Summary of Study ST003014

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 IDST003014
Study TitleNMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma (part-Ⅲ)
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
Radiology Department, Second Affiliated Hospital, Shantou University Medical College
Last NameLin
First NameYan
AddressNo. 69, Dongxia North Road, Shantou, Guangdong, China, Shantou, Guangdong, China, 515041, China
Email994809889@qq.com
Phone+86 18823992148
Submit Date2023-12-15
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2024-02-08
Release Version1
Yan Lin Yan Lin
https://dx.doi.org/10.21228/M87426
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:SU003128
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 stage
SA327316Urine-Control.43.fid#134HC Urine
SA327317Urine-Control.42.fid#133HC Urine
SA327318Urine-Control.41.fid#132HC Urine
SA327319Urine-Control.44.fid#135HC Urine
SA327320Urine-Control.46.fid#137HC Urine
SA327321Urine-Control.48.fid#139HC Urine
SA327322Urine-Control.47.fid#138HC Urine
SA327323Urine-Control.40.fid#131HC Urine
SA327324Urine-Control.45.fid#136HC Urine
SA327325Urine-Control.38.fid#129HC Urine
SA327326Urine-Control.32.fid#123HC Urine
SA327327Urine-Control.31.fid#122HC Urine
SA327328Urine-Control.14.fid#121HC Urine
SA327329Urine-Control.33.fid#124HC Urine
SA327330Urine-Control.35.fid#126HC Urine
SA327331Urine-Control.49.fid#140HC Urine
SA327332Urine-Control.37.fid#128HC Urine
SA327333Urine-Control.36.fid#127HC Urine
SA327334Urine-Control.39.fid#130HC Urine
SA327335Urine-Control.34.fid#125HC Urine
SA327336Urine-Control.65.fid#154HC Urine
SA327337Urine-Control.64.fid#153HC Urine
SA327338Urine-Control.61.fid#152HC Urine
SA327339Urine-Control.66.fid#155HC Urine
SA327340Urine-Control.67.fid#156HC Urine
SA327341Urine-Control.50.fid#141HC Urine
SA327342Urine-Control.70.fid#159HC Urine
SA327343Urine-Control.69.fid#158HC Urine
SA327344Urine-Control.60.fid#151HC Urine
SA327345Urine-Control.68.fid#157HC Urine
SA327346Urine-Control.52.fid#143HC Urine
SA327347Urine-Control.59.fid#150HC Urine
SA327348Urine-Control.51.fid#142HC Urine
SA327349Urine-Control.54.fid#145HC Urine
SA327350Urine-Control.53.fid#144HC Urine
SA327351Urine-Control.56.fid#147HC Urine
SA327352Urine-Control.57.fid#148HC Urine
SA327353Urine-Control.58.fid#149HC Urine
SA327354Urine-Control.55.fid#146HC Urine
SA327355EC Urine-20220608.1.fid#87Post-operation Urine
SA327356EC Urine-20220608.1.fid#85Post-operation Urine
SA327357EC Urine-20220608.1.fid#86Post-operation Urine
SA327358EC Urine-20220608.1.fid#89Post-operation Urine
SA327359EC Urine-20220608.1.fid#90Post-operation Urine
SA327360EC Urine-20220608.1.fid#84Post-operation Urine
SA327361EC Urine-20220608.1.fid#91Post-operation Urine
SA327362EC Urine-20220608.1.fid#88Post-operation Urine
SA327363EC Urine-20220608.1.fid#79Post-operation Urine
SA327364EC Urine-20220608.1.fid#77Post-operation Urine
SA327365EC Urine-20220608.1.fid#92Post-operation Urine
SA327366EC Urine-20220608.1.fid#76Post-operation Urine
SA327367EC Urine-20220608.1.fid#78Post-operation Urine
SA327368EC Urine-20220608.1.fid#80Post-operation Urine
SA327369EC Urine-20220608.1.fid#82Post-operation Urine
SA327370EC Urine-20220608.1.fid#81Post-operation Urine
SA327371EC Urine-20220608.1.fid#83Post-operation Urine
SA327372EC Urine-20220608.1.fid#102Post-operation Urine
SA327373EC Urine-20220608.1.fid#105Post-operation Urine
SA327374EC Urine-20220608.1.fid#104Post-operation Urine
