#METABOLOMICS WORKBENCH Linyan_20231215_041621 DATATRACK_ID:4523 STUDY_ID:ST003014 ANALYSIS_ID:AN004947 PROJECT_ID:PR001876 VERSION 1 CREATED_ON December 18, 2023, 10:18 am #PROJECT PR:PROJECT_TITLE NMR- and MS-based omics reveal characteristic metabolome atlas and optimize PR:PROJECT_TITLE biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma PR:PROJECT_SUMMARY Metabolic changes precede malignant histology. However, it remains unclear PR:PROJECT_SUMMARY whether detectable characteristic metabolome exists in esophageal squamous cell PR:PROJECT_SUMMARY carcinoma (ESCC) tissues and biofluids for early diagnosis. We conducted NMR- PR:PROJECT_SUMMARY and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- PR:PROJECT_SUMMARY and one-week post-operative sera and urines from 560 participants across three PR:PROJECT_SUMMARY hospitals, with machine learning, logistic regression and WGCNA. Aberrations in PR:PROJECT_SUMMARY 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout PR:PROJECT_SUMMARY the ESCC evolution, and were reflected in 16 serum and 10 urine metabolic PR:PROJECT_SUMMARY signatures that were consistently identified by NMR and MS in both discovery and PR:PROJECT_SUMMARY validation sets. NMR-based simplified panels of any five serum or urine PR:PROJECT_SUMMARY metabolites outperformed clinical serological tumor markers (AUC = 0.984 and PR:PROJECT_SUMMARY 0.930, respectively), and were effective in distinguishing early-stage ESCC in PR:PROJECT_SUMMARY test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, PR:PROJECT_SUMMARY NMR-based biofluid screening can reveal characteristic metabolic events of ESCC PR:PROJECT_SUMMARY and be feasible for early detection (ChiCTR2300073613). PR:INSTITUTE Radiology Department, Second Affiliated Hospital, Shantou University Medical PR:INSTITUTE College PR:LAST_NAME Lin PR:FIRST_NAME Yan PR:ADDRESS No. 69, Dongxia North Road, Shantou, Guangdong, China, 515041, China PR:EMAIL 994809889@qq.com PR:PHONE +86 18823992148 #STUDY ST:STUDY_TITLE NMR- and MS-based omics reveal characteristic metabolome atlas and optimize ST:STUDY_TITLE biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma ST:STUDY_TITLE (part-Ⅲ) ST:STUDY_SUMMARY Metabolic changes precede malignant histology. However, it remains unclear ST:STUDY_SUMMARY whether detectable characteristic metabolome exists in esophageal squamous cell ST:STUDY_SUMMARY carcinoma (ESCC) tissues and biofluids for early diagnosis. We conducted NMR- ST:STUDY_SUMMARY and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- ST:STUDY_SUMMARY and one-week post-operative sera and urines from 560 participants across three ST:STUDY_SUMMARY hospitals, with machine learning, logistic regression and WGCNA. Aberrations in ST:STUDY_SUMMARY 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout ST:STUDY_SUMMARY the ESCC evolution, and were reflected in 16 serum and 10 urine metabolic ST:STUDY_SUMMARY signatures that were consistently identified by NMR and MS in both discovery and ST:STUDY_SUMMARY validation sets. NMR-based simplified panels of any five serum or urine ST:STUDY_SUMMARY metabolites outperformed clinical serological tumor markers (AUC = 0.984 and ST:STUDY_SUMMARY 0.930, respectively), and were effective in distinguishing early-stage ESCC in ST:STUDY_SUMMARY test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, ST:STUDY_SUMMARY NMR-based biofluid screening can reveal characteristic metabolic events of ESCC ST:STUDY_SUMMARY and be feasible for early detection (ChiCTR2300073613). ST:INSTITUTE Radiology Department, Second Affiliated Hospital, Shantou University Medical ST:INSTITUTE College ST:LAST_NAME Lin ST:FIRST_NAME Yan ST:ADDRESS No. 69, Dongxia North Road, Shantou, Guangdong, China, Shantou, Guangdong, ST:ADDRESS China, 515041, China ST:EMAIL 994809889@qq.com ST:PHONE +86 18823992148 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - EC Urine-20220608.1.fid#1 stage:Pre-operation Urine RAW_FILE_NAME=Raw_ESCC Urine.1.fid SUBJECT_SAMPLE_FACTORS - EC Urine-20220608.1.fid#2 stage:Pre-operation Urine RAW_FILE_NAME=Raw_ESCC Urine.2.fid SUBJECT_SAMPLE_FACTORS - EC Urine-20220608.1.fid#3 stage:Pre-operation Urine RAW_FILE_NAME=Raw_ESCC Urine.3.fid SUBJECT_SAMPLE_FACTORS - EC Urine-20220608.1.fid#4 stage:Pre-operation Urine RAW_FILE_NAME=Raw_ESCC Urine.4.fid SUBJECT_SAMPLE_FACTORS - 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Urine-Control.57.fid#148 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.57.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.58.fid#149 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.58.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.59.fid#150 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.59.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.60.fid#151 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.60.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.61.fid#152 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.61.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.64.fid#153 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.64.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.65.fid#154 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.65.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.66.fid#155 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.66.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.67.fid#156 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.67.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.68.fid#157 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.68.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.69.fid#158 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.69.fid SUBJECT_SAMPLE_FACTORS - Urine-Control.70.fid#159 stage:HC Urine RAW_FILE_NAME=Raw_HC Urine.70.fid #COLLECTION CO:COLLECTION_SUMMARY Urine samples: Patients were instructed on morning midstream urine collection. CO:COLLECTION_SUMMARY After mild centrifugation, the urine was aliquoted into storage tubes, promptly CO:COLLECTION_SUMMARY frozen in liquid nitrogen, and stored at −80°C until analysis. CO:COLLECTION_PROTOCOL_FILENAME NMR_Urine collection_uploaded.pdf CO:SAMPLE_TYPE Urine #TREATMENT TR:TREATMENT_SUMMARY None #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Urine preparation: A total of 500 μL of urine was mixed with 50 μL of PBS/D2O SP:SAMPLEPREP_SUMMARY buffer (pH 7.4, 1.5 M, containing 0.05% TSP) using vortexing to ensure thorough SP:SAMPLEPREP_SUMMARY mixing. The mixture was then centrifuged at 10,000 rpm for 10 min at 4°C. After SP:SAMPLEPREP_SUMMARY centrifugation, 500 μL of the supernatant was transferred into a 5 mm NMR tube SP:SAMPLEPREP_SUMMARY for further analysis. SP:SAMPLEPREP_PROTOCOL_FILENAME Urine_preparation_uploaded.pdf #ANALYSIS AN:ANALYSIS_TYPE NMR #NMR NM:INSTRUMENT_NAME 600 MHz Bruker Avance III NM:INSTRUMENT_TYPE FT-NMR NM:NMR_EXPERIMENT_TYPE 1D-1H NM:SPECTROMETER_FREQUENCY 600 MHz NM:NMR_SOLVENT H2O+D2O NM:NMR_RESULTS_FILE ST003014_AN004947_Results.txt UNITS:gauss #END