Summary of Study ST003013

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 IDST003013
Study TitleNMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma (part-Ⅱ)
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
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:SU003127
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
SA327121HC2.28.fid#158HC
SA327122HC2.29.fid#159HC
SA327123HC2.31.fid#161HC
SA327124HC2.27.fid#157HC
SA327125HC2.30.fid#160HC
SA327126HC2.26.fid#156HC
SA327127HC2.23.fid#153HC
SA327128HC2.24.fid#154HC
SA327129HC2.25.fid#155HC
SA327130HC2.32.fid#162HC
SA327131HC2.34.fid#164HC
SA327132HC2.39.fid#169HC
SA327133HC2.40.fid#170HC
SA327134HC2.42.fid#172HC
SA327135HC2.43.fid#173HC
SA327136HC2.38.fid#168HC
SA327137HC2.37.fid#167HC
SA327138HC2.22.fid#152HC
SA327139HC2.35.fid#165HC
SA327140HC2.36.fid#166HC
SA327141HC2.33.fid#163HC
SA327142HC2.20.fid#150HC
SA327143HC2.6.fid#136HC
SA327144HC2.7.fid#137HC
SA327145HC2.8.fid#138HC
SA327146HC2.9.fid#139HC
SA327147HC2.5.fid#135HC
SA327148HC2.4.fid#134HC
SA327149HC2.1.fid#131HC
SA327150HC2.2.fid#132HC
SA327151HC2.3.fid#133HC
SA327152HC2.10.fid#140HC
SA327153HC2.11.fid#141HC
SA327154HC2.17.fid#147HC
SA327155HC2.18.fid#148HC
SA327156HC2.19.fid#149HC
SA327157HC2.44.fid#174HC
SA327158HC2.16.fid#146HC
SA327159HC2.15.fid#145HC
SA327160HC2.12.fid#142HC
SA327161HC2.13.fid#143HC
SA327162HC2.14.fid#144HC
SA327163HC2.21.fid#151HC
SA327164HC2.41.fid#171HC
SA327165HC2.73.fid#203HC
SA327166HC2.74.fid#204HC
SA327167HC2.75.fid#205HC
SA327168HC2.76.fid#206HC
SA327169HC2.72.fid#202HC
SA327170HC2.71.fid#201HC
SA327171HC2.67.fid#197HC
SA327172HC2.68.fid#198HC
SA327173HC2.69.fid#199HC
SA327174HC2.45.fid#175HC
SA327175HC2.77.fid#207HC
SA327176HC2.78.fid#208HC
SA327177HC2.84.fid#214HC
SA327178HC2.85.fid#215HC
SA327179HC2.86.fid#216HC
SA327180HC2.87.fid#217HC
SA327181HC2.83.fid#213HC
SA327182HC2.82.fid#212HC
SA327183HC2.79.fid#209HC
SA327184HC2.80.fid#210HC
SA327185HC2.81.fid#211HC
SA327186HC2.66.fid#196HC
SA327187HC2.70.fid#200HC
SA327188HC2.65.fid#195HC
SA327189HC2.52.fid#182HC
SA327190HC2.53.fid#183HC
SA327191HC2.54.fid#184HC
SA327192HC2.50.fid#180HC
SA327193HC2.49.fid#179HC
SA327194HC2.46.fid#176HC
SA327195HC2.47.fid#177HC
SA327196HC2.48.fid#178HC
SA327197HC2.55.fid#185HC
SA327198HC2.51.fid#181HC
SA327199HC2.62.fid#192HC
SA327200HC2.63.fid#193HC
SA327201HC2.56.fid#186HC
SA327202HC2.61.fid#191HC
SA327203HC2.64.fid#194HC
SA327204HC2.60.fid#190HC
SA327205HC2.58.fid#188HC
SA327206HC2.57.fid#187HC
SA327207HC2.59.fid#189HC
SA327208EC Sera-20220608.1.fid#102Post-operation
SA327209EC Sera-20220608.1.fid#103Post-operation
SA327210EC Sera-20220608.1.fid#101Post-operation
SA327211EC Sera-20220608.1.fid#104Post-operation
SA327212EC Sera-20220608.1.fid#100Post-operation
SA327213EC Sera-20220608.1.fid#107Post-operation
SA327214EC Sera-20220608.1.fid#99Post-operation
SA327215EC Sera-20220608.1.fid#108Post-operation
SA327216EC Sera-20220608.1.fid#106Post-operation
SA327217EC Sera-20220608.1.fid#105Post-operation
SA327218EC Sera-20220608.1.fid#98Post-operation
SA327219EC Sera-20220608.1.fid#70Post-operation
SA327220EC Sera-20220608.1.fid#69Post-operation
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Collection:

Collection ID:CO003120
Collection Summary:Serum samples: Fasting blood was drawn into additive-free vacuum blood collection tubes, taking care to avoid hemolysis. Samples were left to clot naturally for 30 minutes and then centrifuged for 10 minutes at 3000 rpm and 4°C. Following centrifugation, the serum supernatant was aliquoted into storage tubes, promptly frozen in liquid nitrogen, and stored at −80°C until analysis.
Collection Protocol Filename:NMR_Serum_collection_uploaded.pdf
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003136
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP003133
Sampleprep Summary:Serum preparation: A total of 400 μL of serum was combined with 200 μL of PBS/D2O buffer (pH 7.4, containing 0.9% NaCl) using vortexing to ensure thorough mixing. The resulting mixture was then centrifuged at 10,000 rpm for 10 min at 4°C. Finally, the supernatant, which amounted to 550 μL, was carefully transferred into a 5 mm NMR tube for further analysis.
Sampleprep Protocol Filename:Serum_preparation_uploaded.pdf
Processing Storage Conditions:4℃
Extract Storage:4℃

Analysis:

Analysis ID:AN004946
Analysis Type:NMR
Results File:ST003013_AN004946_Results.txt
Units:gauss

NMR:

NMR ID:NM000271
Analysis ID:AN004946
Instrument Name:6000 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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