SA327375EC Urine-20220608.1.fid#103Post-operation Urine
SA327376EC Urine-20220608.1.fid#106Post-operation Urine
SA327377EC Urine-20220608.1.fid#107Post-operation Urine
SA327378EC Urine-20220608.1.fid#75Post-operation Urine
SA327379EC Urine-20220608.1.fid#108Post-operation Urine
SA327380EC Urine-20220608.1.fid#101Post-operation Urine
SA327381EC Urine-20220608.1.fid#100Post-operation Urine
SA327382EC Urine-20220608.1.fid#95Post-operation Urine
SA327383EC Urine-20220608.1.fid#94Post-operation Urine
SA327384EC Urine-20220608.1.fid#96Post-operation Urine
SA327385EC Urine-20220608.1.fid#97Post-operation Urine
SA327386EC Urine-20220608.1.fid#99Post-operation Urine
SA327387EC Urine-20220608.1.fid#98Post-operation Urine
SA327388EC Urine-20220608.1.fid#93Post-operation Urine
SA327389EC Urine-20220608.1.fid#74Post-operation Urine
SA327390EC Urine-20220608.1.fid#61Post-operation Urine
SA327391EC Urine-20220608.1.fid#62Post-operation Urine
SA327392EC Urine-20220608.1.fid#63Post-operation Urine
SA327393EC Urine-20220608.1.fid#60Post-operation Urine
SA327394EC Urine-20220608.1.fid#58Post-operation Urine
SA327395EC Urine-20220608.1.fid#55Post-operation Urine
SA327396EC Urine-20220608.1.fid#56Post-operation Urine
SA327397EC Urine-20220608.1.fid#57Post-operation Urine
SA327398EC Urine-20220608.1.fid#64Post-operation Urine
SA327399EC Urine-20220608.1.fid#59Post-operation Urine
SA327400EC Urine-20220608.1.fid#72Post-operation Urine
SA327401EC Urine-20220608.1.fid#73Post-operation Urine
SA327402EC Urine-20220608.1.fid#65Post-operation Urine
SA327403EC Urine-20220608.1.fid#70Post-operation Urine
SA327404EC Urine-20220608.1.fid#71Post-operation Urine
SA327405EC Urine-20220608.1.fid#66Post-operation Urine
SA327406EC Urine-20220608.1.fid#68Post-operation Urine
SA327407EC Urine-20220608.1.fid#67Post-operation Urine
SA327408EC Urine-20220608.1.fid#69Post-operation Urine
SA327409EC Urine-20220608.1.fid#19Pre-operation Urine
SA327410EC Urine-20220608.1.fid#20Pre-operation Urine
SA327411EC Urine-20220608.1.fid#18Pre-operation Urine
SA327412EC Urine-20220608.1.fid#17Pre-operation Urine
SA327413EC Urine-20220608.1.fid#16Pre-operation Urine
SA327414EC Urine-20220608.1.fid#21Pre-operation Urine
SA327415EC Urine-20220608.1.fid#27Pre-operation Urine
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Collection:

Collection ID:CO003121
Collection Summary:Urine samples: Patients were instructed on morning midstream urine collection. After mild centrifugation, the urine was aliquoted into storage tubes, promptly frozen in liquid nitrogen, and stored at −80°C until analysis.
Collection Protocol Filename:NMR_Urine collection_uploaded.pdf
Sample Type:Urine

Treatment:

Treatment ID:TR003137
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP003134
Sampleprep Summary:Urine preparation: A total of 500 μL of urine was mixed with 50 μL of PBS/D2O buffer (pH 7.4, 1.5 M, containing 0.05% TSP) using vortexing to ensure thorough mixing. The mixture was then centrifuged at 10,000 rpm for 10 min at 4°C. After centrifugation, 500 μL of the supernatant was transferred into a 5 mm NMR tube for further analysis.
Sampleprep Protocol Filename:Urine_preparation_uploaded.pdf

Analysis:

Analysis ID:AN004947
Analysis Type:NMR
Results File:ST003014_AN004947_Results.txt
Units:gauss

NMR:

NMR ID:NM000272
Analysis ID:AN004947
Instrument Name:600 MHz Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Spectrometer Frequency:600 MHz
NMR Solvent:H2O+D2O
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