#METABOLOMICS WORKBENCH Linyan_20231215_005254 DATATRACK_ID:4522 STUDY_ID:ST003013 ANALYSIS_ID:AN004946 PROJECT_ID:PR001876 VERSION 1 CREATED_ON December 18, 2023, 10:28 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, Shantou PR:LAST_NAME Lin PR:FIRST_NAME Yan PR:ADDRESS No. 69, Dongxia North Road, Shantou, Guangdong, 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-Ⅱ) 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, Shantou ST:LAST_NAME Lin ST:FIRST_NAME Yan ST:ADDRESS No. 69, Dongxia North Road, Shantou, Guangdong, 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 Sera-20220608.1.fid#1 Fator:Pre-operation RAW_FILE_NAME=Raw_ESCC Serum.1.fid SUBJECT_SAMPLE_FACTORS - EC Sera-20220608.1.fid#2 Fator:Pre-operation RAW_FILE_NAME=Raw_ESCC Serum.2.fid SUBJECT_SAMPLE_FACTORS - EC Sera-20220608.1.fid#3 Fator:Pre-operation RAW_FILE_NAME=Raw_ESCC Serum.3.fid SUBJECT_SAMPLE_FACTORS - EC Sera-20220608.1.fid#4 Fator:Pre-operation RAW_FILE_NAME=Raw_ESCC Serum.4.fid SUBJECT_SAMPLE_FACTORS - EC Sera-20220608.1.fid#5 Fator:Pre-operation RAW_FILE_NAME=Raw_ESCC Serum.5.fid SUBJECT_SAMPLE_FACTORS - 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HC2.36.fid#166 Fator:HC RAW_FILE_NAME=Raw_HC Sera.36.fid SUBJECT_SAMPLE_FACTORS - HC2.37.fid#167 Fator:HC RAW_FILE_NAME=Raw_HC Sera.37.fid SUBJECT_SAMPLE_FACTORS - HC2.38.fid#168 Fator:HC RAW_FILE_NAME=Raw_HC Sera.38.fid SUBJECT_SAMPLE_FACTORS - HC2.39.fid#169 Fator:HC RAW_FILE_NAME=Raw_HC Sera.39.fid SUBJECT_SAMPLE_FACTORS - HC2.40.fid#170 Fator:HC RAW_FILE_NAME=Raw_HC Sera.40.fid SUBJECT_SAMPLE_FACTORS - HC2.41.fid#171 Fator:HC RAW_FILE_NAME=Raw_HC Sera.41.fid SUBJECT_SAMPLE_FACTORS - HC2.42.fid#172 Fator:HC RAW_FILE_NAME=Raw_HC Sera.42.fid SUBJECT_SAMPLE_FACTORS - HC2.43.fid#173 Fator:HC RAW_FILE_NAME=Raw_HC Sera.43.fid SUBJECT_SAMPLE_FACTORS - HC2.44.fid#174 Fator:HC RAW_FILE_NAME=Raw_HC Sera.44.fid SUBJECT_SAMPLE_FACTORS - HC2.45.fid#175 Fator:HC RAW_FILE_NAME=Raw_HC Sera.45.fid SUBJECT_SAMPLE_FACTORS - HC2.46.fid#176 Fator:HC RAW_FILE_NAME=Raw_HC Sera.46.fid SUBJECT_SAMPLE_FACTORS - HC2.47.fid#177 Fator:HC RAW_FILE_NAME=Raw_HC Sera.47.fid SUBJECT_SAMPLE_FACTORS - HC2.48.fid#178 Fator:HC RAW_FILE_NAME=Raw_HC Sera.48.fid SUBJECT_SAMPLE_FACTORS - HC2.49.fid#179 Fator:HC RAW_FILE_NAME=Raw_HC Sera.49.fid SUBJECT_SAMPLE_FACTORS - HC2.50.fid#180 Fator:HC RAW_FILE_NAME=Raw_HC Sera.50.fid SUBJECT_SAMPLE_FACTORS - HC2.51.fid#181 Fator:HC RAW_FILE_NAME=Raw_HC Sera.51.fid SUBJECT_SAMPLE_FACTORS - HC2.52.fid#182 Fator:HC RAW_FILE_NAME=Raw_HC Sera.52.fid SUBJECT_SAMPLE_FACTORS - HC2.53.fid#183 Fator:HC RAW_FILE_NAME=Raw_HC Sera.53.fid SUBJECT_SAMPLE_FACTORS - HC2.54.fid#184 Fator:HC RAW_FILE_NAME=Raw_HC Sera.54.fid SUBJECT_SAMPLE_FACTORS - HC2.55.fid#185 Fator:HC RAW_FILE_NAME=Raw_HC Sera.55.fid SUBJECT_SAMPLE_FACTORS - HC2.56.fid#186 Fator:HC RAW_FILE_NAME=Raw_HC Sera.56.fid SUBJECT_SAMPLE_FACTORS - HC2.57.fid#187 Fator:HC RAW_FILE_NAME=Raw_HC Sera.57.fid SUBJECT_SAMPLE_FACTORS - HC2.58.fid#188 Fator:HC RAW_FILE_NAME=Raw_HC Sera.58.fid SUBJECT_SAMPLE_FACTORS - HC2.59.fid#189 Fator:HC RAW_FILE_NAME=Raw_HC Sera.59.fid SUBJECT_SAMPLE_FACTORS - HC2.60.fid#190 Fator:HC RAW_FILE_NAME=Raw_HC Sera.60.fid SUBJECT_SAMPLE_FACTORS - HC2.61.fid#191 Fator:HC RAW_FILE_NAME=Raw_HC Sera.61.fid SUBJECT_SAMPLE_FACTORS - HC2.62.fid#192 Fator:HC RAW_FILE_NAME=Raw_HC Sera.62.fid SUBJECT_SAMPLE_FACTORS - HC2.63.fid#193 Fator:HC RAW_FILE_NAME=Raw_HC Sera.63.fid