003743
Instrument Name:SHIMADZU GC2030
Column Name:Agilent HP5-MS (30m x 0.25mm, 0.25 um)
Column Temperature:475°C
Flow Gradient:-
Flow Rate:350-400
Solvent A:-
Solvent B:-
Chromatography Type:GC

MS:

MS ID:MS004700
Analysis ID:AN004960
Instrument Name:SHIMADZU
Instrument Type:GC2030-QP2020
MS Type:EI
MS Comments:The quantitative results are calculated from the following formula: Calculation formula: C（con）= (Cs∗V1∗V3)/(M∗V2) *1000 C (con) : content of the target compound in the sample, μg/g; Cs: target compound concentration in extract, mg/l; V1: Volume of extract solution added, ML; V2: Take Out pure water supernatant volume, ML; V3: Volume of pure water added, ML; M: weighing sample, MG.
Ion Mode:POSITIVE
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