Summary of Study ST003015

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 IDST003015
Study TitleNMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma (part-Ⅰ)
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 Date2023-12-16
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

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:SU003129
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
SA32746320220725.73.fid#73Normal tissue
SA32746420220725.74.fid#74Normal tissue
SA32746520220725.72.fid#72Normal tissue
SA32746620220725.71.fid#71Normal tissue
SA32746720220725.70.fid#70Normal tissue
SA32746820220725.75.fid#75Normal tissue
SA32746920220725.77.fid#77Normal tissue
SA32747020220725.80.fid#80Normal tissue
SA32747120220725.81.fid#81Normal tissue
SA32747220220725.79.fid#79Normal tissue
SA32747320220725.78.fid#78Normal tissue
SA32747420220725.69.fid#69Normal tissue
SA32747520220725.76.fid#76Normal tissue
SA32747620220725.68.fid#68Normal tissue
SA32747720220725.60.fid#60Normal tissue
SA32747820220725.61.fid#61Normal tissue
SA32747920220725.59.fid#59Normal tissue
SA32748020220725.58.fid#58Normal tissue
SA32748120220725.57.fid#57Normal tissue
SA32748220220725.62.fid#62Normal tissue
SA32748320220725.63.fid#63Normal tissue
SA32748420220725.67.fid#67Normal tissue
SA32748520220725.66.fid#66Normal tissue
SA32748620220725.65.fid#65Normal tissue
SA32748720220725.64.fid#64Normal tissue
SA32748820220725.82.fid#82Normal tissue
SA32748920220725.84.fid#84Normal tissue
SA32749020220725.100.fid#100Normal tissue
SA32749120220725.101.fid#101Normal tissue
SA32749220220725.99.fid#99Normal tissue
SA32749320220725.98.fid#98Normal tissue
SA32749420220725.97.fid#97Normal tissue
SA32749520220725.102.fid#102Normal tissue
SA32749620220725.103.fid#103Normal tissue
SA32749720220725.107.fid#107Normal tissue
SA32749820220725.108.fid#108Normal tissue
SA32749920220725.106.fid#106Normal tissue
SA32750020220725.105.fid#105Normal tissue
SA32750120220725.104.fid#104Normal tissue
SA32750220220725.96.fid#96Normal tissue
SA32750320220725.95.fid#95Normal tissue
SA32750420220725.87.fid#87Normal tissue
SA32750520220725.88.fid#88Normal tissue
SA32750620220725.86.fid#86Normal tissue
SA32750720220725.85.fid#85Normal tissue
SA32750820220725.56.fid#56Normal tissue
SA32750920220725.89.fid#89Normal tissue
SA32751020220725.90.fid#90Normal tissue
SA32751120220725.94.fid#94Normal tissue
SA32751220220725.93.fid#93Normal tissue
SA32751320220725.92.fid#92Normal tissue
SA32751420220725.91.fid#91Normal tissue
SA32751520220725.83.fid#83Normal tissue
SA32751620220725.55.fid#55Normal tissue
SA32751720220725.19.fid#19Tumor tissue
SA32751820220725.20.fid#20Tumor tissue
SA32751920220725.18.fid#18Tumor tissue
SA32752020220725.17.fid#17Tumor tissue
SA32752120220725.16.fid#16Tumor tissue
SA32752220220725.21.fid#21Tumor tissue
SA32752320220725.22.fid#22Tumor tissue
SA32752420220725.26.fid#26Tumor tissue
SA32752520220725.27.fid#27Tumor tissue
SA32752620220725.25.fid#25Tumor tissue
SA32752720220725.24.fid#24Tumor tissue
SA32752820220725.23.fid#23Tumor tissue
SA32752920220725.15.fid#15Tumor tissue
SA32753020220725.14.fid#14Tumor tissue
SA32753120220725.5.fid#5Tumor tissue
SA32753220220725.6.fid#6Tumor tissue
SA32753320220725.4.fid#4Tumor tissue
SA32753420220725.3.fid#3Tumor tissue
SA32753520220725.2.fid#2Tumor tissue
SA32753620220725.7.fid#7Tumor tissue
SA32753720220725.8.fid#8Tumor tissue
SA32753820220725.12.fid#12Tumor tissue
SA32753920220725.13.fid#13Tumor tissue
SA32754020220725.11.fid#11Tumor tissue
SA32754120220725.10.fid#10Tumor tissue
SA32754220220725.9.fid#9Tumor tissue
SA32754320220725.28.fid#28Tumor tissue
SA32754420220725.29.fid#29Tumor tissue
SA32754520220725.46.fid#46Tumor tissue
SA32754620220725.47.fid#47Tumor tissue
SA32754720220725.45.fid#45Tumor tissue
SA32754820220725.44.fid#44Tumor tissue
SA32754920220725.43.fid#43Tumor tissue
SA32755020220725.48.fid#48Tumor tissue
SA32755120220725.49.fid#49Tumor tissue
SA32755220220725.53.fid#53Tumor tissue
SA32755320220725.54.fid#54Tumor tissue
SA32755420220725.52.fid#52Tumor tissue
SA32755520220725.51.fid#51Tumor tissue
SA32755620220725.50.fid#50Tumor tissue
SA32755720220725.42.fid#42Tumor tissue
SA32755820220725.41.fid#41Tumor tissue
SA32755920220725.33.fid#33Tumor tissue
SA32756020220725.34.fid#34Tumor tissue
SA32756120220725.32.fid#32Tumor tissue
SA32756220220725.31.fid#31Tumor tissue
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Collection:

Collection ID:CO003122
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.
Collection Protocol Filename:Tissue_collection_uploaded.pdf
Sample Type:Tissue
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003138
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP003135
Sampleprep Summary:Tissue homogenate preparation: Tissue samples weighing 300 mg were ground using a 60 Hz grinder at 4 °C for 1 min in a mixture of 4 mL/g of CH3OH and 2 mL/g of ultrapure water. The resulting homogenate was then subjected to vortexing for 1 min after adding 4 mL/g of CHCl3 and 4 mL/g of ultrapure water. The mixture was allowed to settle on ice for 15 mins and subsequently centrifuged at 10,000 rpm for 10 mins at 4 °C. The supernatant was carefully transferred to a new 5 mL Eppendorf (EP) tube and treated with running nitrogen to remove the methanol. The resulting liquid was freeze-dried at −80°C until further analysis. The freeze-dried powder was dissolved in 550 μL of PBS/D2O buffer (pH 7.4, 150 mM), which contained 0.05% TMSP-2,2,3,3-D4 (D, 98%) SODIUM-3-TRIMETHYLSILYLPROPIONATE (TSP, Cambridge Isotope Laboratories (CIL), Inc. #DLM-48, CAS #24493-21-8)). After thorough mixing, the solution was centrifuged at 10,000 rpm for 10 min at 4 °C. Finally, 500 μL of the supernatant was transferred into a 5 mm NMR tube (NORELL, #S55 SECURE SERIES) for analysis.
Sampleprep Protocol Filename:Tissue_preparation.pdf
Processing Storage Conditions:4℃
Extract Storage:4℃

Analysis:

Analysis ID:AN004948
Analysis Type:NMR
Results File:ST003015_AN004948_Results.txt
Units:gauss

NMR:

NMR ID:NM000273
Analysis ID:AN004948
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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