SUBJECT_SAMPLE_FACTORS - HC2.64.fid#194 Fator:HC RAW_FILE_NAME=Raw_HC Sera.64.fid SUBJECT_SAMPLE_FACTORS - HC2.65.fid#195 Fator:HC RAW_FILE_NAME=Raw_HC Sera.65.fid SUBJECT_SAMPLE_FACTORS - HC2.66.fid#196 Fator:HC RAW_FILE_NAME=Raw_HC Sera.66.fid SUBJECT_SAMPLE_FACTORS - HC2.67.fid#197 Fator:HC RAW_FILE_NAME=Raw_HC Sera.67.fid SUBJECT_SAMPLE_FACTORS - HC2.68.fid#198 Fator:HC RAW_FILE_NAME=Raw_HC Sera.68.fid SUBJECT_SAMPLE_FACTORS - HC2.69.fid#199 Fator:HC RAW_FILE_NAME=Raw_HC Sera.69.fid SUBJECT_SAMPLE_FACTORS - HC2.70.fid#200 Fator:HC RAW_FILE_NAME=Raw_HC Sera.70.fid SUBJECT_SAMPLE_FACTORS - HC2.71.fid#201 Fator:HC RAW_FILE_NAME=Raw_HC Sera.71.fid SUBJECT_SAMPLE_FACTORS - HC2.72.fid#202 Fator:HC RAW_FILE_NAME=Raw_HC Sera.72.fid SUBJECT_SAMPLE_FACTORS - HC2.73.fid#203 Fator:HC RAW_FILE_NAME=Raw_HC Sera.73.fid SUBJECT_SAMPLE_FACTORS - HC2.74.fid#204 Fator:HC RAW_FILE_NAME=Raw_HC Sera.74.fid SUBJECT_SAMPLE_FACTORS - HC2.75.fid#205 Fator:HC RAW_FILE_NAME=Raw_HC Sera.75.fid SUBJECT_SAMPLE_FACTORS - HC2.76.fid#206 Fator:HC RAW_FILE_NAME=Raw_HC Sera.76.fid SUBJECT_SAMPLE_FACTORS - HC2.77.fid#207 Fator:HC RAW_FILE_NAME=Raw_HC Sera.77.fid SUBJECT_SAMPLE_FACTORS - HC2.78.fid#208 Fator:HC RAW_FILE_NAME=Raw_HC Sera.78.fid SUBJECT_SAMPLE_FACTORS - HC2.79.fid#209 Fator:HC RAW_FILE_NAME=Raw_HC Sera.79.fid SUBJECT_SAMPLE_FACTORS - HC2.80.fid#210 Fator:HC RAW_FILE_NAME=Raw_HC Sera.80.fid SUBJECT_SAMPLE_FACTORS - HC2.81.fid#211 Fator:HC RAW_FILE_NAME=Raw_HC Sera.81.fid SUBJECT_SAMPLE_FACTORS - HC2.82.fid#212 Fator:HC RAW_FILE_NAME=Raw_HC Sera.82.fid SUBJECT_SAMPLE_FACTORS - HC2.83.fid#213 Fator:HC RAW_FILE_NAME=Raw_HC Sera.83.fid SUBJECT_SAMPLE_FACTORS - HC2.84.fid#214 Fator:HC RAW_FILE_NAME=Raw_HC Sera.84.fid SUBJECT_SAMPLE_FACTORS - HC2.85.fid#215 Fator:HC RAW_FILE_NAME=Raw_HC Sera.85.fid SUBJECT_SAMPLE_FACTORS - HC2.86.fid#216 Fator:HC RAW_FILE_NAME=Raw_HC Sera.86.fid SUBJECT_SAMPLE_FACTORS - HC2.87.fid#217 Fator:HC RAW_FILE_NAME=Raw_HC Sera.87.fid #COLLECTION CO:COLLECTION_SUMMARY Serum samples: Fasting blood was drawn into additive-free vacuum blood CO:COLLECTION_SUMMARY collection tubes, taking care to avoid hemolysis. Samples were left to clot CO:COLLECTION_SUMMARY naturally for 30 minutes and then centrifuged for 10 minutes at 3000 rpm and CO:COLLECTION_SUMMARY 4°C. Following centrifugation, the serum supernatant was aliquoted into storage CO:COLLECTION_SUMMARY tubes, promptly frozen in liquid nitrogen, and stored at −80°C until CO:COLLECTION_SUMMARY analysis. CO:COLLECTION_PROTOCOL_FILENAME NMR_Serum_collection_uploaded.pdf CO:SAMPLE_TYPE Blood (serum) CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY None #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Serum preparation: A total of 400 μL of serum was combined with 200 μL of SP:SAMPLEPREP_SUMMARY PBS/D2O buffer (pH 7.4, containing 0.9% NaCl) using vortexing to ensure thorough SP:SAMPLEPREP_SUMMARY mixing. The resulting mixture was then centrifuged at 10,000 rpm for 10 min at SP:SAMPLEPREP_SUMMARY 4°C. Finally, the supernatant, which amounted to 550 μL, was carefully SP:SAMPLEPREP_SUMMARY transferred into a 5 mm NMR tube for further analysis. SP:SAMPLEPREP_PROTOCOL_FILENAME Serum_preparation_uploaded.pdf SP:PROCESSING_STORAGE_CONDITIONS 4℃ SP:EXTRACT_STORAGE 4℃ #ANALYSIS AN:ANALYSIS_TYPE NMR #NMR NM:INSTRUMENT_NAME 6000 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 ST003013_AN004946_Results.txt UNITS:gauss #END